Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 151 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 2432 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 52 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 41 SARS 36 COVID-19 15 covid-19 9 MERS 8 patient 8 Hajj 7 China 5 case 4 respiratory 4 Korea 4 Ebola 4 Africa 3 virus 3 influenza 3 RNA 3 PCR 3 Health 3 HIV 3 East 2 study 2 measure 2 gathering 2 day 2 child 2 asymptomatic 2 Wuhan 2 Taiwan 2 TCZ 2 RSV 2 Middle 2 Hubei 2 HCQ 2 H1N1 1 viral 1 vaccine 1 travel 1 test 1 swab 1 standard 1 saharan 1 risk 1 rate 1 precaution 1 pool 1 pneumonia 1 pilgrim 1 personal 1 pandemic 1 outbreak 1 oral Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 2616 patient 2085 % 1847 case 1833 study 1692 infection 1323 disease 1042 virus 962 r 761 health 754 day 749 o 739 influenza 738 coronavirus 708 risk 650 outbreak 632 time 632 p 632 group 615 datum 606 country 542 pneumonia 534 treatment 534 transmission 529 epidemic 506 number 501 rate 488 analysis 486 child 485 result 481 hospital 471 test 453 syndrome 438 symptom 411 n 405 sample 403 year 403 population 403 control 402 cell 401 level 397 pandemic 395 measure 383 l 365 e 356 age 345 response 339 factor 337 vaccine 331 care 330 mortality Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1383 al 1371 SARS 1298 COVID-19 1074 et 1031 . 975 CoV-2 551 China 493 MERS 472 J 438 Hajj 398 CoV 354 Health 318 Wuhan 259 PCR 225 Coronavirus 204 Africa 203 Korea 196 East 183 Middle 179 March 178 Disease 174 RT 172 Ebola 171 South 168 RNA 159 HIV 153 World 151 Dis 150 Int 143 Table 139 January 139 February 133 Saudi 130 Organization 125 H1N1 122 Kawasaki 122 ICU 116 April 116 A 115 Arabia 109 Hubei 108 Rt 105 sha 105 RSV 104 Hospital 99 r 98 S. 98 CT 95 CI 93 May Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 883 we 583 it 275 they 100 he 88 them 58 i 57 she 36 us 18 themselves 13 you 7 one 6 itself 3 her 2 ours 1 yourself 1 www.cdc.gov/flu 1 ws 1 theirs 1 ourselves 1 oneself 1 igm/ 1 em Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 10562 be 2317 have 947 use 689 include 686 report 540 show 426 associate 420 infect 386 increase 380 base 358 find 346 detect 344 confirm 338 compare 308 identify 307 do 270 develop 269 follow 251 require 239 cause 229 receive 226 provide 225 reduce 223 consider 210 indicate 206 suggest 204 collect 194 perform 187 treat 187 estimate 186 present 183 emerge 182 relate 175 test 174 give 166 occur 166 conduct 159 observe 156 take 156 need 155 declare 153 lead 151 remain 151 hospitalize 151 determine 144 assess 141 make 139 spread 139 know 138 describe Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1171 respiratory 916 not 845 high 758 - 732 clinical 729 severe 642 other 611 viral 597 more 565 covid-19 480 acute 466 also 445 low 427 first 408 such 397 positive 375 human 369 most 366 however 346 early 321 public 321 only 299 infectious 294 novel 291 asymptomatic 290 well 289 different 267 significant 225 non 225 medical 223 new 223 negative 210 global 206 effective 206 common 204 significantly 199 many 194 large 184 potential 183 important 181 respectively 179 as 177 likely 177 available 176 old 174 specific 170 mild 169 standard 162 similar 160 local Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 143 most 88 high 49 Most 43 good 39 least 28 low 25 large 9 late 8 early 8 bad 7 big 6 great 3 young 3 near 3 long 3 common 3 cold 2 strong 2 safe 2 old 2 new 2 heavy 2 hard 2 -42.94 1 wet 1 tight 1 theb 1 strict 1 short 1 severe 1 quiet 1 poor 1 p=0.016 1 northernmost 1 montelukast 1 manif 1 hot 1 easy 1 deep 1 cord-276445-m5vjo3ym 1 close 1 bright 1 -displayed Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 226 most 66 least 5 well 2 hard 1 lowest 1 highest 1 early Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 6 doi.org 2 www.r-project.org 2 www.pandora-id.net 2 www.chictr.org.cn 2 ncov.dxy.cn 2 github.com 2 dx.doi.org 2 coronavirus.jhu.edu 1 www.who.int 1 www.fda.gov 1 www.eviews.com 1 www.ecdc.europa.eu 1 www.cslm.org.cn 1 www.cebm.net 1 www.cdc.gov 1 www 1 unfccc.int 1 sustainabledevelopment.un.org 1 statista 1 ipscell.com 1 files.ssi.dk 1 fchampalimaud.org 1 en.wondfo.com.cn 1 en-author-services.edanzgroup.com 1 clinicaltrials.gov Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www.chictr.org.cn/ 2 http://ncov.dxy.cn/ncovh5/view/pneumonia 2 http://coronavirus.jhu.edu/map.html 1 http://www.who.int/emergencies/ 1 http://www.r-project.org/ 1 http://www.r-project.org 1 http://www.pandora-id.net/partners).AZ 1 http://www.pandora-id.net/ 1 http://www.fda.gov/consumers/consumer-updates/fda-warns-about-stem-cell-therapies 1 http://www.eviews.com/ 1 http://www.ecdc.europa.eu/en/publicationsdata/download-todays-data-geographic-distribution-covid-19-cases-worldwide 1 http://www.cslm.org.cn/cn/news.asp?id=74.html 1 http://www.cebm.net/ 1 http://www.cdc.gov/hai/outbreaks/stem-cell-products.html 1 http://www 1 http://unfccc.int/2860.php) 1 http://sustainabledevelopment.un.org/ 1 http://statista 1 http://ipscell.com/rmat-list 1 http://github.com/jihoo-kim/Data-Science-for-COVID-19 1 http://github.com/Jiasong-Duan/COVID-19-epidemic-trajectories 1 http://files.ssi.dk/COVID19-overvaagningsrapport-12032020 1 http://fchampalimaud.org/covid19/aci 1 http://en.wondfo.com.cn/product/wondfo-sars-cov-2-antibody-test-lateral-flowmethod-2/ 1 http://en-author-services.edanzgroup.com/ 1 http://dx.doi.org/10.1016/j.ijid.2014.02.019 1 http://dx.doi.org/10.1016/j.ijid.2012.03.015 1 http://doi.org/10.1038/s41591-020-0868-6 1 http://doi.org/10.1016/j.ijid.2020.04.017 1 http://doi.org/10.1016/j.ijid.2020.03.062 1 http://doi.org/10.1016/j.ijid.2019.02.003 1 http://doi.org/10.1016/j.ijid.2018.08.001 1 http://doi.org/10.1016/j.ijid.2018.03.005 1 http://clinicaltrials.gov/ct2/who_table Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 2 naeem.mubarak@lmdc.edu.pk 1 teshima@med.hokudai.ac.jp 1 taco155485@hotmail.com 1 eskild.petersen@gmail.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 7 pneumonia requiring hospitalization 7 study has several 6 coronavirus indicating person 5 patients were positive 4 cov-2 infected patients 4 patients received tcz 3 % had knowledge 3 % were male 3 cases are asymptomatic 3 cases is still 3 days following tocilizumab 3 disease is not 3 group was significantly 3 outbreaks were common 3 patient did not 3 patients are very 3 patients had at 3 patients is not 3 patients was significantly 3 patients were co 3 patients were mild 3 studies have also 3 study does not 3 study included patients 3 study is not 3 virus was subsequently 2 % had at 2 case report date 2 case report first 2 case report form 2 cases are mild 2 cases are not 2 cases had more 2 cases is comparable 2 cases was higher 2 cases was not 2 cases were also 2 cases were mainly 2 cases were negative 2 coronavirus was initially 2 countries are now 2 countries including liberia 2 cov-2 does not 2 cov-2 is critical 2 cov-2 is not 2 cov-2 was significantly 2 covid-19 are also 2 covid-19 confirmed cases 2 covid-19 is higher 2 data are anonymous Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 cov-2 is not clear 2 infection are not identical 2 patients is not well 2 viruses are no longer 1 cases are not apparent 1 cases have not yet 1 cases is not clear 1 china showed no significant 1 cov-2 does not only 1 data indicated no vaccine 1 data suggest no increase 1 disease is not always 1 groups showed no significant 1 infection is not appropriate 1 infection is not uncommon 1 infection were not clearly 1 infections are not distinguishable 1 infections have not previously 1 patient was not different 1 patients had no symptoms 1 patients have no obvious 1 patients is not yet 1 patients showed no typical 1 study had no role 1 study is not exempt 1 study is not flawless 1 study received no external 1 study received no funding 1 treatment does no harm 1 treatments were not randomly A rudimentary bibliography -------------------------- id = cord-279581-d2l4nnex author = Abuhabib, A.A. title = Unique situation of Gaza Strip dealing with COVID-19 crisis date = 2020-09-03 keywords = Gaza summary = Constructively, this study follows direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario within a limited time frame covering the period from 22 March to 05 July 2020. This study follows the direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario likelihood determination and consequences identification within a limited time frame covering the period from 22 March to 05 July 2020. doi = 10.1016/j.ijid.2020.08.070 id = cord-308114-68cgub5o author = Afrin, Lawrence B. title = Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome date = 2020-09-10 keywords = MCAS; covid-19 summary = MCs, present in all vascularized tissues but dominantly at the environmental interfaces and in vessel walls (Akin and Metcalfe, 2004) , are activated by the SARS-Cov-2 coronavirus which causes Covid-19 infection (Kritas et al., 2020; Theoharides, 2020; Zhou et al., 2020) , leading to MC activation and resulting release of various subsets of the MC''s >1000 potent multi-action mediators (Ibelgaufts, 2020) (including biogenic amines (e.g., histamine), proteases (e.g., tryptase and chymase), cytokines (e.g., interleukins and TNF-α), eicosanoids (e.g., prostaglandins and leukotrienes), heparin, and growth factors) increasingly thought to play a key role in driving the hyperinflammation of severe Covid-19 illness (Kempuraj et al., 2020; Valent et al., 2020) . doi = 10.1016/j.ijid.2020.09.016 id = cord-305788-z75yv88e author = Agergaard, Charlotte Nielsen title = Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date = 2020-09-28 keywords = SARS summary = Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. doi = 10.1016/j.ijid.2020.09.1442 id = cord-318181-xxc7vdnt author = Ahmed, Anwar E. title = Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date = 2018-03-14 keywords = East; MERS; Middle summary = A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient''s clinical status, ''yes/no'', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). doi = 10.1016/j.ijid.2018.03.005 id = cord-324231-nik7xizn author = Aitsi-Selmi, Amina title = Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction date = 2016-04-07 keywords = Framework; Sendai; health summary = The following actions with a public health focus are agreed in the Sendai Framework with local, national, regional, and global partners as relevant: ''''Enhancing the resilience of national health systems through training and capacity development; strengthening the design and implementation of inclusive policies and social safety-net mechanisms, including access to basic health care services towards the eradication of poverty; finding durable solutions in the post-disaster phase to empower and assist people disproportionately affected by disasters, including those with life-threatening and chronic disease; enhancing cooperation between health authorities and other relevant stakeholders to strengthen country capacity for disaster risk management for health; the implementation of the International Health Regulations (2005) and the building of resilient health systems; improving the resilience of new and existing critical infrastructure, including hospitals, to ensure that they remain safe, effective and operational during and after disasters, to provide live-saving and essential services; establishing a mechanism of case registry and a database of mortality caused by disaster to improve the prevention of morbidity and mortality and enhancing recovery schemes to provide psychosocial support and mental health services for all people in need''''. doi = 10.1016/j.ijid.2016.04.006 id = cord-257073-dm80bxnd author = Akmatov, Manas K. title = E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date = 2011-08-17 keywords = respiratory; study; swab summary = OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. doi = 10.1016/j.ijid.2011.07.005 id = cord-317399-693q80xo author = Al Wahaibi, Adil title = COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date = 2020-08-20 keywords = COVID-19; China summary = title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population In this study, we will analyse the dynamics of COVID-19 infection transmissibility in Oman in the different populations (Omani and non-Omani) and the effects of the introduction of the nonpharmaceutical measures on disease transmissibility. With the increasing numbers of COVID-19 cases in Oman, our study showed the feasibility of using the time-varying Rt to assess and explain transmissibility dynamics and epidemic progression. However, the use of timevarying Rt in assessing the transmissibility dynamics and epidemic progression was a crucial tool to know how the mitigation measures influenced Rt. Nevertheless, a study from China demonstrated that changes in reporting rates substantially affect estimates of Rt. 23 Thus, the initial Rt is influenced by testing frequency, contact tracing, and reporting of mild cases outside hospital. doi = 10.1016/j.ijid.2020.08.039 id = cord-266253-oyid5haj author = Al-Abaidani, I.S. title = Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman date = 2014-10-29 keywords = MERS summary = Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. doi = 10.1016/j.ijid.2014.10.003 id = cord-275191-lgze4zex author = Al-Sadeq, Duaa W. title = The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date = 2020-07-02 keywords = SARS; asymptomatic; covid-19 summary = AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. doi = 10.1016/j.ijid.2020.06.098 id = cord-343789-6tq0kcfd author = Al-Tawfiq, Jaffar A. title = Ribavirin and interferon therapy in patients infected with the Middle East respiratory syndrome coronavirus: an observational study date = 2014-01-06 keywords = MERS; day summary = doi = 10.1016/j.ijid.2013.12.003 id = cord-323455-26xi2lqf author = AlBarrak, Ali title = Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date = 2018-02-21 keywords = Hajj; cap summary = This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. pneumoniae among adult Hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with Hajj and inform vaccination policy-making. General pattern of community-acquired pneumonia (CAP) case admissions to hospitals during the study period. It was aimed to systematically enroll all hospitalized X-ray-confirmed CAP cases among Hajj pilgrims during the study period. doi = 10.1016/j.ijid.2018.02.008 id = cord-282421-yialyuav author = Alcoba-Florez, Julia title = Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date = 2020-08-01 keywords = SARS summary = In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. doi = 10.1016/j.ijid.2020.07.058 id = cord-254377-j8e8gb0l author = Ali, Sadaf title = Acute cor pulmonale from saddle pulmonary embolism in a patient with previous Covid-19 – should we prolong prophylactic anticoagulation? date = 2020-06-13 keywords = Covid-19; patient summary = However, the risk associated with mild and moderate illness from Covid-19 is unknown, and there is no current recommendation for prophylaxis against thromboembolism in patients after hospital treatment unless there are established thrombophilic risk factors. We report the case of a 52-year old woman, who presented with massive saddle pulmonary embolism after one week of initial hospital discharge, successfully thrombolysed that raises the question of consideration of extended prophylactic anticoagulation even in low risk Covid-19 cases. 3 We report a case of acute massive PE successfully managed by thrombolysis in a patient who was discharged after one week of initial hospital treatment for Covid-19 pneumonia which raises serious concerns about the indication for extended prophylactic anticoagulation in such cases. Emerging data and clinical experience suggest an increased prevalence of venous thromboembolic events (VTE) in COVID-19, especially in patients with severe disease requiring hospitalization, and even among those who are not critically ill. doi = 10.1016/j.ijid.2020.06.039 id = cord-347907-0nrejsgr author = Alqahtani, Amani S. title = Exploring barriers to and facilitators of preventive measures against infectious diseases among Australian Hajj pilgrims: cross-sectional studies before and after Hajj date = 2016-02-10 keywords = Australian; Hajj; pilgrim summary = doi = 10.1016/j.ijid.2016.02.005 id = cord-024631-yvek5vjz author = Althaus, T. title = Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date = 2020-05-11 keywords = Asia; CRP; Southeast; test summary = OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. In this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in Southeast Asia, and to evaluate the performance of CRP for discriminating between bacteria and viruses. Specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of C-reactive protein (CRP) testing on antibiotic prescription in primary care [38] . We investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of CRP in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. Investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. doi = 10.1016/j.ijid.2020.05.016 id = cord-330819-vfagxsdz author = Althouse, Benjamin M title = Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date = 2018-08-14 keywords = ARI; RSV summary = Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. doi = 10.1016/j.ijid.2018.08.001 id = cord-301085-tk2vvxj7 author = Askarian, Mehrdad title = Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran date = 2006-07-11 keywords = knowledge summary = title: Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. [2] [3] [4] The purpose of our study was to measure the level of knowledge, attitude, and practice in surgeons and physicians in Shiraz University of Medical Sciences affiliated hospitals. doi = 10.1016/j.ijid.2006.01.006 id = cord-289304-9srk0ohb author = Bagnato, Sergio title = Critical illness myopathy after COVID-19 date = 2020-08-05 keywords = COVID-19; ICU summary = We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 (COVID-19). We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 . The patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (EMG) of the proximal and distal muscles, and direct muscle stimulation (DMS). In this report, we describe neurophysiological findings from a patient who developed severe muscular weakness, likely due to CIM, after hospitalization for COVID-19. The patient described here had myopathy, with greater involvement of the proximal muscles in the lower limbs, probably reflecting ICU-acquired weakness. Since rehabilitation programs can be effective to reverse muscle weakness caused by CIM, health systems must plan to provide adequate access to rehabilitative facilities for patients requiring both pulmonary and motor rehabilitative treatment after COVID-19. doi = 10.1016/j.ijid.2020.07.072 id = cord-355480-mx9dbm73 author = Bajunirwe, Francis title = Long distance truck drivers and the increasing risk of COVID-19 spread in Uganda date = 2020-06-29 keywords = Uganda; case summary = doi = 10.1016/j.ijid.2020.06.085 id = cord-255901-nl9k8uwd author = Barasheed, Osamah title = Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date = 2016-03-29 keywords = Hajj; facemask; respiratory; study summary = Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. doi = 10.1016/j.ijid.2016.03.023 id = cord-323696-0lq8ql6n author = Bearman, Gonzalo title = Reflections on the COVID-19 Pandemic in the USA: Will We Better Prepared Next Time? date = 2020-05-20 keywords = COVID-19; healthcare summary = We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. 1 We reflect on the US and its response to the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. doi = 10.1016/j.ijid.2020.05.059 id = cord-271495-5906wju4 author = Beldomenico, Pablo M. title = Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date = 2020-05-11 keywords = SARS; viral summary = Data and modelling supported the existence of ''superspreaders'' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. doi = 10.1016/j.ijid.2020.05.025 id = cord-283812-ocfjj79v author = Blumberg, Lucille title = Hosting of mass gathering sporting events during the 2013–2016 Ebola virus outbreak in West Africa: experience from three African countries date = 2016-06-15 keywords = Africa; EVD; Ebola summary = • The 2013–2016 Ebola virus disease (EVD) outbreak in West Africa that resulted in over 28 637 cases and 11 315 deaths required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of EVD. 7, 8 The unprecedented Ebola virus disease (EVD) epidemic in West Africa 9 and the ongoing Zika virus (ZIKV) outbreak in South America 10, 11 were declared Public Health Emergencies of International Concern (PHEIC) by the World Health Organization (WHO) in August 2014 and February 2016, respectively. 4, 14, 15 The 2013-2016 EVD outbreak in West Africa, which resulted in over 28 637 cases and 11 315 deaths, 16 required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of viral haemorrhagic fever (VHF). doi = 10.1016/j.ijid.2016.06.011 id = cord-349418-98sgr5iv author = Bo, Yacong title = Effectiveness of non-pharmaceutical interventions on COVID-19 transmission in 190 countries from 23 January to 13 April 2020 date = 2020-10-29 keywords = COVID-19; npi summary = doi = 10.1016/j.ijid.2020.10.066 id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 keywords = SARS; bat; figure; human; virus summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . doi = 10.1016/j.ijid.2020.08.050 id = cord-355343-dtdsd8j2 author = Buonsenso, Danilo title = Social consequences of COVID-19 in a low resource setting in Sierra Leone, West Africa date = 2020-06-01 keywords = Africa summary = doi = 10.1016/j.ijid.2020.05.104 id = cord-261058-yu2qw02l author = Burgner, David title = Kawasaki disease: What is the epidemiology telling us about the etiology? date = 2005-06-03 keywords = Kawasaki; coronary; disease summary = Thus in genetically susceptible children, acute infections such as those causing fever and rash, may result in unrecognised damage to the cardiovascular system that later manifests itself as adult cardiovascular disease. 3 The consensus view is that KD results from a widely distributed infectious agent (or possibly agents) that causes the clinical syndrome in genetically susceptible children. Kawasaki disease is more common in boys (male:female ratio 1.6:1) 1 a feature observed in many infectious diseases 30, 31 and also in coronary atherosclerosis, where sex differences in immune responses are suggested to mediate susceptibility. A recent report of an association between the presence of genetic material from a novel coronavirus and Kawasaki disease in a handful of cases 48 remains unproven and may reflect an epiphenomenon; the putative etiological agent is a relatively common viral pathogen in young children and it is unclear how long the DNA persists. doi = 10.1016/j.ijid.2005.03.002 id = cord-347499-7q47jh14 author = Burrel, Sonia title = Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date = 2020-10-25 keywords = SARS summary = doi = 10.1016/j.ijid.2020.10.040 id = cord-272179-wvw5mmy3 author = Calderaro, Adriana title = Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date = 2020-10-02 keywords = SARS; respiratory summary = title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children doi = 10.1016/j.ijid.2020.09.1473 id = cord-277640-vy7ex5lv author = Calderaro, Adriana title = SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date = 2020-05-14 keywords = SARS summary = The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. doi = 10.1016/j.ijid.2020.05.035 id = cord-293630-zc8huo1j author = Capone, Alessandro title = Simultaneous circulation of COVID-19 and flu in Italy: potential combined effects on the risk of death? date = 2020-08-05 keywords = COVID-19; Italy summary = Based on data updated to May 20, 2020, in Italy the total recorded number of patients who died due to COVID-19-related reasons is 31,851. While some of the excess mortality reported in the ILI group may be attributable to COVID-19, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? It would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from COVID-19 or influenza. While some of the excess mortality reported in the ILI group (in over 65) may be attributable to COVID-19 infection actually, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? doi = 10.1016/j.ijid.2020.07.077 id = cord-311413-uiwjrvru author = Chanda-Kapata, Pascalina title = COVID-19 and malaria: A symptom screening challenge for malaria endemic countries date = 2020-04-27 keywords = COVID-19; malaria summary = COVID-19 currently imposes an additional burden to the already overstretched, resource strapped health services which are grappling to bring under control the high burden of existing infectious and non-infectious diseases, including TB, HIV, and malaria. Health care workers and community members alike are faced with an important challenge of quickly identifying symptoms and taking appropriate steps for laboratory investigation in line with the case definition based on surveillance or clinical characterisation (WHO, 2020a) . Key steps to identifying a COVID-19 case ultimately involves symptomatic or high risk patients presenting to health providers with complaints of any of the following symptoms or travel history: fever, cough, shortness of breath, fatigue, headache and others of acute onset or history of travel to affected areas or contact with an infected person. Thus, current screening approaches for COVID-19 are likely to miss approximately 50% of the infected cases even in countries with good health systems and available diagnostic capacities (Gostic et al., 2020) . doi = 10.1016/j.ijid.2020.04.007 id = cord-283590-xvnv17zy author = Chen, Dabiao title = Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date = 2020-03-05 keywords = RNA; SARS summary = Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People''s Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). doi = 10.1016/j.ijid.2020.03.003 id = cord-317624-qdzhncs0 author = Choi, Min Joo title = Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study date = 2020-10-27 keywords = COVID-19; HCQ; LPV summary = METHODS: Nationwide retrospective case-control study was conducted to compare the effect of HCQ and LPV/r on viral shedding duration among patients with mild-to-moderate COVID-19 using the reimbursement data of National Health Insurance Service. This study aimed to compare the effect of HCQ and LPV/r on the viral shedding duration among patients with mild-to-moderate COVID-19 cases using South Korea''s National Health J o u r n a l P r e -p r o o f Insurance Service (NHIS) database. Among these, only mild-to-moderate grade 1 patients were included in the analysis, and the effect of LPV/r or HCQ use on viral shedding duration was evaluated ( Figure 1 ). In the previous studies including mild COVID-19 patients in CTCs, the mean viral shedding duration from symptom onset was 21-24.5 days, which is longer than the results of our control group , Noh et al., 2020 . doi = 10.1016/j.ijid.2020.10.062 id = cord-258669-ubw6mdzi author = Colebunders, Robert title = A call for strengthened evidence on targeted, non-pharmaceutical interventions against COVID-19 for the protection of vulnerable individuals in sub-Saharan Africa date = 2020-08-27 keywords = Africa; covid-19; saharan summary = We suggest investigating the feasibility, acceptability, and efficacy of distributing COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. Here, we call for the generation and strengthening of evidence to guide non-pharmaceutical interventions for COVID-19, which we illustrate with a practical proposal for assessing the impact of targeted protection of at-risk individuals in settings in sub-Saharan Africa. Although the early implementation of lockdown measures for COVID-19 control may have contributed to the (initially) low mortality observed in most sub-Saharan Africa countries, the collateral damage resulting from this strategy is becoming increasingly apparent. We therefore propose to complement the extant containment measures in sub-Saharan Africa with more targeted protection strategies, aiming at protecting people at risk of severe COVID-19 disease. One strategy could be to distribute COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. doi = 10.1016/j.ijid.2020.08.060 id = cord-268883-nf4fm7r7 author = Corchuelo, Jairo title = Oral manifestations in a patient with a history of asymptomatic COVID-19. Case Report date = 2020-09-01 keywords = COVID-19; oral summary = This case shows that the problems that arise in the oral mucosa in patients with suspected or confirmed SARS-CoV-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technology currently available worldwide. Due to the use of intensified therapeutic methods possibly aggravated by SARS-CoV-2, an increase in cases with oropharyngeal symptoms / conditions, dental-oral problems associated with soft tissues, saliva production (dry mouth) as side effects, could be predicted, even after recovering from COVID-19. Taking into account that Candida albicans is part of the oral microbiome and that there were favorable events for its pathological development, such as the decrease in salivation manifested in the patient by the sensation of dry mouth, in addition to the frequent use of antibiotics and a mild predisposing factor such as the female sex (Zegarelli 1993) and the successful response to nystatin treatment, we can clinically confirm candida infection The hyperpigmentation of the gums in the anterior teeth due to the aesthetic problem that it represents for the patient is the one that causes of most concern. doi = 10.1016/j.ijid.2020.08.071 id = cord-272015-1anph6qi author = Dauby, Nicolas title = The unfinished story of hydroxychloroquine in COVID-19: the right anti-inflammatory dose at the right moment? date = 2020-10-17 keywords = COVID-19 summary = The observation by Lammers et al (Lammers et al.) that early HCQ treatment after admission at low dosage (2400 mg in total) is associated with lower risk of admission in intensive care unit coincides with large observational studies showing a lower mortality rate in patients exposed to HCQ therapy compared to no or other treatment. Another recent large cohort study of patients on low-dose HCQ for inflammatory disorders reported an association between chronic HCQ use and reduced mortality following SARS-CoV-2 infection (Gentry et al. The association of treatment with hydroxychloroquine and hospital mortality in COVID-19 patients Low-dose hydroxychloroquine therapy and mortality in hospitalised patients with COVID-19: a nationwide observational study of 8075 participants Use of hydroxychloroquine in hospitalised COVID-19 patients is associated with reduced mortality: Findings from the observational multicentre Italian CORIST study Longterm hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study doi = 10.1016/j.ijid.2020.10.032 id = cord-338225-8dlxnpcn author = De Meyer, Sandra title = Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date = 2020-05-29 keywords = SARS summary = Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. doi = 10.1016/j.ijid.2020.05.085 id = cord-274028-dvsvtsn0 author = Del Brutto, Oscar H. title = SARS-CoV-2-related mortality in a rural Latin American population date = 2020-08-08 keywords = SARS summary = Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . doi = 10.1016/j.ijid.2020.08.003 id = cord-328459-nmd81sue author = Dioscoridi, Lorenzo title = Covid-19 exposure risk for family members of healthcare workers: an observational study date = 2020-07-04 keywords = SRT summary = However, no available papers discussed the risk of exposure of family members (FM) of HWs. Aims The present study collected the data of SARS-COV-2 positive FM of HWs using serological rapid IgM/IgG tests (SRT) compared with positive HWs at SRT and serological quantitative IgG test (SQT). The key element of our study was to assess the total number of family members (FM) of HWs positive to SARS-COV-2 infection and the number of positive HWs working in a COVID-19 hospital. The SRT studied both IgG and IgM with a declared sensitivity of 100% for IgG and 85% for IgM SQT used in the study was ELISA test researching IgG anti-S1/anti-S2 for SARS-CoV-2, available and validated for HWs screening in the region of the study (Lombardia, Italy). For both HWs and FMs, exposure to COVID-19 cases, onset of suspicious symptoms (also before the study period since the 1 st February 2020), photos of the serological tests after 10 minutes, serological tests'' platforms, past medical history, drugs and clinical course were registered. doi = 10.1016/j.ijid.2020.06.106 id = cord-262310-z0m6uuzf author = Effenberger, Maria title = Association of the COVID-19 pandemic with Internet Search Volumes: A Google TrendsTM Analysis date = 2020-04-17 keywords = Google; Trends summary = Methods We performed a Google TrendsTM search for "Coronavirus" and compared Relative Search Volumes (RSV) indices to the number of reported COVID-19 cases by the European Center for Disease Control (ECDC) using time-lag correlation analysis. The worldwide Google TrendsTM index reached its peak on the 12th of March 2020 at a time when numbers of infected patients started to increase in Europe and COVID-19 was declared a pandemic. In European countries, especially in Italy, a small peak in the Google Trends TM analysis was found during the outbreak in China and a climax was found on February 23 rd 2020, a few days before the numbers of newly COVID-19 started to increase exponentially. The peak of search queries was March 3 rd a new increase in RSV is found in Brazil, followed by increasing numbers of newly confirmed cases of COVID-19 ( Figure 2 ). doi = 10.1016/j.ijid.2020.04.033 id = cord-293247-ltxt2dfv author = Elachola, Habida title = Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings date = 2015-10-09 keywords = Hajj; gathering summary = title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings Although current GHSA is yet to specifically highlight mass gathering preparedness as a strategic priority even in countries with high participant contribution to mass gatherings, the 12 Global Health Security Agenda action packages and the strategies to minimize the implications of mass gathering on public health are similar. Given that two-thirds of the emerging diseases are zoonotic, human-animal interaction during some mass gatherings such as the Hajj further increases the risk, and Saudi Arabia imports sacrifice animals from 6 countries. Mass gatherings offer opportunities to implement, test, and assess GHSA objectives in its entirety and can contribute significantly to health security of individuals, nations, and the world. Mass gatherings medicine and global health security doi = 10.1016/j.ijid.2015.10.003 id = cord-268037-szhzmzys author = Eshaghi, A. title = A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains date = 2008-12-17 keywords = H1N1 summary = authors: Eshaghi, A.; Blair, J.; Burton, L.; Lombos, E.; Choi, K.; De Lima, C.; Drews, S.J. title: A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains The purpose of this brief investigation was to determine whether nasopharyngeal specimens from patients infected with strains of influenza A (H1N1) carrying the H274Y mutation were more likely than not to contain other commonly circulating respiratory viral pathogens. Isolate sequences were compared to sequences with described H274Y mutations: GenBank accession No. 7 Specimens corresponding to H274Y mutant and H274 wild-type isolates were blinded and chosen at random for a retrospective investigation for other respiratory viral pathogens (adenovirus, coronavirus 229E/NL63, coronavirus OC43, influenza A/B, parainfluenza virus 1/2/3, respiratory syncytial virus A/B, rhinovirus A) using the Seeplex 1 RV detection kit protocol (Seegene, Inc., Rockville, MD). doi = 10.1016/j.ijid.2008.07.026 id = cord-340279-bq5owwot author = Espíndola, Otávio de Melo title = Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date = 2020-06-04 keywords = SARS summary = key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection doi = 10.1016/j.ijid.2020.05.123 id = cord-330136-o8df8szx author = Fan, Hua title = Cardiac injuries in patients with coronavirus disease 2019: Not to be ignored date = 2020-05-11 keywords = COVID-19; patient summary = 40 non-survivors had test result of hs-TnI，they were divided into two groups based on cardiac injury，Further analysis revealed that non-survivors with elevated hs-TnI levels on admission had shorter duration from symptom onset to death, and TnI elevation was related to the dismal prognosis. The mortality of critically ill COVID-19 patients is high, but its mechanism is not clear at present, and it might be related to the virus-induced acute lung injury, inflammatory factor storm. Our study discovered that the level of hs-TnI increased in many patients on admission, indicating that cardiac injury occurred in the early stage of the disease.The incidence rate of cardiac injury among patients at admission was 16.44%, with the non-survivors having an incidence rate of as high as 25.53%. Association of Cardiac Injury With Mortality in Hospitalized Patients With COVID-19 in Wuhan, China doi = 10.1016/j.ijid.2020.05.024 id = cord-320902-1hfxju5f author = Filocamo, Giovanni title = Use of anakinra in severe COVID-19: a case report date = 2020-05-11 keywords = COVID-19; SARS summary = As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still''s disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient''s critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). doi = 10.1016/j.ijid.2020.05.026 id = cord-340410-s9haq8y1 author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-06-26 keywords = SARS summary = doi = 10.1016/j.ijid.2020.06.074 id = cord-292092-o6s5nw49 author = Furuse, Yuki title = Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date = 2015-09-30 keywords = MERS summary = title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. 5 The laboratory diagnosis of MERS-CoV infection is mainly performed using real-time reverse transcription PCR (RT-PCR) to detect viral RNA in specimens. This study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the RT-PCR protocols for the molecular diagnosis of MERS-CoV infections. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Table 1 Conservation of the primer and probe region sequences of the WHO-recommended assays for the molecular diagnosis of MERS-CoV doi = 10.1016/j.ijid.2015.09.018 id = cord-339576-0d6sa9pe author = Guallar, María Pilar title = Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date = 2020-06-14 keywords = SARS; covid-19 summary = Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure doi = 10.1016/j.ijid.2020.06.035 id = cord-311479-8pjoz64q author = He, Daihai title = The relative transmissibility of asymptomatic cases among close contacts date = 2020-04-18 keywords = case summary = A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. 28 29 Keywords: COVID-19; asymptomatic cases; relative transmissibility 30 31 32 33 Main text 35 Nishiura et al (Nishiura et al, 2020 ) estimated the asymptomatic ratio of COVID-19 was 41.6% 36 (5 out of 12 confirmed cases) among 565 Japanese individuals evacuated from Wuhan, China. The odds ratio (OR) is estimated 109 In summary, we conclude that the relatively transmissibility of asymptomatic case could be 127 significantly smaller than that of the symptomatic cases. Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-158 19) Estimating the asymptomatic 161 proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess 162 cruise ship doi = 10.1016/j.ijid.2020.04.034 id = cord-330692-rqwkkfp0 author = He, Daihai title = Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date = 2020-06-26 keywords = SARS summary = doi = 10.1016/j.ijid.2020.06.075 id = cord-273090-fdzkfo1u author = He, Susu title = Relationship between Chest CT manifestations and immune response in COVID-19 patients date = 2020-06-20 keywords = IL-6; patient summary = In critically ill patients, the decrease of absolute value of CD4 + T cells and increase of IL-6 level are significantly correlated with the volume of lung lesions. There have been many reports that most of the 2019-nCoV patients have chest CT manifestations of pneumonia, typically showing bilateral ground-glass shadows and patchy shadows, and a few can also appear as consolidation shadows and interstitial lesions, the laboratory showed that the lymphocytes count in most patients decreased [6] [7] [8] [9] , with gradually worsened the disease, the lymphocytes absolute count continued to decline [9] , and has been There are reports in the literature that the proinflammatory cytokines IL-2, IL-6, IL-8, IL-10, and TNF-α are elevated in some 2019-nCoV patients [7] [8] . The purpose of this study is to investigate changes in lymphocytes counts and cytokines levels induced by 2019-nCoV and their effects on lung lesions, to determine the severity of the disease, and to select markers that could prompt early clinical intervention. doi = 10.1016/j.ijid.2020.06.059 id = cord-320829-uepneyug author = He, Zhongping title = Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date = 2005-08-10 keywords = CD8; SARS summary = title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS doi = 10.1016/j.ijid.2004.07.014 id = cord-300774-5mrkmctl author = Hernández-Mora, Miguel Górgolas title = Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date = 2020-10-25 keywords = SARS; TCZ; Tocilizumab; patient summary = INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . doi = 10.1016/j.ijid.2020.10.045 id = cord-258250-zueo1xfa author = Hirotsu, Yosuke title = Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date = 2020-08-12 keywords = PCR; SARS summary = title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . doi = 10.1016/j.ijid.2020.08.029 id = cord-265146-j0n3a4m6 author = Hsieh, Ying-Hen title = Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan date = 2013-02-12 keywords = HIV; IDU; Taiwan summary = Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. RESULTS: Model fit revealed a two-wave epidemic during April 2004–March 2007. Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. Results: Model fit revealed a two-wave epidemic during April 2004-March 2007. Correlation analysis was performed in an attempt to determine the relationship between the male and female IDUs. The data used here were extracted from the monthly reported HIV case data between April 2004 and March 2007, for a total of 36 months, made available by the Taiwan Centers for Disease Control and Prevention (TCDC) on the TCDC website. The monthly time series data of reported HIV cases for male IDUs, female IDUs, and all IDUs in Taiwan were fit to the Richards model as in Figure 1 and Table 1 The effective reproduction number R was computed for each wave. doi = 10.1016/j.ijid.2013.01.002 id = cord-283891-m36un1y2 author = Hu, Bisong title = First, second and potential third generation spreads of the COVID-19 epidemic in mainland China: an early exploratory study incorporating location-based service data of mobile devices date = 2020-05-17 keywords = China; Hubei; Wuhan summary = Methods We used spatiotemporal data of COVID-19 cases in mainland China and two categories of location-based service (LBS) data of mobile devices from the primary and secondary epidemic sources to calculate Pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. Here, using location-based service (LBS) data of mobile devices, we analyzed the spatiotemporal association of the confirmed COVID-19 cases and human movements from the sources of the epidemic outbreak, and revealed the first, second and potential third generation spreads of the COVID-19 epidemic in mainland China. Based on the above datasets of COVID-19 cases in mainland China and two categories of location-based service data of mobile devices from the epidemic sources, we calculated their Pearson correlation coefficient, r, and spatial stratified heterogeneity (SSH), q, statistics. doi = 10.1016/j.ijid.2020.05.048 id = cord-258078-k7y8k1vx author = Jang, Sukbin title = Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy date = 2020-05-26 keywords = COVID-19; March summary = title: Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy We report three cases of COVID-19 pneumonia who progressed while using antiviral drugs and needed supplementary oxygen therapy, improved after treatment with nafamostat. Three COVID-19 patients had the following conditions: pneumonia with progression despite antiviral treatment; were elderly, over 65 years; and had underlying diseases that were known as high risk J o u r n a l P r e -p r o o f factors. On admission, he was not dyspneic or cyanotic, with a body temperature of 37.0°C, respiratory rate of 20 breaths per minute, heart rate of 75 beats per minute, and blood pressure of 140/90 mmHg. Initial laboratory results were as follows: white blood cell (WBC) count 5,150/μL (65% segmented neutrophil), and C-reactive protein (CRP) 2.61 mg/dL. doi = 10.1016/j.ijid.2020.05.072 id = cord-315860-9j667c03 author = Jullien, Sophie title = Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study date = 2020-04-10 keywords = Bhutan; child; pneumonia summary = METHODS: This prospective study enrolled children aged 2–59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital with World Health Organization (WHO)-defined clinical pneumonia. CONCLUSION: Respiratory viral infections predominated among this cohort of WHO-defined clinical pneumonia cases, whereas bacterial aetiologies were uncommon, highlighting the epidemiologic transition that Bhutan seems to have reached. We conducted this prospective hospital-based observational study to describe the epidemiology, aetiology, and clinical and radiological presentation of World Health Organization (WHO)defined pneumonia among children aged between 2 and 59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital in Thimphu. All children aged 2-59 months hospitalized with WHO-defined pneumonia (irrespective of severity) were eligible for recruitment (World Health Organization, 2014) (see Box 1). Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study doi = 10.1016/j.ijid.2020.04.017 id = cord-259837-5tbdqzxr author = Kalcioglu, Mahmut Tayyar title = May COVID-19 cause sudden sensorineural hearing loss? date = 2020-09-29 keywords = COVID-19 summary = title: May COVID-19 cause sudden sensorineural hearing loss? In previous studies, viral infections have been reported to have an important role in the etiology of sudden sensorineural hearing loss (SSNHL) (Cohen et al., 2014) . Moreover, recently, studies on the effects of SARS-CoV-2 virus on central and peripheral nervous systems have been published. Some of these studies have reported Guillain -Barré syndrome (Toscano et al., 2020) and impaired olfactory function (Eliezer et al., 2020) to be related to SARS-CoV-2. Another recently published study reported neurologic changes in 58 of 64 patients with COVID-19 (Helms et al., 2020) . Therefore, we investigated the possibility of SARS-CoV-2 infection in these J o u r n a l P r e -p r o o f patients. Sudden and Complete Olfactory Loss Function as a Possible Symptom of COVID-19 An investigation into SARS-COV-2 in the etiology of sudden sensorineural hearing loss doi = 10.1016/j.ijid.2020.09.1468 id = cord-268389-0agwvsrv author = Kaminski, Monica A. title = Tocilizumab Therapy of COVID-19: A Comparison of Subcutaneous and Intravenous Therapies date = 2020-09-28 keywords = COVID-19 summary = This study aimed to compare the effects of intravenous (IV) and subcutaneous (SC) tocilizumab, an IL-6 receptor antagonist, on respiratory parameters and clinical outcome in patients with COVID 19. C-reactive protein levels were significantly higher in patients in the IV group that did not respond (Table 2) Lastly, laboratory markers of inflammation were analyzed before and during the seven days following tocilizumab therapy to identify trends that correlated with response involving the respiratory parameters (Table 3) . Tocilizumab has been found to be associated with improved outcomes in patients with COVID-19 related respiratory disease, particularly for patients with critical illness (i.e., requiring mechanical ventilation) (Rossotti et al., 2020 , Somers et al., 2020 . In our report, levels of C-reactive protein fell acutely in both patients that did and did not have improvement in respiratory parameters seven days following tocilizumab therapy. doi = 10.1016/j.ijid.2020.09.1447 id = cord-291638-oatrjbo3 author = Kang, Dayun title = Spatial epidemic dynamics of the COVID-19 outbreak in China date = 2020-04-03 keywords = COVID-19; China summary = This study described the spatio-temporal pattern and measured the spatial association of the early stages of the COVID-19 epidemic in mainland China from 16 January–06 February 2020. The results showed that most of the models, except medical-care-based connection models, indicated a significant spatial association of COVID-19 infections from around 22 January 2020. There are 31 provinces in mainland China, and this study used 3 weeks'' data from 16 January to 06 February 2020, which was during the early stages of COVID-19 in China. Because COVID-19 spread from Hubei Province, the epicentre of the outbreak, the number of newly confirmed cases in the provinces neighbouring Hubei was investigated. It used Moran''s I statistic, a measure of spatial association, for the number of confirmed cases with different types of neighbourhoods. On 22 January Models 1-4 first detected a significant spatial dependency on the number of newly confirmed cases. Since approximately 24 January, the number of newly confirmed cases show significant spatial dependency in Models 1 and 2. doi = 10.1016/j.ijid.2020.03.076 id = cord-351740-779g8tr1 author = Khaba, Moshawa Calvin title = COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date = 2020-09-25 keywords = COVID-19; HIV summary = doi = 10.1016/j.ijid.2020.09.1435 id = cord-321412-6g3obmzc author = Khamis, Faryal title = Therapeutic Plasma Exchange in Adults with Severe COVID-19 Infection date = 2020-06-23 keywords = TPE; covid-19 summary = doi = 10.1016/j.ijid.2020.06.064 id = cord-261672-0cresfn8 author = Kim, Sungchan title = Evaluation of COVID-19 epidemic outbreak caused by temporal contact-increase in South Korea date = 2020-05-14 keywords = Korea summary = OBJECTIVES: On March 15, 2020, 61.3% of the confirmed cases of COVID-19 infection are associated with the worship service that was organized on February 9 in the Shincheonji Church of Jesus in Daegu, South Korea. METHOD: Using opened data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model. The effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on February 9 in the Shincheonji Church of Jesus, Daegu. However, the effective reproduction number decreased to less than unity after February 28 owing to the implementation of high-level preventive control interventions in South Korea, coupled with voluntary prevention actions by citizens. In this study, we aimed to evaluate the effects of mass infection due to temporal increases in contacts and assess the preventive control interventions using the confirmed cases and deaths data associated with COVID-19 in Korea. doi = 10.1016/j.ijid.2020.05.036 id = cord-259501-iggw1exl author = Kim, Yong Yean title = Acute Respiratory Illness in Rural Haiti date = 2019-02-14 keywords = Haiti; child summary = Earlier studies in resource-poor settings have identified Streptococcus pneumoniae, Haemophilus influenzae type B and Staphylococcus aureus as important bacterial causes of ARI, and respiratory syncytial virus (RSV) and Influenza as important viral causes (Rudan et al., 2008) . A multicountry study that included Haiti showed that agents detected in hospitalized children less than 5 years of age who had pneumonia included RSV, Influenza A and B, Parainfluenza viruses, Adenovirus and Human metapneumovirus (HMPV) (Bénet et al., 2017) . Analysis of specific viral or bacterial agents detected showed more children with FluA or FluB had LRTI (33%) compared to URTI (15%) [ Table 5 ]. The overall findings of RV as the most common virus detected followed by Influenza in Haiti is comparable to that found in studies of children in other tropical, resource-poor countries (Hoffman et al., 2012; Schlaudecker et al., 2012; Taylor et al., 2017) . doi = 10.1016/j.ijid.2019.02.003 id = cord-311453-l6quzef6 author = Klopfenstein, Timothée title = Impact of Tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 COVID-19 patients date = 2020-08-13 keywords = COVID-19; TCZ summary = CONCLUSION: Despite the small sample size in the group TCZ, this result suggests that TCZ reduces mortality and/or IMV requirement in patients with severe SARS-CoV-2 pneumonia. We have recently published a retrospective study including 45 patients treated in our hospital, which shows that TCZ seems to reduce the number of COVID-19 severe cases and/or mortality (11) . Based on the medical literature, we checked several criteria before starting TCZ treatment: no contraindication to TCZ, confirmed COVID-19 with real-time reverse transcription (RT)-PCR SARS-CoV-2 RNA, failure of standard treatment, period since symptoms onset ≥ 5 days, oxygen therapy ≥ 4 liters/min, ≥ 25% of lung damages on chest computed tomography (CT) scan, and ≥ 2 parameters of inflammation or biological markers of mortality (with a high level) such as ferritin, CRP, D-dimer, lymphopenia, and/or lactate dehydrogenase. doi = 10.1016/j.ijid.2020.08.024 id = cord-300583-0krbrj4w author = Koh, Wee Chian title = Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis date = 2020-08-13 keywords = case; measure summary = METHODS: We identified three distinct physical distancing measures with varying intensity and implemented at different times—international travel controls, restrictions on mass gatherings, and lockdown-type measures—based on the Oxford COVID-19 Government Response Tracker. INTERPRETATION: A combination of physical distancing measures, if implemented early, can be effective in containing COVID-19—tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak. is the average reproduction number of country over the 14 days following the date of the 100 th case; is country ''s physical distancing measure of type on the date of the 100 th case; represents the country characteristic (income level, population density, age structure, and temperature) of country ; is a constant term, ''s are the regression coefficients, and denotes the error term. doi = 10.1016/j.ijid.2020.08.026 id = cord-304743-0bsdahh6 author = Kortepeter, Mark G title = Marburg Virus Disease: a Summary for Clinicians date = 2020-08-03 keywords = Ebola; Marburg summary = Abstract Objectives This article is a summary of countermeasures for Marburg virus disease focusing on pathogenesis, clinical features, and diagnostics, with an emphasis on therapies and vaccines that have demonstrated potential for use in an emergency situation, through their evaluation in nonhuman primates (NHPs) and/or in humans. Results We identified six treatments and four vaccine platforms that have demonstrated potential benefit for treating or preventing infection in humans, through their efficacy in NHPs. Conclusion We provide succinct summaries of Marburg countermeasures to give the busy clinician a head start in reviewing the literature if faced with a patient with Marburg virus disease. Postexposure protection against Marburg haemorrhagic fever with recombinant vesicular stomatitis virus vectors in non-human primates: an efficacy assessment Vesicular stomatitis virus-based vaccines protect nonhuman primates against aerosol challenge with Ebola and Marburg viruses. Single-injection vaccine protects nonhuman primates against infection with Marburg virus and three species of ebola virus doi = 10.1016/j.ijid.2020.07.042 id = cord-305763-160heazx author = Lai, Chih-Cheng title = Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date = 2020-10-09 keywords = COVID-19; SARS summary = One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. doi = 10.1016/j.ijid.2020.10.011 id = cord-286743-z0e5arlm author = Langer-Gould, Annette title = Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab date = 2020-08-06 keywords = COVID19-CS; anakinra; patient summary = Subsequently, a shift in practice by clinicians at some of our medical centers aimed to identify early COVID19-CS through laboratory abnormalities in patients with increasing O2 requirements and to initiate combined treatment with anakinra and corticosteroids occurred. Data were extracted by manual reviewing the EHR, including onset of dyspnea and other COVID-19 symptoms, age, sex, comorbidities, smoking status, tocilizumab and anakinra use, other J o u r n a l P r e -p r o o f treatments rendered for hydroxychloroquine, and/or corticosteroids) , fever (>100.4F), hypotension requiring pressors, dates of admission, intubation, extubation, discharge and/or death. The primary purpose of analyses was to describe clinical outcomes among tocilizumab-or anakinra-treated COVID-19 patients and to examine whether differences in outcomes could be accounted for by COVID19-CS severity and/or duration at the time of treatment initiation (baseline). doi = 10.1016/j.ijid.2020.07.081 id = cord-008219-ng9xb46c author = Lassmann, Britta title = Highlights from the 6(th) International Meeting on Emerging Diseases and Surveillance (IMED 2016) Vienna, Austria from Nov 3 to 7, 2016 date = 2016-12-09 keywords = Health summary = c o m / l o c a t e / i j i d During the oral abstract presentation session on One Health -Diseases Across Species Boundaries, Toph Allen from EcoHealth Alliance and colleagues shared results from an updated model assessing the global distribution of zoonotic emerging infectious disease risk. Professor [ 1 7 _ T D $ D I F F ] Daniel Lucey summarized the commissions'' recommendations including the importance of strengthening national health systems, consolidating and strengthening World Health Organization (WHO) emergency and outbreak response activities, and enhancing research and development. In a separate session, the challenges posed by climate change on infectious disease outbreaks and how to best prevent and track diseases in mobile populations were discussed. The importance of the food chain as a source for emergence and spread of antimicrobial resistance between animals and humans was highlighted in a nation-wide study in Lebanon. doi = 10.1016/j.ijid.2016.12.008 id = cord-276445-m5vjo3ym author = Lee, Hyojung title = Recrudescence of Ebola virus disease outbreak in West Africa, 2014–2016 date = 2017-09-20 keywords = Health summary = For the Ebola virus disease (EVD) outbreak in West Africa from 2014 to 2016, the World Health Organization (WHO) recommended securing 42 days (World Health Organization, 2015) , or twice the observed maximum incubation period, from the time at which the last case was found negative for the virus at second testing. WHO reports and other sources were reviewed in an analysis of all known recrudescence events occurring from 2014 to 2016 (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . A total of five cases of recrudescence were identified ( Figure 1 ): three occurred in Liberia and one each in Guinea and Sierra Leone (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . doi = 10.1016/j.ijid.2017.09.013 id = cord-349645-6o8773c5 author = Li, He title = Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date = 2020-06-02 keywords = SARS; covid-19 summary = doi = 10.1016/j.ijid.2020.05.076 id = cord-275866-m89hgf41 author = Li, Ping title = Clinical Features and Short-term Outcomes of Elderly Patients With COVID-19 date = 2020-05-31 keywords = COVID-19 summary = Methods 204 elderly patients (≥60 years old) diagnosed with COVID-19 in Renmin Hospital of Wuhan University from January 31st to February 20th, 2020 were included in this study. Multivariate analysis showed that dyspnea (hazards ratio (HR) 2.2, 95% confidence interval (CI) 1.414 to 3.517;p < 0.001), older age (HR 1.1, 95% CI 1.070 to 1.123; p < 0.001), neutrophilia (HR 4.4, 95% CI 1.310 to 15.061; p = 0.017) and elevated ultrasensitive cardiac troponin I (HR 3.9, 95% CI 1.471 to 10.433; p = 0.006) were independently associated with death. Univariate analysis showed age of 70 years or older, comorbidity (hypertension, J o u r n a l P r e -p r o o f cardiovascular disease, COPD, chronic renal failure), onset of dyspnea, and several laboratory indices abnormalities were associated with poor outcome. This study suggests that the elderly patients of COVID-19 have a rapid course of the disease and a higher case fatality ratio. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China doi = 10.1016/j.ijid.2020.05.107 id = cord-274845-pqvlh3eg author = Li, Yan title = Characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in Beijing date = 2020-05-07 keywords = Flu summary = Here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory virus infection. COVID-19 group (83.33%) had higher rate of pneumonia in chest CT scan than Flu A and B virus infection groups. There was no statistical difference in complete blood count parameters between Similar to what was reported in COVID-19 [9] , fever was the most common symptom in the respiratory virus infection patients. In this study, the ratio of fever and the highest temperature were higher in Flu A virus infection patients than in COVID-19 patients. And in this study, it showed that COVID-19 patients even had lower WBC count and neutrophil count than Flu A virus and RSV infection group. Also, it was reported that they had low lymphocyte count [9, 10] , but this study found that the lymphocyte count was higher in COVID-19 than in Flu A and B virus infection patients. doi = 10.1016/j.ijid.2020.05.008 id = cord-318808-1cfwj5uq author = Li, Ying title = Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years date = 2020-06-12 keywords = covid-19; patient summary = title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years Abstract Background Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. Therefore, the aim of this study was to compare the different clinical Page 5 of 15 J o u r n a l P r e -p r o o f 5 presentations between patients with infected with COVID-19 pneumonia versus influenza A pneumonia, to provide some recommendations for their differential diagnosis. Our present study revealed that COVID-19 manifested as mild, severe pneumonia were less than influenza A patients. In conclusion, COVID-19 patients were mild not only in clinical symptoms but also in laboratory examinations which including lymphocyte, CRP, PCT, D-dimer in the children under 5 years. doi = 10.1016/j.ijid.2020.06.026 id = cord-332348-yi85sfks author = Liang, Yujie title = Neurosensory dysfunction: a diagnostic marker of early COVID-19 date = 2020-06-29 keywords = COVID-19; SARS summary = Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. doi = 10.1016/j.ijid.2020.06.086 id = cord-290206-fmy4zrim author = Lim, Jue Tao title = The Costs of an Expanded Screening Criteria for COVID-19: A Modelling Study date = 2020-08-12 keywords = ESC; PIR; case summary = The screening process should therefore maximise sensitivity to minimise the number of missed cases and risk of nosocomial transmission, which occurred in Singapore during another coronavirus outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003. Using ESC, NUH clinicians were able to identify and isolate 13 patients who did not fit the WHO SARS criteria but were eventually confirmed to have SARS, who would have otherwise been potential spreaders (the number of positive and negative cases for SARS are presented in Supplementary Table 1.) 12 Clinicians responded to the COVID-19 crisis similarly, implementing ESC on 7 th February 2020, which was approximately three weeks after the first imported case. At an of 2.5 and incubation period (IP) of 4 days, approximate to estimates by Wu and colleagues 29 for Wuhan, an estimated 240 (95% CI: 200-290) cases would be prevented over 150 days through ESC by isolating patients presenting fever or respiratory symptoms such as cough with their travel and exposure profile not considered (Table 2) . doi = 10.1016/j.ijid.2020.08.025 id = cord-354780-yzyixucr author = Lin, Chih-Yen title = Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date = 2020-06-13 keywords = SARS; Taiwan summary = doi = 10.1016/j.ijid.2020.06.031 id = cord-282177-8l7zukg4 author = Lin, Yi-Chun title = A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date = 2020-05-26 keywords = SARS summary = title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 doi = 10.1016/j.ijid.2020.05.070 id = cord-320785-42p8292o author = Lobo, Andréa de Paula title = COVID-19 epidemic in Brazil: where we at? date = 2020-06-16 keywords = COVID-19 summary = Abstract Objetive to analyze the trends of COVID-19 in Brazil in 2020 by Federal Units (FU). Joinpoint regression models were applied to identify points of inflection in COVID-19 trends, considering the days since the 50th confirmed case as time unit. Conclusions In summary, our results show that all FUs in Brazil present upward trends of COVID-19. Discussion: Although all FUs presented upward trends in the number of cumulative cases of COVID-19, 18 out of 27 FUs showed a reduction in the pace of the trend in the last segment. Even though the FUs from the Southeast region presented most of the confirmed cases, the highest ADPC values were found in the Northeast and North regions. (36.9;58.8) 3-11 13.8*(12.7;14.9) 11-20 8.1*(7.2;9.0 • All of Federative Units in Brazil shows a upward in accumulated cases of COVID-19. • Each Federative Unit in Brazil is at a different stage of the COVID-19 pandemic. doi = 10.1016/j.ijid.2020.06.044 id = cord-254776-m4makxr8 author = Luo, Shiua title = A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China date = 2020-06-01 keywords = covid-19 summary = title: A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China The 2019 novel coronavirus disease (COVID-19) epidemic has clearly entered a new stage with rapid spread in countries outside China [1] . Currently, a large number of COVID-19 patients in Wuhan have been cured and discharged. In Wuhan, China, all cured patients with COVID-19 are required to quarantine in either a designated hotel room or at home for 14 days [3] . We retrospectively evaluated the data of the recovered patients with COVID-19 in two different designated fever clinics in Wuhan, with a goal to provide relevant information about these patients. In this study, only 7.7‰ patients experienced recurrence during isolation and observation, and all presented with mild symptoms. Serological tests to identify antibodies played a key role in surveillance of recurrence of COVID-19 [4] . Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) doi = 10.1016/j.ijid.2020.05.119 id = cord-323332-vu2cre8k author = Luo, Yang title = Factors impacting compliance with standard precautions in nursing, China date = 2010-11-10 keywords = compliance; precaution; standard summary = doi = 10.1016/j.ijid.2009.03.037 id = cord-255021-acgfwjwi author = Luo, Ying title = Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus date = 2020-05-01 keywords = NCPP summary = title: Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus Abstract Background The differential diagnosis between novel coronavirus pneumonia patients (NCPP) and influenza patients (IP) remains a challenge in clinical practice. We observed that NCPP had significantly decreased white blood cells, alkaline phosphatase, and d-dimer, compared with IP. Conclusions Some routine laboratory results had statistical difference between NCPP and IP. A diagnostic model based on combination of routine laboratory results provides an adjunct approach in the differential diagnosis between NCPP and IP. We observed that NCPP had 37 significantly decreased white blood cells, alkaline phosphatase, and d-dimer, The Lancet, 2020). Epidemiological and clinical 307 characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a 308 descriptive study Clinical features of patients 312 infected with 2019 novel coronavirus in Wuhan doi = 10.1016/j.ijid.2020.04.078 id = cord-304872-hnxmtbrf author = Lv, Hao title = Prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with COVID‑19 in Wuhan, China date = 2020-09-17 keywords = COVID-19 summary = OBJECTIVES: To investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (COVID-19) in Wuhan using a telephone interview. The characteristics of the patient''s disease course and recovery time for olfactory and/or gustatory dysfunctions (OD and/or GD) were collected by telephone interview. Two hypotheses might explain the low prevalence of OD and/ or GD reported in the Chinese study: First, the number of Chinese patients with COVID-19 who exhibit olfactory or gustatory disorders is indeed lower. Furthermore, all previous studies were limited to the acute phase with a short follow-up period, which might not reflect the recovery regularity of olfactory and/or gustatory impairment in patients with COVID 19. The aim of this study was to investigate the occurrence and recovery time of olfactory and/or gustatory dysfunction in patients with COVID-19 infection who were discharged from non-intensive care units 3 months earlier in China. doi = 10.1016/j.ijid.2020.09.039 id = cord-310691-6danlh8h author = Ma, Simin title = Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date = 2020-05-26 keywords = SARS; covid-19 summary = title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. doi = 10.1016/j.ijid.2020.05.068 id = cord-278406-n5e3a09i author = Macauley, Precious title = CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date = 2020-08-21 keywords = COVID-19; SARS summary = Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). doi = 10.1016/j.ijid.2020.08.051 id = cord-297715-qcwp2jdv author = Machida, Masaki title = Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak date = 2020-05-17 keywords = measure; personal summary = title: Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak Participants were asked how often they implemented the 5 personal protective measures recommended by the World Health Organization (hand hygiene, social distancing, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) in the baseline and follow-up surveys. In that study, we found that in the early phase of COVID-19 there was J o u r n a l P r e -p r o o f low prevalence among ordinary Japanese citizens in the implementation of social distancing measures and avoiding touching the eyes, nose and mouth, 2 of the 5 personal protective measures recommended by the World Health Organization (WHO) (WHO, 2020a The company, then invited the 2,400 respondents of the baseline survey to participate in a follow-up survey by email on April 1, 2020. doi = 10.1016/j.ijid.2020.05.039 id = cord-029882-kufs0fxe author = Malviya, Amit title = The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials date = 2020-07-29 keywords = HCQ summary = HCQ is touted for treatment of Covid 19 primarily based on its anti-viral properties, thus the timing of administration becomes very important for a meaning full assessment of study results. Recently it been shown that this score is not accurate for predicting severity of disease in Covid 19 patients . Covid 19 is a multisystem disease and the disease itself promotes proarrhythmic milieu with prolonged QT intervals at baseline .5,6 Risk assessment of HCQ therapy is not complete if such patients are excluded. Finally , mechanism of action of HCQ against is a part of its broad anti-viral and immunomodulatory properties and no specific pharmacologic actions are described for SARS-CoV-2 infection. 9,10 Weather HCQ as initial anti-viral agent prevents progression to severe disease is not known clearly . Ventricular arrhythmia risk due to chloroquine / hydroxychloroquine treatment for COVID-19: Should it be given Effects of chloroquine on viral infections: an old drug against today''s diseases? doi = 10.1016/j.ijid.2020.07.054 id = cord-318315-r6wqywwe author = Memish, Ziad A. title = Etiology of severe community-acquired pneumonia during the 2013 Hajj—part of the MERS-CoV surveillance program date = 2014-06-23 keywords = Hajj; MERS summary = We aimed to screen Hajj pilgrims admitted to healthcare facilities in 2013 with severe community-acquired pneumonia (CAP) for MERS-CoV and to determine other etiologies. METHODS: Sputum samples were collected from all pilgrims admitted to 15 healthcare facilities in the cities of Makkah and Medina, Saudi Arabia, who were diagnosed with severe CAP on admission, presenting with bilateral pneumonia. 7, 10 In recent years, the Middle East respiratory syndrome coronavirus (MERS-CoV) has also emerged as a cause of serious illness including severe pneumonia. Respiratory tract infections are common illnesses during the Hajj, 15 and pneumonia is the leading cause of hospital admission, including admission to the ICU, during the pilgrimage. 16 In the current study, as part of the Saudi MoH MERS-CoV surveillance, we investigated the etiology of severe CAP in pilgrims attending the 2013 Hajj requiring hospitalization. 7,10 Studies performed during previous Hajj seasons have reported the organism as a cause of respiratory tract infections including penumonia. doi = 10.1016/j.ijid.2014.06.003 id = cord-292256-jp80u828 author = Moriguchi, Takeshi title = A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date = 2020-04-03 keywords = CoV-2; SARS summary = We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient''s nasopharyngeal specimen is negative. doi = 10.1016/j.ijid.2020.03.062 id = cord-315059-l6guql8q author = Mubarak, Naeem title = Corona and Clergy: The missing link for an effective social distancing in Pakistan. Time for some unpopular decisions date = 2020-04-30 keywords = Pakistan summary = title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. To begin with, more than half of the COVID-19 cases in Malaysia received virus 11 in a congregation of 16000 believers from 30 countries. Pakistan''s case is of concern due to a fragile healthcare system, poor hygiene practices, 20 limited access to healthcare, and steep rise in the number of local cases in a population bigger 21 than Italy and Iran combined. Evidence supports the substantial impact of social distancing as 22 a viable practice to contain the spread of the virus. In Pakistan, the practice of social distancing 24 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 Muslim world, and cancelled Umrah (pilgrimage). for Pakistan to implement social distancing in the holy month of Ramadan (26 th April) when 46 influx in mosques increases many-fold for daily prayers and Tarawih (an additional prayer in 47 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 79 80 COVID-19: Pakistan to allow mosques prayers in 70 doi = 10.1016/j.ijid.2020.04.067 id = cord-273961-ja8xggnd author = Nakagawara, Kensuke title = Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date = 2020-07-26 keywords = SARS summary = title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . doi = 10.1016/j.ijid.2020.07.034 id = cord-297396-r1p7xn3a author = Ng, Ming-Yen title = Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date = 2020-09-15 keywords = COVID-19; CXR; PCR summary = OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.  Developed two simple-to use nomograms for identifying COVID-19 positive patients  Probabilities are provided to allow healthcare leaders to decide suitable cut-offs  Variables are age, white cell count, chest x-ray appearances and contact history  Model variables are easily available in the general hospital setting. To develop: (1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. Thus, a COVID-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such RT-PCR availability is constrained. doi = 10.1016/j.ijid.2020.09.022 id = cord-340992-88t1c0zs author = Nikolai, Lea A title = Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date = 2020-09-03 keywords = COVID-19; SARS; asymptomatic summary = Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection doi = 10.1016/j.ijid.2020.08.076 id = cord-356074-kw8c2fgk author = Oboh, Mary Aigbiremo title = Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks date = 2020-08-13 keywords = ACDC; Africa summary = doi = 10.1016/j.ijid.2020.08.027 id = cord-288167-976qxja2 author = Park, Wan Beom title = Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date = 2018-05-09 keywords = MERS; RNA summary = title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. In the present study, replicative MERS-CoV was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in MERS-CoV-infected patients with severe pneumonia. In conclusion, replicative MERS-CoV was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic RNA. In upper respiratory tract specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. Middle East respiratory syndrome coronavirus (MERS-CoV) genomic RNA (upE) titers in sputum and transtracheal aspirates with vs. doi = 10.1016/j.ijid.2018.05.003 id = cord-276254-q04hqra2 author = Paul, Kishor Kumar title = Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh date = 2020-06-02 keywords = Bangladesh; case; outbreak summary = title: Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh In this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. (Khatun et al., 2015 , Salje et al., 2016b Here we use the results from a detailed investigation of an outbreak of chikungunya virus in a village in Tangail, Bangladesh where the outbreak team visited every household in the community and interviewed all members in each household. This investigation suggests that chikungunya virus has become an emerging public health problem in Bangladesh, and outbreak investigations of emerging infections often have the objective of estimating attack rates of diseases and identifying the risk factors that lead to infection. doi = 10.1016/j.ijid.2020.05.111 id = cord-306200-d5qn65k0 author = Petersen, Eskild title = COVID-19 travel restrictions and the International Health Regulations – call for an open debate on easing of travel restrictions date = 2020-04-17 keywords = covid-19; travel summary = doi = 10.1016/j.ijid.2020.04.029 id = cord-311026-mpr3xb2a author = Petersen, Eskild title = COVID-19–We urgently need to start developing an exit strategy date = 2020-04-29 keywords = COVID-19; Hong; Kong; PDF; SARS summary = Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state''s strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. doi = 10.1016/j.ijid.2020.04.035 id = cord-317080-kn56oov6 author = Quadri, Sayed. A. title = COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens date = 2020-05-07 keywords = COVID-19 summary = title: COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens Gathering of large number of people in close approximation could be a fertile ground for the spread of novel pathogens. COVID 19 is spread through droplet and basic reproduction rate, a 23 measure of transmissibility of the virus, ranges from 2.24 to 3.58 (Zhao et al., 2020) . Public 24 gatherings will evidently increase transmission and therefore social distancing was touted as the 25 foremost preventive strategy.  Suspension of communal gatherings must be promptly done as a preventive strategy 196 whenever novel pathogens emerge, in order to contain its spread.  An international regime of containment measures with regards to suspension of religious 198 congregations during infectious disease outbreaks must be devised. Preliminary estimation of the basic reproduction number of novel 185 coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the 186 early phase of the outbreak doi = 10.1016/j.ijid.2020.05.007 id = cord-338576-gh1plurq author = Regen, Francesca title = A Simple Approach to Optimum Pool Size for Pooled SARS-CoV-2 Testing date = 2020-08-28 keywords = pool summary = Finally, we derive a simple-to-use formula and table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. Here we provide a simple strategy to estimate the optimum pool size for a two-staged pooling based on a known target prevalence. The optimum pool size for a given frequency is defined by the local minima of the isolines in figure 1A and can be more precisely determined by the first derivative of equation 1 Results from our analysis clearly demonstrate the relation between target prevalence rates and optimum pool sizes in a two staged pooling strategy. The relation between the estimated analyses per specimen and a pool size are given for various target prevalence rates as defined by equation 1 (isolines; A). Local minima suggest optimum pool sizes at the respective target prevalence rate (isolines; A). doi = 10.1016/j.ijid.2020.08.063 id = cord-280060-gzby85u9 author = Rello, Jordi title = Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() date = 2016-04-28 keywords = ESCMID; infection; patient; risk summary = 2 A International Journal of Infectious Diseases 48 (2016) 104-112 significant number of immunocompromised patients may also be migrants who may return to their countries of origin to visit friends and relatives, and may acquire travel-associated infections. 26 Cases of Chagas disease (Trypanosoma cruzi) either as a consequence of reactivation of a latent infection not identified at the time of transplant (because an unrecorded travel history or stay in an endemic area) or by transmission through the organ donor, can also be associated with a high mortality. There have also been case reports of severe disease from other travel-associated infections, such as salmonellosis, Vibrio parahaemolyticus, and visceral leishmaniasis in immunocompromised patients. Less common pathogens such as Staphylococcus aureus, avian influenza viruses such as H7N9 and H5N1, the Middle East respiratory syndrome coronavirus (MERS-CoV), and Gram-negative rods such as Burkholderia pseudomallei must also be considered, as well as a few other pathogens that do not usually cause pneumonia, such as malaria. doi = 10.1016/j.ijid.2016.04.020 id = cord-344478-5gp7v1uh author = Rosenberg, Eli S. title = Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 date = 2020-07-29 keywords = Hydroxychloroquine summary = title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 The study from Arshad et al on the use of hydroxychloroquine, with and without azithromycin, for the treatment of inpatients with COVID-19 in one healthcare system (Henry Ford Health System) is a new entrant into the rapidly expanding literature on the treatment of this disease [1, 2] . Treatment with Hydroxychloroquine, Azithromycin, and Combination in Patients Hospitalized with COVID-19 Observational Study of Hydroxychloroquine in Hospitalized Patients with Covid-19 Association of Treatment With Hydroxychloroquine or Azithromycin With In-Hospital Mortality in Patients With COVID-19 in Treatment with Hydroxychloroquine Cut Death Rate Significantly in COVID-19 Patients, Henry Ford Health System Study Shows doi = 10.1016/j.ijid.2020.07.055 id = cord-253102-z15j8izi author = Ross, Allen G.P. title = Planning for the Next Global Pandemic date = 2015-08-04 keywords = Ebola; global; pandemic summary = The West African Ebola virus pandemic has shown us yet again that the world is ill prepared to respond to a global health emergency. The national health systems in West Africa, and for most low and middle income countries (LMICs), would not meet IHR standards (despite claims by some member WHA nations) and it is unlikely that following the Ebola pandemic much will change. This editorial discusses many issues including priority emerging and reemerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the One Health approach to future pandemic planning. The PEF would 22 If the WHO contingency fund (100 million US dollars) and the World Bank pandemic emergency facility cannot be utilised to strengthen national health systems in LMICs in order to meet IHRs core capabilities, then how can this be achieved? doi = 10.1016/j.ijid.2015.07.016 id = cord-316209-juvmabdq author = Rutayisire, Erigene title = What works and what does not work in response to COVID-19 prevention and control in Africa date = 2020-06-12 keywords = COVID-19; african summary = The lower number of COVID-19 cases in most African countries is attributed to inadequate health systems, low-to-absent testing capacity, poor reporting system and insufficient number of medical staff. On 11 March 2020, the World Health Organization (WHO) had declared COVID-19 a pandemic, pointing to the over 118,000 cases of the coronavirus illnesses in over 110 countries and territories around the world and the sustained risk of further global spread. Africa Centers for Diseases Control and Prevention (Africa CDC), World Health Organization and other international agencies are providing support and guidance to many African countries in response to COVID-19 pandemic. Despite reported low case-fatality of COVID-19, the pandemic is likely to cause more deaths in Africa if the compliance to COVID-19 prevention and control measures continues to be ignored as observed in some African countries. doi = 10.1016/j.ijid.2020.06.024 id = cord-305782-gnzwe2z2 author = Satici, Celal title = Performance of Pneumonia Severity Index and CURB-65 in Predicting 30-day mortality in patients with COVID-19 date = 2020-06-14 keywords = COVID-19; CURB-65; PSI summary = Abstract Objective The aim of the study was to analyze the usefulness of the CURB-65 and pneumonia severity index (PSI) in predicting 30-day mortality in patients with COVID-19 and to identify other factors associated with higher mortality. Conclusion In a large group of hospitalized patients with COVID-19, we found that PSI performed better than CURB-65 in predicting mortality. According to the Health Ministry Guideline, any suspected case who is over 50 years old or has any comorbidity should be hospitalized irrespective of vital signs, laboratory results and computed tomography (CT) findings (Bilim Kurulu, 2020) Thus, a large proportion of patients with COVID-19 meet criteria for admission as an inpatient. In this study, we aimed to assess whether CURB-65 or PSI is useful tool to predict 30-day mortality and to identify other factors that are associated with higher mortality in patients with COVID-19. doi = 10.1016/j.ijid.2020.06.038 id = cord-317500-ufo2qgj4 author = Scialpi, Michele title = Pulmonary thromboembolism in criticall ill COVID-19 patients date = 2020-04-24 keywords = COVID-19 summary = Dear Editor, the outbreak of novel Coronavirus disease 2019 in the city of Wuhan, Hubei province of China, has been declared a pandemic by the World Health Organization (WHO) on March 21 st , and has since then forced the scientific community to consider two fundamental aspects: first off, SARS-CoV-2 does not only cause pneumonia and second, the death of many critical ill patients is caused by multiple organ failure (involving the heart, liver, kidneys, blood and immune system). A novel coronavirus from patients with pneumonia in China Acute pulmonary embolism and COVID-19 pneumonia: a random association? COVID-19 Complicated by Acute Pulmonary Embolism Radiology: Cardiothoracic Imaging Findings of Acute Pulmonary Embolism in COVID-19 Patients Management strategy of novel coronavirus (COVID-19) pneumonia in the radiology department: a Chinese experience The Authors declare no conflicts of interest associated for the manuscript entiltled "Pulmonary thromboembolism in criticall ill COVID-19 patients doi = 10.1016/j.ijid.2020.04.056 id = cord-346461-eqyte6ko author = Scialpi, Michele title = Pneumonia misinterpretation in COVID-19: revisitation and update date = 2020-08-28 keywords = COVID-19 summary = doi = 10.1016/j.ijid.2020.08.067 id = cord-341775-mucatzaa author = Shafi, Shuja title = The annual Hajj pilgrimage—minimizing the risk of ill health in pilgrims from Europe and opportunity for driving the best prevention and health promotion guidelines date = 2016-06-22 keywords = Hajj; KSA summary = Mass gathering sporting and religious events pose important public health challenges, including the transmission of infectious diseases, exacerbation of non-communicable diseases, and disorders related to climate change. [1] [2] [3] [4] [5] Every year, the Kingdom of Saudi Arabia (KSA) hosts the Hajj pilgrimage, which is the largest mass gathering in the world held on a recurrent annual basis. Mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. doi = 10.1016/j.ijid.2016.06.013 id = cord-284652-7npya3yx author = Shim, Eunha title = Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020 date = 2020-10-08 keywords = Korea; Province; South summary = Results At the regional level, Seoul and Gyeonggi Province have experienced the first peak of COVID-19 in early March, followed by the second wave in early June, withRt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. Therefore, since 10 July, the government banned churches from organizing small gatherings other than regular worship services (KCDC, 2020a To estimate the regional and temporal variability in the reproduction number of COVID-19 in South Korea, including the second wave concentrated in the greater Seoul areas, we analysed the spatiotemporal progression of the epidemic in the country from mid-February to mid-July 2020. In this report, we estimated the doubling time and the effective reproduction number involving two epidemic waves of the COVID-19 epidemic in South Korea by employing the time series of cases by date of symptoms onset for the four most affected Korean regions: Seoul, Gyeonggi Province, Gyeongbuk Province, and Daegu. doi = 10.1016/j.ijid.2020.10.007 id = cord-336954-rh88lod0 author = Shim, Eunha title = Transmission potential and severity of COVID-19 in South Korea date = 2020-03-18 keywords = COVID-19; Korea summary = OBJECTIVES: Since the first case of 2019 novel coronavirus (COVID-19) identified on Jan 20, 2020 in South Korea, the number of cases rapidly increased, resulting in 6,284 cases including 42 deaths as of March 6, 2020. However, the number of confirmed cases of SARS-CoV-2 infection started to increase rapidly on February 19, 2020 with a total of 6,284 confirmed COVID-19 cases including 42 deaths reported as of March 6, 2020 according to the Korea Centers for Disease Control and Prevention (KCDC) (KCDC, 2020) ( Table 1 ). Under the empirical reporting delay distribution from early Korean cases with available dates of onset, the intrinsic growth rate (r) was estimated at 0.6 (95% CI: 0.6, 0.7) and the scaling of growth parameter (p) was estimated at 0.8 (95% CI: 0.7, 0.8), indicating sub-exponential growth dynamics of COVID-19 doi = 10.1016/j.ijid.2020.03.031 id = cord-308080-1heu9vuv author = Simulundu, Edgar title = First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date = 2020-10-06 keywords = COVID-19; SARS; Zambia summary = title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient''s household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient''s SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. doi = 10.1016/j.ijid.2020.09.1480 id = cord-325325-xw7627x9 author = Skeik, Nedaa title = Influenza viruses and the evolution of avian influenza virus H5N1 date = 2007-10-02 keywords = H5N1; influenza; virus summary = While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. doi = 10.1016/j.ijid.2007.07.002 id = cord-254872-w6d397js author = Stein, Richard A. title = Methicillin-resistant Staphylococcus aureus—the new zoonosis date = 2008-11-30 keywords = MRSA; Staphylococcus summary = The surge in community-associated MRSA, at a time when reports of animal-to-human transmission are increasing, might not be merely coincidental, 12, 13 and according to a recent study conducted in the Netherlands, MRSA that entered from an animal reservoir into the human population is now responsible for over 20% of the strains isolated. 14 Findings that have accumulated in recent years make it necessary to define three additional patient groups at high risk for zoonotic MRSA: individuals in contact with farm animals, contacts of household pets, and veterinarian staff. Moreover, it is important to note that MRSA strains of animal origin have been isolated from people lacking previous documented direct animal contacts, supporting the possibility that direct human-to-human transmission occurs subsequent to one person''s colonization/infection. Methicillin (oxacillin)-resistant Staphylococcus aureus strains isolated from major food animals and their potential transmission to humans An outbreak of methicillin-resistant Staphylococcus aureus skin infections resulting from horse to human transmission in a veterinary hospital doi = 10.1016/j.ijid.2008.09.008 id = cord-279892-37vyazby author = Sun, Guanghao title = Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases date = 2017-01-16 keywords = IRT; rate summary = This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. These systems have already been installed at most major international airports, and they can remotely sense several vital signs, including body temperature and heart and respiration rates, thereby facilitating the rapid and accurate screening of people who are suspected of carrying infectious diseases. To distinguish between patients with infectious influenza and healthy control subjects, logistic regression discriminant analysis was used to establish a classification model based on the three derived vital signs. The classification model was established using the data that described the three vital signs from the 16 influenza virus-infected patients and the 22 healthy control subjects using multivariable logistic regression. doi = 10.1016/j.ijid.2017.01.007 id = cord-345275-h0hvaxgx author = Sun, Mengyao title = Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date = 2020-07-04 keywords = Ebola; SARS summary = title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection doi = 10.1016/j.ijid.2020.06.107 id = cord-293942-n5ypkftc author = Takoi, Hiroyuki title = Favipiravir-induced fever in coronavirus disease 2019: A report of two cases date = 2020-09-28 keywords = COVID-19 summary = title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases Favipiravir, an antiviral agent, is undergoing clinical trials for treating novel coronavirus disease 2019 (COVID-19). We report two cases of COVID-19 with favipiravir-induced fever. Favipiravir, a promising antiviral agent, is undergoing clinical trials as an alternative drug for treating COVID-19 (Arab-Zozani et al., 2020) in several countries, including China (Chen et al., 2020) , Iran, Germany, and Japan. We experienced two cases of favipiravir-induced fever in patients hospitalized with COVID-19. Drug-induced fever was suspected and favipiravir was discontinued on Day 10. This preliminary report may help differentiate paradoxical fever in patients receiving favipiravir therapy for COVID-19. Favipiravir for treating patients with novel coronavirus (COVID-19): protocol for a systematic review and meta-analysis of randomised clinical trials Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: A case series doi = 10.1016/j.ijid.2020.09.1450 id = cord-301079-n1nytr6k author = Tan, Li title = Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date = 2020-07-27 keywords = HCP; SARS; patient summary = Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. doi = 10.1016/j.ijid.2020.07.027 id = cord-262017-utvy0i8l author = Tobar Vega, Pool title = Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date = 2019-06-21 keywords = HIV; Histoplasma summary = title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. Endemic to Southeast Asia, East Asia and China, Talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (Supparatpinyo et al., 1994) . In the U.S. patients with HIV infection usually undergo testing for endemic fungal infections such as Blastomyces, Histoplasma, Coccidioides and Paracoccidioides. To our knowledge, this is the first case reporting systemic mycosis due toTalaromyces marneffei with associated hyponatremia secondary to SIADH and cross-reactivity with Blastomyces and Histoplasma in urine antigen testing. doi = 10.1016/j.ijid.2019.06.018 id = cord-260332-tnz6k2z1 author = Tran, Tu Anh title = CT scan does not make a diagnosis of Covid-19: a cautionary case report() date = 2020-09-02 keywords = covid-19 summary = key: cord-260332-tnz6k2z1 title: CT scan does not make a diagnosis of Covid-19: a cautionary case report() Here, we report the clinical case of a 12-year-old girl presenting with flu-like symptoms, cough, anosmia, ageusia, breathing difficulties, patchy ground glass opacities on TDM chest scan who turned out to be Coronavirus 229E-infected. This case must draw attention on the risk of false COVID-19 diagnosis when relying overly on CT scan imaging. RT-PCR assays of nasopharyngeal samples at admittance and 24 hours later, were negative for SARS-CoV-2. In this case report, parents'' anosmia and ageusia as well as chest scanner could have been misleading. According to Kim et al., scanner screening of patients with suspected COVID-19 in low-prevalence countries has a poor positive prediction value (1%-31%) 2 . The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. doi = 10.1016/j.ijid.2020.08.073 id = cord-326881-3j2e92dj author = Vassallo, M. title = Patients with Covid-19 exhibit different immunological profiles according to their clinical presentation date = 2020-09-28 keywords = CD10; covid-19 summary = Conclusions In a population of elderly patients recently infected with Covid-19, CD10 + B cell levels were inversely correlated with clinical severity. However, clinical expression of Covid-19 is extremely variable, with, in some cases, asymptomatic or mild forms [15] , while in other subjects severe forms culminating in acute respiratory distress syndrome (ARDS) have been described, requiring patients to be transferred to Intensive Care Units. The aim of this study was to retrospectively analyze the immunological profile of patients at early stages of Covid-19 in order to identify potential risk factors for subsequent clinical deterioration. We conducted an observational, retrospective cohort study on patients admitted to the Internal Medicine and Infectious Diseases Department in Cannes General Hospital, from March to May 2020, with confirmed Covid-19 infection. In a population of elderly patients at a very early stage of Covid-19, we found that levels of CD10+ B lymphocyte cells were predictive of the clinical severity. doi = 10.1016/j.ijid.2020.09.1438 id = cord-306682-01q775up author = Vijgen, Leen title = Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date = 2004-06-22 keywords = APN; PCR summary = In this study we examined whether polymorphisms could be detected in the HCoV-229E binding domain of APN in a Caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in HCoV-229E attachment to human cells. A total of 100 healthy unrelated Belgian individuals were screened for polymorphisms in the human aminopeptidase N domain that is essential for its HCoV-229E receptor activity. All individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the APN gene. In our search for polymorphisms in the APN domain that is essential for its HCoV-229E receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. Three polymorphisms in APN exon 4 (C956T, G978T and G987A) in association with an intron 3 variation (C389T), were identified at a relatively high allele frequency (8.5%) in our Belgian population. doi = 10.1016/j.ijid.2004.03.004 id = cord-302409-40ktyt5q author = Wang, Jie title = SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date = 2020-04-18 keywords = RNA; SARS summary = OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs'' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. doi = 10.1016/j.ijid.2020.04.024 id = cord-258881-74aijckl author = Wang, Maomao title = Case Report: One Case of Coronavirus Desease 2019(COVID-19) in Patient Co-nfected by HIV With a Low CD4+ T Cell Count date = 2020-04-23 keywords = Cov-2 summary = Abstract The ongoing outbreak of COVID-19 that began in Wuhan, China has become an emergency of international concern When thousands of peolple were infected around the world.We report a case infected by SARS-Cov-2 and HIV simultaneously,which showed a longer course of disease and slower generation of specific antibody. Here we report a patient infected by SARS-Cov-2 , who had a relatively long course of disease with unstable state. Then eight markers of infectious diseases was checked and the result showed that abtibodies to HIV and syphilis were positive .Then the patient was transferred to specialty hospital for further treatment on March 8. People are generally susceptible to SARS-Cov-2 infection, especially the elderly patients and those with underlying diseases [2] . The author suggested that SARS-Cov-2 might damage lymphocytes, especially T lymphocytes, and the immune system was impaired during the period of disease [2] . In conclusion, we report the clinical features of a patient infected by SARS-Cov-2 and HIV. doi = 10.1016/j.ijid.2020.04.060 id = cord-326143-6ndqgxy8 author = Wang, Qiang title = Successful recovery of severe COVID-19 with cytokine storm treating with extracorporeal blood purification date = 2020-05-26 keywords = day summary = COVID-19 associated cytokine storm could induce ARDS rapidly and the patients would require the support of mechanic ventilation. We present a case of severe SARS-CoV-2 infection who recovered from cytokine storm. The patients with confirmed COVID-19 progressed to acute respiratory distress syndrome (ARDS) rapidly in an incident rate as high as 41.8% 1 , and many of them require mechanic ventilation. Cytokines could be eliminated effectively by extracorporeal blood purification (EBP) 4 , which thus could interrupt the initiation and progression of inflammation cascade in the scenario of COVID-19. IL-6 (198.66 pg/ml) was almost 10 folds of normal range (≤5.9 pg/ml) which indicated an initiation of cytokine storm on day 12 ( Figure 1 ). The patient was largely stable until the chest distress exacerbated and blood in phlegm developed on day 14. Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease doi = 10.1016/j.ijid.2020.05.065 id = cord-280627-dfnc9g2c author = Wang, Xiong title = Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date = 2020-04-18 keywords = China; SARS summary = The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). doi = 10.1016/j.ijid.2020.04.023 id = cord-290100-wnjjqqn5 author = Wong, Samuel Y.S. title = Primary care physicians’ response to pandemic influenza in Hong Kong: a mixed quantitative and qualitative study date = 2012-07-11 keywords = H1N1; influenza summary = OBJECTIVES: The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. RESULTS: We found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among GOPC doctors during the study period. The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. doi = 10.1016/j.ijid.2012.03.015 id = cord-257737-obadq502 author = Wu, Di title = Positive effects of COVID-19 control measures on influenza prevention date = 2020-04-10 keywords = China summary = title: Positive effects of COVID-19 control measures on influenza prevention This article aims to alert clinicians of the presence of co-infection with these two viruses and to describe the effect of the measures taken to fight COVID-19 on influenza prevention and control. [ 4 ] have reported the case of a patient co-infected with SARS-CoV-2 and influenza A virus. Also, Li and Wang [ 5 ] have reported the need to be alert to the superposed effect of seasonal influenza while fighting pneumonia caused by the novel coronavirus. Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention Coronavirus disease 2019 (COVID-19) Situation Report -71 Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia Be alert to superposed effect of seasonal influenza while fighting against novel coronavirus pneumonia doi = 10.1016/j.ijid.2020.04.009 id = cord-275250-ilmgy7ce author = Xia, Yong title = Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date = 2020-05-17 keywords = SARS summary = As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. doi = 10.1016/j.ijid.2020.05.042 id = cord-279976-juz9jnfk author = Xie, Mingxuan title = Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date = 2020-04-01 keywords = China; MERS; SARS; Wuhan summary = METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". doi = 10.1016/j.ijid.2020.03.071 id = cord-347349-caz5fwl1 author = Yu, Xinhua title = Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea date = 2020-07-02 keywords = Korea; covid-19; epidemic summary = doi = 10.1016/j.ijid.2020.06.101 id = cord-320860-qt84oicg author = Zhang, Aining title = Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date = 2020-09-15 keywords = COVID-19; SARS summary = title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis doi = 10.1016/j.ijid.2020.09.021 id = cord-282360-byqhzyzi author = Zhang, Dingmei title = Enterovirus 71 vaccine: close but still far date = 2010-04-18 keywords = EV71; VP1; vaccine summary = To overcome the potential problem of reversion to virulence of attenuated strain vaccine, subunit vaccines consisting of only one or a few ''subunit'' proteins of the pathogen that can stimulate immune responses directed at the intact virus have been developed using recombinant DNA technology. 21 have described a recombinant VP1 protein expressed in Escherichia coli BL21, showing that the VP1 protein with a complete adjuvant is able to elicit a neutralizing antibody response, enhance T helper cell proliferation, and induce high levels of interleukin (IL)-10 and interferon (IFN)-g in mice, providing direct evidence that the VP1 protein contains neutralizing epitopes independent of other viral capsid proteins; this paves the way for the use of VP1 as a backbone antigen for developing subunit vaccines against EV71. Protection against lethal enterovirus 71 infection in newborn mice by passive immunization with subunit VP1 vaccines and inactivated virus doi = 10.1016/j.ijid.2009.12.002 id = cord-319814-tyqb473m author = Zhang, Dingmei title = Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date = 2014-06-11 keywords = RSV; respiratory; virus summary = METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. doi = 10.1016/j.ijid.2014.02.019 id = cord-297829-aynigoud author = Zhang, Li title = Post-pandemic assessment of public knowledge, behavior, and skill on influenza prevention among the general population of Beijing, China date = 2014-04-13 keywords = Beijing; influenza summary = doi = 10.1016/j.ijid.2014.01.003 id = cord-274230-old0xmcc author = Zhao, Qianwen title = Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis date = 2020-05-04 keywords = covid-19 summary = title: Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis Mean difference (MD) of lymphocyte count in COVID-19 patients with or without severe disease and odds ratio (OR) of lymphopenia for severe form of COVID-19 was evaluated with this meta-analysis. The pooled analysis showed that lymphocyte count was significantly lower in severe COVID-19 patients (MD -0.31×109/L; 95%CI: -0.42 to -0.19×109/L). After the significant clinical heterogeneity was excluded, the 130 randomized effects model was used for meta-analysis. Severe Outcomes Among Patients with Coronavirus Disease 2019 (COVID-19) -United States Risk Factors Associated With Acute Respiratory Distress Syndrome 284 and Death in Patients With Coronavirus Disease Retrospective study on the epidemiological 300 characteristics of 139 patients with novel coronavirus pneumonia on the effects of Severity Effects of severe acute respiratory syndrome (SARS) coronavirus 311 infection on peripheral blood lymphocytes and their subsets Lymphopenia predicts disease severity of COVID-19: a 322 descriptive and predictive study doi = 10.1016/j.ijid.2020.04.086 id = cord-257265-lkzytud0 author = Zheng, Fang title = SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date = 2020-08-03 keywords = Lopinavir; Novaferon; SARS summary = According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. doi = 10.1016/j.ijid.2020.07.053 id = cord-309032-idjdzs97 author = Zhou, Feng title = Epidemiological Characteristics and Factors Associated with Critical Time Intervals of COVID-19 in Eighteen Provinces, China: A Retrospective Study date = 2020-10-09 keywords = COVID-19; China; Hubei summary = Several studies conducted in China, Italy and the United States have reported some epidemiological characteristics of COVID-19 in the initial phase (Grasselli et al., 2020 , Liang et al., 2020 , Price-Haywood et al., 2020 , Richardson et al., 2020 , Wu and McGoogan, 2020 , However, there is still a lack of research on the space-time characteristics in the populations of imported and local cases respectively which is of great significance. In this study, we described the spatiotemporal distribution of the COVID-19 in eighteen provinces of China (outside Hubei province) and investigated the epidemiological characteristics in the population of imported cases and local cases, from the beginning of this epidemic until it was under good control. We further assessed the critical influence factors associated with time interval from symptom onset to hospitalization (TOH) and length of hospital stay (LOS), including demographic and temporal and spatial characteristics. doi = 10.1016/j.ijid.2020.09.1487 id = cord-257200-q0vqlerz author = Zumla, A. title = What is the experience from previous mass gathering events? Lessons for Zika virus and the Olympics 2016 date = 2016-06-15 keywords = Hajj; gathering; mass summary = 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. The spread of severe acute respiratory syndrome coronavirus (SARS-CoV) from China to Hong Kong and further to Canada was not due to a mass gathering, but to infected individuals travelling late in the incubation period or just after the onset of symptoms. A review in this issue discusses the need for vaccines for mass gatherings and draws attention to immunization against pneumococcal infections in elderly pilgrims and highlights that polio may be a risk. Communicable diseases as health risks at mass gatherings other than Hajj: what is the evidence? doi = 10.1016/j.ijid.2016.06.010 id = cord-260518-mswb3q67 author = Zumla, Alimuddin title = Taking forward a ‘One Health’ approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential date = 2016-06-15 keywords = East; Health; MERS; Middle summary = Since the Kingdom of Saudi Arabia is host to millions of pilgrims each year travelling from all continents, 29 tackling the threat of MERS and other infectious diseases with epidemic potential will require enhanced closer cooperation between those who provide human health, animal health, and environmental health services, locally, nationally, regionally, and internationally: the Middle Eastern, European, African, Asian, and American governments, veterinary groups, the WHO, the Food and Agriculture Organization (FAO), the African Union, the United Nations International Children''s Emergency Fund (UNICEF), The World Bank, Office International des Epizooties (OIE), CDC, Public Health England, the newly formed Africa CDC, and funding agencies among others. The persistence of MERS-CoV 4 years since its first discovery has created major opportunities for each of the Middle Eastern and African countries to take leadership of the ''One Health'' approach with a view to bringing this under regional and global umbrellas, to tackle new emerging and re-emerging infectious diseases with epidemic potential. doi = 10.1016/j.ijid.2016.06.012 id = cord-291367-rtmsrh16 author = Zumla, Alimuddin title = Middle East Respiratory Syndrome - need for increased vigilance and watchful surveillance for MERS-CoV in sub-Saharan Africa date = 2015-07-02 keywords = East; MERS summary = 4, 5 The recent unprecedented outbreak of the MERS 6, 7 in South Korea which arose consequential to the importation of MERS-CoV by a South Korean traveler to the Middle East, alarmed global public health authorities and highlights the potential of MERS-CoV to spread across the globe and cause local outbreaks. National surveillance systems should be on alert for the low but long-lasting risk of MERS-CoV infected pilgrims returning from the Umrah throughout the year, and also for the large numbers of refugees at several conflict zones in the Middle East (those migrating from Syria to Turkey and from the Yemen border into Saudi Arabia and beyond). The Hajj pilgrimage and surveillance for Middle East Respiratory syndrome coronavirus in pilgrims from African countries Infection prevention and control during health care for probable or confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. doi = 10.1016/j.ijid.2015.06.020 id = cord-292988-q1yz9y8k author = Zumla, Alimuddin title = Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date = 2020-05-17 keywords = MSC; SARS; cell; covid-19 summary = title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . doi = 10.1016/j.ijid.2020.05.040 id = cord-311654-ixn65hxb author = Zumla, Alimuddin title = COVID-19 and the scaled-down 2020 Hajj Pilgrimage - Decisive, logical and prudent decision making by Saudi authorities overcomes pre-Hajj public health concerns date = 2020-08-08 keywords = Hajj; Saudi summary = Apart from generic prevention and control issues of public health and lockdown measures to limit epidemic spread, specific issues of Mass Gathering (MG) sporting and religious events came under specific spotlight (Alzahrani et al, 2020; Baloch et al, 2020; McCloskey et al, 2020; . WHO with global MG partners, developed comprehensive key recommendations for COVID-19, and since end of February, 2020, there was a stepwise increase in cancellation, temporary suspension or postponement of international and national religious, sporting, musical, and other MGs, as countries worldwide took public health and other measures (WHO, 2020b; McCloskey et al, 2020; Petersen, McCloskey et al, 2020) . The successful completion of the 2020 Hajj is a major tribute to the leadership and commitment of the Saudi authorities, and it reflects their extensive experience of organising the annual Hajj pilgrimage, and continued commitment to improvement public health issues related to mass gatherings events. doi = 10.1016/j.ijid.2020.08.014 id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 keywords = HLA; MHC; SARS summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. doi = 10.1016/j.ijid.2020.07.016 id = cord-303417-1237ykxt author = d’Arminio Monforte, Antonella title = Effectiveness of Hydroxychloroquine in COVID-19 disease: A done and dusted situation? date = 2020-07-29 keywords = Alessandro summary = Arshad et al show evidence for a reduced mortality in Covid-19 patients taking hydroxychloroquine alone or with azithromycin in an observational study in USA [1] . We divided a subset of our cohort in three groups who started treatment a median of 1 day after admission: those receiving hydroxycholoroquine alone (N=197), those receiving hydroxycholoroquine+azithromycin (N=94), and those receiving neither (controls) (N=92). After adjusting for a number of key confounders (see table) , the use of hydroxycholoroquine+azithromycin was associated with a 66% reduction in risk of death as compared to controls; the analysis also suggested a larger effectiveness of hydroxychloroquine in patients with less severe COVID-19 disease (PO2/FiO2>300, interaction p-value<.0001). Treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalised with COVID-19 Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomised clinical trial Hydroxychloroquine in patients mainly with mild to moderate COVID-19: an open-label, randomised, controlled trial An observational cohort study of hydroxychloroquine and azithromycin for COVID-19: (Can''t get no) satisfaction doi = 10.1016/j.ijid.2020.07.056