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?' ---------------------------------------------------------- 141 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 31 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 34 SARS 12 patient 11 virus 11 PCR 10 influenza 8 respiratory 7 infection 7 OC43 7 COVID-19 6 figure 5 cell 5 NL63 4 vaccine 4 covid-19 4 MERS 4 HRV 3 RSV 3 IFN 3 HIV 3 Ebola 2 viral 2 cryptosporidium 2 TNF 2 TIV 2 RNA 2 NAI 2 LRT 2 HKU1 2 HCoV 2 HCV 2 HAI 2 H1N1 2 CoV 2 Africa 2 ARI 1 Ϫ/Ϫ 1 Δ1313 1 year 1 trial 1 treatment 1 torovirus 1 sample 1 response 1 research 1 protein 1 pregnant 1 pigeon 1 pfu 1 outbreak 1 nkg2d Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 3613 virus 2993 infection 2469 patient 2229 % 1940 study 1890 cell 1621 influenza 1277 antibody 1132 disease 1128 sample 1002 day 957 vaccine 900 response 858 group 785 coronavirus 747 p 732 analysis 696 year 679 datum 677 child 636 figure 635 case 634 time 633 result 616 control 591 protein 572 assay 559 illness 553 c 548 serum 535 treatment 534 specimen 530 test 516 t 505 detection 481 titer 469 level 463 pneumonia 459 use 456 symptom 450 risk 427 age 420 number 418 pandemic 415 adult 392 sequence 392 population 391 rate 383 syndrome 383 mouse Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1451 SARS 551 PCR 548 HCoV 542 CoV-2 537 CoV 368 RNA 367 MERS 340 RSV 319 COVID-19 298 OC43 259 A 238 RT 211 C 210 S 208 H1N1 205 T 205 HRV 196 al 184 Health 184 HBoV 183 NL63 165 J 162 M 162 CD4 157 Table 156 et 156 China 147 A(H1N1)pdm09 146 HIV 145 PfSRA 140 United 140 HCoV-229E 140 Dis 139 HKU1 139 B 137 a 134 sha 132 IFN 130 Supplementary 130 CI 129 Influenza 128 HI 125 Coronavirus 124 u 122 s 121 sera 118 States 117 ELISA 114 LRT 110 Vero Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1341 we 622 it 272 they 178 i 63 them 45 he 32 us 17 she 15 one 11 themselves 10 itself 5 you 4 ourselves 4 em 3 me 1 ≥110 1 Ϫ238 1 Ϫ20Њc 1 wg320 1 s 1 ours 1 her 1 eba-175 1 cord-262840-fhfxnr76 1 cord-007375-hqmyund4 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 13847 be 2558 have 1330 use 727 show 713 associate 703 infect 649 include 618 detect 535 report 512 do 447 compare 423 find 415 test 406 identify 401 suggest 386 increase 379 observe 368 follow 355 describe 339 base 335 perform 329 collect 319 provide 315 obtain 307 determine 305 cause 294 occur 262 confirm 256 indicate 246 develop 239 require 238 induce 237 produce 234 neutralize 227 consider 226 receive 216 hospitalize 213 relate 213 contain 200 demonstrate 198 evaluate 197 define 192 reduce 191 assess 189 isolate 185 bind 184 remain 173 examine 168 give 165 treat Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1820 respiratory 1407 not 1177 viral 1062 human 795 other 749 clinical 741 high 730 acute 713 also 703 severe 608 low 597 positive 562 - 529 more 464 however 455 only 405 specific 393 first 382 significant 360 immune 349 most 329 different 328 such 319 well 289 similar 278 old 266 negative 266 available 260 present 256 significantly 250 previously 250 novel 243 potential 243 infectious 233 respectively 226 asymptomatic 224 new 222 same 221 early 209 important 205 likely 204 further 203 chronic 200 large 198 common 192 syncytial 186 several 185 as 184 infected 179 real Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 126 most 100 least 64 high 37 Most 30 good 18 low 15 large 15 great 9 strong 7 early 3 late 3 close 3 bad 2 short 2 old 2 near 2 mild 1 young 1 wide 1 small 1 slight 1 new 1 long 1 deadly 1 common 1 broad 1 bright 1 big 1 /OD 1 -update 1 -CTTTGGACTTAATGACA 1 -CTCTTGCAGGTAT 1 -CTAGTTCTTCTGGT Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 223 most 30 least 9 well 1 highest 1 hard 1 furthest 1 -gagcgg Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 10 jid.oxfordjournals.org 2 www.ncbi.nlm.nih.gov 2 www.ebi.ac.uk 1 www.trialregister.nl 1 www.nottingham.ac.uk 1 www.ncbi 1 www.megasofware.net 1 www.influenzareagentresource.org 1 www.hra.nhs.uk 1 www.fda.gov 1 www.covig-19plasmaalliance.org 1 www.cbs.dtu.dk 1 www.audubon.org 1 www.r-project.org 1 tree.bio.ed.ac 1 tree 1 sfbay.craigslist.org 1 lalashan 1 jbloomlab.github.io 1 health 1 blast.ncbi.nlm.nih.gov Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 5 http://jid.oxfordjournals.org/ 5 http://jid.oxfordjournals.org 2 http://www.ncbi.nlm.nih.gov/geo/ 1 http://www.trialregister.nl 1 http://www.nottingham.ac.uk/research/groups/healthprotection/projects/pride.aspx 1 http://www.ncbi 1 http://www.megasofware.net 1 http://www.influenzareagentresource.org/ 1 http://www.hra.nhs.uk/covid-19-research/approved-covid-19-research/281317/ 1 http://www.fda.gov/media/136049 1 http://www.ebi.ac.uk/services/proteins 1 http://www.ebi.ac.uk/Tools/ 1 http://www.covig-19plasmaalliance.org 1 http://www.cbs.dtu.dk 1 http://www.audubon.org/field-guide/bird/ 1 http://www.R-project.org 1 http://tree.bio.ed.ac 1 http://tree 1 http://sfbay.craigslist.org/ 1 http://lalashan 1 http://jbloomlab.github.io/neutcurve/ 1 http://health 1 http://blast.ncbi.nlm.nih.gov/Blast.cgi Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 11 samples were available 9 cells were then 9 patients did not 7 cells were also 7 data are available 7 samples were also 6 virus was not 5 data are consistent 4 % were boys 4 % were infants 4 cells were negatively 4 data do not 4 infection did not 4 infection was significantly 4 patients do not 4 results were not 4 samples were not 4 studies have also 4 studies reported outcomes 4 study provides evidence 4 study using real 3 % had influenza 3 % were male 3 analysis did not 3 antibodies detect multiple 3 cases were fatal 3 cells were not 3 diseases included chronic 3 patients were available 3 response following infection 3 results were also 3 results were negative 3 results were statistically 3 samples were then 3 studies did not 3 study did not 3 study was not 3 vaccine is immunogenic 2 % had cough 2 % were aged 2 % were female 2 antibodies are also 2 antibodies are more 2 antibodies did not 2 antibodies was higher 2 antibodies were inhibitory 2 assays do not 2 cases was not 2 cells did not 2 cells is dependent Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 patients do not always 1 analyses were not available 1 antibodies were not detectable 1 antibody had no effect 1 antibody had no significant 1 antibody is not type 1 cases do not readily 1 cases was not large 1 cells had no appreciable 1 cells showed no significant 1 cells was not significantly 1 controls were not symptomatic 1 coronavirus are not atypical 1 data are not available 1 data do not necessarily 1 data show no evidence 1 data showing no significant 1 disease is not well 1 disease was not substantial 1 disease were no longer 1 group do not necessarily 1 group was not significantly 1 groups showed no detectable 1 groups were not statistically 1 infection have not yet 1 infection is not very 1 infection was not more 1 infections are not pathogenic 1 infections is not surprising 1 patient had no significant 1 patient is not infectious 1 patient reported no exacerbations 1 patients did not always 1 patients did not significantly 1 patients is not weak 1 patients were not anemic 1 protein is not normally 1 response was not sufficient 1 result was not due 1 results were not likely 1 results were not readable 1 results were not surprising 1 samples is not sufficient 1 samples was not as 1 samples were not available 1 samples were not reactive 1 sars did not apparently 1 sars does not closely 1 sars had no antinucleocapsid 1 sars showed no consistent A rudimentary bibliography -------------------------- id = cord-332175-d5suvj8g author = Allen, Jawara title = My Future in Medicine: How COVID-19 Is Inspiring the Next Generation of Infectious Disease Specialists date = 2020-04-11 keywords = COVID-19 summary = Three weeks later-on the day I was scheduled to start the clinical portion of my medical training-there were 418 700 confirmed cases of COVID-19 globally [1] . By that time, many courses had started remote instruction, most research laboratories had been closed to all nonessential personnel, and medical school core clerkships had been temporarily canceled, all in an effort to decrease student exposure to COVID-19 and help "flatten the curve. But as a medical student eager to reenter the world of clinical care, the personal stories from the communities that would be most impacted by this relentless pathogen soon consumed my thoughts. Few other events before have so poignantly highlighted the global nature of health, the vulnerability of certain populations around the world, and the need for more infectious disease specialists. But the importance of infectious disease specialists will not end once the number of newly diagnosed COVID-19 cases starts to decrease. To protect those communities, we need more infectious disease specialists. doi = 10.1093/infdis/jiaa178 id = cord-003115-y40knklf author = Amlabu, Emmanuel title = Functional Characterization of Plasmodium falciparum Surface-Related Antigen as a Potential Blood-Stage Vaccine Target date = 2018-09-01 keywords = PfSRA; Plasmodium; figure summary = The antibodies (α-PfSRA P1, α-PfSRA P2, and α-PfSRA P3) consistently detected multiple processed fragments (17, 32 , and 58 kDa) of the native PfSRA in ring-stage invasion supernatants ( Figure 1B , II-V) or parasite culture supernatants ( Figure 1C , I-IV) and schizont lysates ( Figure 1D , I-IV). falciparum asexual stages by IFAs showed that all α-PfSRA peptide antibodies labeled the surface membranes of merozoites in intact schizonts and released merozoites, respectively (Figure 2A -C). The 3 PfSRA peptide antibodies from rabbits specifically detected breakdown products of native PfSRA in ring-stage invasion supernatant or parasite culture supernatant and schizont lysates. Sequential processing of merozoite surface proteins during and after erythrocyte invasion by Plasmodium falciparum Plasmodium falciparum merozoite surface antigen, PfRH5, elicits detectable levels of invasion-inhibiting antibodies in humans Analysis of antibodies directed against merozoite surface protein 1 of the human malaria parasite Plasmodium falciparum doi = 10.1093/infdis/jiy222 id = cord-011710-rz23ozxb author = Aoki, Fred Y. title = The Beneficial Effects of Neuraminidase Inhibitor Drug Therapy on Severe Patient Outcomes During the 2009–2010 Influenza A Virus Subtype H1N1 Pandemic date = 2013-02-15 keywords = H1N1; NAI summary = doi = 10.1093/infdis/jis727 id = cord-003171-z22ekgtv author = Babu, Tara M title = Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment date = 2018-10-01 keywords = H2N2; HAI; Hong summary = doi = 10.1093/infdis/jiy291 id = cord-290277-ndfoppoq author = Bahl, Prateek title = Airborne or droplet precautions for health workers treating COVID-19? date = 2020-04-16 keywords = SARS; droplet summary = doi = 10.1093/infdis/jiaa189 id = cord-288821-nalulzfo author = Bastien, Nathalie title = Human Coronavirus NL63 Infection in Canada date = 2005-02-15 keywords = ARI; NL63 summary = doi = 10.1086/426869 id = cord-329061-1xut73dq author = Bhatt, Pravin N. title = Characterization of the Virus of Sialodacryoadenitis of Rats: A Member of the Coronavirus Group date = 1972-08-17 keywords = SDA; mouse summary = The virus that causes sialodacryoadenitis in rats has been isolated in mice and in primary cultures of rat-kidney cells and has been characterized as a heat-labile RNA virus that is sensitive to lipid solvents and is relatively stable at pH 3.0. Rats were inoculated intranasally with 0.1 ml of virus-infected salivary-gland suspension, observed daily for evidence of overt illness, and sacrificed at various intervals. Monolayers obtained from explant cultures of submaxillary, parotid, Harderian, and exorbital glands of germfree rats, monolayers of trypsin-dispersed brain cells of infant mice, and a line of polyoma-transformed mouse cells (Py-AL/N) [6J were also tested. The neutralization (N) test with sera immune to murine viruses was performed in infant mice, and these animals were observed for 14 days after inoculation. Infectious virus or viral antigen was not detected when tissue-culture fluids from infected-mouse-brain and Py-AL/N cultures were inoculated ic into infant mice or when monolayers were examined by indirect immunofluorescence. E. Shope tested 118 viral antigens prepared from infected mouse brains with antiserum to SDA virus. doi = 10.1093/infdis/126.2.123 id = cord-007220-nlsduenh author = Black, R. E. title = A Two-Year Study of Bacterial, Viral, and Parasitic Agents Associated with Diarrhea in Rural Bangladesh date = 1980-11-17 keywords = ETEC; year summary = Although classic enteric bacterial pathogens are not isolated from most patients with diarrhea, recent studies indicate that enterotoxigenic Escherichia coli (ETEC) and rotaviruses may frequently cause diarrhea [2] [3] [4] . We therefore studied patients during a two-year period at a treatment center in rural Bangladesh to determine the frequency, severity, and seasonality of diarrhea associated with ETEC, rotavirus, and other enteric agents. V. cholerae group 0: 1 was rarely identified for children less than two years of age but was an important pathogen in older children and adults, while non-group 0: 1 vibrios were found in the stools of 4010-11 010 of the patients of each age group for both years of the study. ETEC organisms were the pathogens most frequently isolated from patients of all ages and were the second most frequently isolated (after rotavirus) from young children coming to the treatment center in rural Bangladesh. doi = 10.1093/infdis/142.5.660 id = cord-258905-0hgdtalg author = Bond, Katherine title = Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date = 2020-08-06 keywords = SARS; covid-19 summary = METHODS: Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). A testing panel was specifically developed to test PoCT devices for this study (Supplementary Material), consisting of 3 patient populations: (1) sera from 91 patients with SARS-CoV-2 detected by RT-PCR from upper and/or lower respiratory tract specimens; (2) sera from 36 patients with seasonal coronavirus infections or other acute infections (eg, dengue, cytomegalovirus, Epstein-Barr virus); and (3) serum from a random cohort (56 patients) of the Australian population obtained in 2018. In this study, we assessed the performance characteristics of 5 serological PoCT, a commercial ELISA, and a commercial novel sVNT against a large serum panel from a cohort of over 100 patients with RT-PCR-confirmed SARS-CoV-2. doi = 10.1093/infdis/jiaa467 id = cord-346411-d2re00r9 author = Boonyaratanakornkit, Jim title = Predictive Value of Respiratory Viral Detection in the Upper Respiratory Tract for Infection of the Lower Respiratory Tract With Hematopoietic Stem Cell Transplantation date = 2020-02-01 keywords = LRT; URT; bal summary = In a small study of adults, the majority of which were HCT recipients or had a hematologic malignancy, with matched NP and BAL specimens, PCR-based NP testing for respiratory viruses in patients with clinical evidence of LRT disease had a high negative predictive value (NPV) and a lower positive predictive value (PPV) [5] . A larger study that included mostly immunocompromised patients concluded that if a pathogen (a respiratory virus or 1 of 3 bacterial pathogens detected by a multiplex PCR panel) was already identified from an NP sample, BAL testing is unlikely to provide additional information; however, a significant number (20%) of subjects had a pathogen detected in the BAL without a positive NP sample [6] . In the present study, we characterized the rates of discordance in respiratory viral detection between matched URT and LRT samples in a large cohort of HCT candidates/recipients who underwent BAL for suspected LRTI and had concomitant URT testing. doi = 10.1093/infdis/jiz470 id = cord-320764-p4ydngag author = Breiman, Robert F. title = Surveillance for Respiratory Infections in Low- and Middle-Income Countries: Experience From the Centers for Disease Control and Prevention's Global Disease Detection International Emerging Infections Program date = 2013-12-15 keywords = Centers; GDD; IEIP summary = doi = 10.1093/infdis/jit462 id = cord-341548-gazsszs6 author = Buscho, R. O. title = Infections with Viruses and Mycoplasma pneumoniae during Exacerbations of Chronic Bronchitis date = 1978-04-17 keywords = exacerbation; infection summary = The association of viral and Mycoplasma pneumoniae infections with acute exacerbations of chronic bronchitis was studied by serologic or isolation techniques in 46 adult men during the five years from 1964 through 1968. Because of the high prevalence and morbidity of chronic bronchitis among patients of Veterans Administration Hospitals, we have conducted surveillance of one of these groups to assess the impact of respiratory tract infections on the natural course of this disease and to investigate further the occurrence and relative importance of viruses and mycoplasmas in exacerbations [3] . Evidence of viral and Mycoplasma pneumoniae infections (obtained mainly by serologic testing and to a lesser extent by isolation of organisms) was correlated with the pattern of clinical disease in patients with chronic bronchitis. pneumoniae were detected in 50 (30.1%) of 166 exacerbations of chronic bronchitis in the 46 adult patients studied (table 2) . doi = 10.1093/infdis/137.4.377 id = cord-007013-tlvgyzft author = Chan, Kok Fei title = Investigating Viral Interference Between Influenza A Virus and Human Respiratory Syncytial Virus in a Ferret Model of Infection date = 2018-08-01 keywords = IFN; figure; infection summary = Previously, we used the ferret model to demonstrate that viral interference can occur following infection with human influenza A and B viruses and will prevent, delay, or limit subsequent infection with an influenza virus of a different type, subtype, or lineage [10, 11] . The peak of hRSV shedding was delayed in ferrets infected with A(H1N1)pdm09 followed by hRSV as compared to control animals infected with hRSV alone (median, 8 vs 6 days; P = .0091 by the Mann-Whitney test; Figure 2Ci ). The median duration of A(H1N1)pdm09 shedding was increased in ferrets infected with hRSV followed by A(H1N1)pdm09 as compared to control animals infected with A(H1N1)pdm09 alone (8 vs 7 days; P = .0196 by the Mann-Whitney test; Figure 2Civ ). Notably, increased expression of inflammatory mediators following infection with influenza virus as compared to hRSV has been observed in studies assessing human clinical samples and in vitro airway epithelial cell cultures [36] [37] [38] [39] . doi = 10.1093/infdis/jiy184 id = cord-335375-n6q70o35 author = Chan, Paul K. S. title = Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date = 2005-07-01 keywords = SARS; sample summary = Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. doi = 10.1086/430615 id = cord-293579-w5sub348 author = Che, Xiao-yan title = Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date = 2005-06-15 keywords = OC43; SARS summary = By use of Western blot analysis, indirect immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA), antigenic cross-reactivity between severe acute respiratory syndrome (SARS)—associated coronavirus (SARS-CoV) and 2 HCoVs (229E and OC43) was demonstrated in immunized animals and human serum. In the present study, we cloned the nucleocapsid genes of SARS-CoV, HCoV-229E, and HCoV-OC43 and produced specific animal antisera to determine if the nucleocapsid protein is responsible for the observed antigenic cross-reactivity. The serum samples from patients with SARS had antibody responses to SARS-CoV as well as to HCoV-229E and HCoV-OC43 when nucleocapsid proteins were used in the Western blot analysis and when CoV-infected cells were used in the IFA. Furthermore, antibodies to SARS-CoV could be detected in only 1 serum sample from a healthy donor by either IFA or nucleocapsid protein-based Western blot analysis, even though patients with SARS had antibodies to HCoV-229E and HCoV-OC43. doi = 10.1086/430355 id = cord-299149-lc2dxvxz author = Chen, I-Cheng Mark title = Evidence for Cross-Protection Against Subsequent Febrile Respiratory Illness Episodes From Prior Infections by Different Viruses Among Singapore Military Recruits 2009–2014 date = 2019-06-15 keywords = BMT; FRI; episode summary = ResPlex II assays and real-time polymerase chain reaction assays were used to detect viral pathogens in nasal wash samples, and survival analyses were performed to determine whether infection with particular viruses conferred short-lived relative cross-protection against FRI. We reanalyzed the Singapore Armed Forces FRI surveillance program data by using survival analyses to assess whether there was any evidence, at the individual level, that infection with particular viruses was conferring short-lived relative cross-protection against subsequent FRI episodes, including those caused by other virus groups. AdV-positive episodes tended to protect against subsequent infection with AdV (P = .090) and also 3 other virus groups All models were adjusted for study year, type of BMT intake, age, ethnicity, smoking history, history of asthma, and influenza vaccination. Infections from the adenovirus and influenza virus families conferred significant cross-protective effects against subsequent FRI episodes relative to other circulating viruses. doi = 10.1093/infdis/jiz046 id = cord-350737-nrtrhq1f author = Chen, Xinchun title = Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date = 2004-04-01 keywords = CoV; SARS; patient summary = A virus from the family Coronaviridae, termed "SARS coronavirus" (SARS CoV), has been identified as the cause [2] [3] [4] [5] [6] [7] , and criteria for laboratory confirmation of SARS CoV infection have been provided by WHO, on the basis of the following methods: (1) detection of SARS CoV RNA by reversetranscription polymerase chain reaction (RT-PCR); (2) serological detection of SARS CoV-related antibody; and (3) isolation of SARS CoV by cell culture [4] . Using an indirect immunofluorescence assay and parallel acute and convalescent serum samples obtained from patients with SARS, tested for IgG antibody to SARS CoV, Peiris et al. In addition, our results indicated that 9 (25.0%) of 36 patients with probable SARS CoV infection had not produced detectable anti-SARS CoV antibody by day 21 after the onset of fever; this implies that 25.0% of patients with SARS might be misdiagnosed by the laboratory confirmation guidelines that WHO currently recommends [5] . doi = 10.1086/380397 id = cord-270205-fw555w1u author = Cillóniz, Catia title = Pure Viral Sepsis Secondary to Community-Acquired Pneumonia in Adults: Risk and Prognostic Factors date = 2019-10-01 keywords = cap; viral summary = title: Pure Viral Sepsis Secondary to Community-Acquired Pneumonia in Adults: Risk and Prognostic Factors We investigated the risk and prognostic factors of pure viral sepsis in adult patients with community-acquired pneumonia (CAP), using the Sepsis-3 definition. We investigated the risk and prognostic factors of pure viral sepsis in adult patients with community-acquired pneumonia (CAP), using the Sepsis-3 definition. Respiratory viruses are detected as etiological agents in almost one third of cases of community-acquired pneumonia (CAP) [2] [3] [4] [5] and in 7%-36% of patients with severe CAP with a defined microbial etiology [2, 3] . We aimed to investigate the prevalence, risks, and prognostic factors associated with pure viral sepsis in adult patients with CAP, using the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) criteria [6] . We observed that viral sepsis was not a risk factor for in-hospital mortality in patients without septic shock. doi = 10.1093/infdis/jiz257 id = cord-315328-8g40ukml author = Clementi, Nicola title = Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection date = 2020-06-19 keywords = IFN; SARS summary = In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In the current study, we assessed its anti-SARS-CoV-2 activity in vitro to give a preclinical background to clinical trials evaluating the possible therapeutic role of IFN-β-1a in patients with coronavirus disease 2019 (COVID-19). Vero E6 cells were treated with concentrations ranging from 5000 to 0.01 IU/mL of IFN-β-1a 1 hour after inoculation with SARS-CoV-2 and monitored for cytopathic effect and real-time-PCR quantitative evaluation at 48, 72, and 96 hours after infection. Our in vitro observations shed light for the first time on that antiviral activity of IFN-β-1a against SARS-CoV-2 when administered after the infection of cells, highlighting its possible efficacy in an early therapeutic setting. doi = 10.1093/infdis/jiaa350 id = cord-007026-ejv0gidp author = Coleman, Kristen K title = Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted? date = 2020-02-15 keywords = HAdV; Singapore summary = METHODS: To understand the epidemiology of HAdV infections in Singapore, we studied 533 HAdV-positive clinical samples collected from 396 pediatric and 137 adult patients in Singapore from 2012 to 2018. CONCLUSIONS: Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of HAdV 4 and 7 vaccine. Clinical samples previously collected from HAdV-positive patients admitted to Singapore General Hospital (SGH) and KK Women''s and Children''s Hospital (KKH) between 2012 and 2015 were preserved at −80°C and transferred to Duke-NUS Laboratory of One Health Research for study. Human adenovirus-C datasets consisted of 4 novel genomes from Singapore and 22 representative virus isolates from different genotypes (HAdV-C1, HAdV-C2, HAdV-C5, and HAdV-C6). doi = 10.1093/infdis/jiz489 id = cord-003567-h8uq5z8b author = Crank, Michelle C title = Preparing for the Next Influenza Pandemic: The Development of a Universal Influenza Vaccine date = 2019-04-15 keywords = influenza; vaccine summary = This issue of The Journal of Infectious Diseases was motivated by the confluence of the 1918 influenza pandemic centenary and the new opportunities afforded by technological advances and breakthroughs along with the improved understanding of influenza biology. 7. Defining the importance of including specific antigenic targets, such as the head or stem domains of hemagglutinin, neuraminidase, or the M2 ectodomain in universal vaccines, and determining whether they are more effective when used in combination or alone could be accomplished through both vaccine protection and natural history studies that provide a better understanding of protective immunity [9] [10] [11] [12] . Improving the characterization of and expanding the reagents for these models would not only benefit influenza vaccine development but would also provide answers to immunological questions relevant to other respiratory virus infections and emerging infectious diseases in general. doi = 10.1093/infdis/jiz043 id = cord-315448-bosazmlm author = Crawford, Katharine H D title = Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection date = 2020-09-30 keywords = SARS summary = Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post symptom onset from a prospective cohort of 32 recovered individuals with asymptomatic, mild, or moderate-severe disease. Most of these studies have reported that over the first three months, antibodies targeting spike decline several fold from a peak reached a few weeks post symptom onset [5, 7, 19] , suggesting that the early dynamics of the antibody response to SARS-CoV-2 are similar to those for other acute viral infections. A c c e p t e d M a n u s c r i p t 5 Here we build on these studies by measuring both the neutralizing and binding antibody levels in serial plasma samples from 32 SARS-CoV-2-infected individuals across a range of disease severity with follow-up as long as 152 days post symptom onset. doi = 10.1093/infdis/jiaa618 id = cord-007188-tcq8lnwg author = Cunningham, Anthony L. title = Gastrointestinal Viral Infections in Homosexual Men Who were Symptomatic and Seropositive for Human Immunodeficiency Virus date = 1988-08-17 keywords = AIDS; HIV summary = Gastrointestinal viruses, predominantly rotaviruses and adenoviruses, were detected by enzyme-linked immunosorbent assay, electron microscopy, or cell culture in >50% of two groups of homosexual men with symptomatic human immunodeficiency virus (HIV) infection, who did (54%) or did not (50%) have diarrhea. We report here the detection of viruses from the stools of a large proportion of patients with symptomatic HIV infection (AIDS, ARC, and POL) and acute or chronic diarrhea when no other microbial pathogen could be identified. In this study we showed that patients with AIDS or ARC may present with acute diarrhea or exacerbations of chronic diarrhea and that in patients with symptomatic HIV infection and diarrhea, >50% excreted gastrointestinal viruses. These high detection rates for rotavirus and adenovirus in patients with ARC or AIDS-OI are similar to those observed in marrow transplant recipients who also have a T cell immunodeficiency and often have gastrointestinal mucosal damage from graft-versus-host disease [4] . doi = 10.1093/infdis/158.2.386 id = cord-313000-as507p4t author = Dare, Ryan K. title = Human Coronavirus Infections in Rural Thailand: A Comprehensive Study Using Real-Time Reverse-Transcription Polymerase Chain Reaction Assays date = 2007-11-01 keywords = NL63; OC43; PCR summary = doi = 10.1086/521308 id = cord-275108-snqbrxgr author = Daverio, Marco title = Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date = 2020-05-22 keywords = SARS summary = doi = 10.1093/infdis/jiaa283 id = cord-266695-ktbgm0p9 author = Dawson, Liza title = SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date = 2020-06-04 keywords = SARS; challenge summary = have recently argued that researchers should consider conducting SARS-CoV-2 human challenge studies to hasten vaccine development [1] . However, we disagree that SARS-CoV-2 challenge studies are ethically appropriate at this time, for three reasons: 1) current scientific knowledge of SARS-CoV-2 infection is insufficient to manage risks; 2) autonomous decision-making, while necessary, does not override concerns about risk; and 3) undertaking challenge studies now would imperil confidence in the research enterprise, potentially undermining the global response to the COVID-19 pandemic. Current scientific knowledge is insufficient to manage the risks of severe disease or death of volunteers in SARS-CoV-2 human challenge studies, especially in terms of selecting low risk volunteers [2] . It is not obvious that the possible benefits of developing a successful vaccine in less time justify the risks SARS-CoV-2 challenge studies, as Eyal and colleagues suggest. However, conducting SARS-CoV-2 human challenge trials now unjustifiably threatens both the well-being of volunteers and confidence in the research enterprise. doi = 10.1093/infdis/jiaa314 id = cord-296197-ohfhnpma author = Deborggraeve, Stijn title = A Simplified and Standardized Polymerase Chain Reaction Format for the Diagnosis of Leishmaniasis date = 2008-11-15 keywords = DNA; Leishmania; PCR summary = doi = 10.1086/592509 id = cord-275863-qos9vu3r author = Dejnirattisai, Wanwisa title = Lectin Switching During Dengue Virus Infection date = 2011-06-15 keywords = SIGN; Vero summary = In this report we have studied the interaction of dengue viruses produced in insect cells, tumor cell lines, and primary human dendritic cells (DCs) with DC-SIGN and L-SIGN. To formally prove that the loss of infection of DCs was a result of the loss of affinity of DC-produced virus for DC-SIGN, we went on to test infection on 3T3 cells expressing DC-SIGN and included in these assays the related C-type lectin L-SIGN ( Figure 3A ), which has also been reported to be a receptor for dengue virus. C6/36-and DC-derived viruses were incubated with increasing levels of pooled convalescent dengue immune serum and subsequently used to infect U937, a monocyte cell line that expresses the Fc receptor and which shows relatively low infectivity without the presence of enhancing antibodies. Viruses produced in both DCs and insect cells were susceptible to enhancement, over the same range of antibody concentrations, showing that DC-produced virus could exploit ADE to replicate in individuals undergoing a secondary dengue infection ( Figure 6A ). doi = 10.1093/infdis/jir173 id = cord-289406-54vyzxjf author = Edwards, Suzanne title = An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date = 1992-01-17 keywords = heart; infection; virus summary = In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. Both Coxsackie Band encephalomyocarditis virus infections in mice may progress to myocarditis and congestive heart failure, and some survi-vors may progress to a dilated cardiomyopathy later in life [5, [14] [15] [16] . Rabbits that died on days 10-12 had pleural effusion, pulmonary edema, ascites, enlarged hearts, dilated right and left ventricular cavities, and congestion in the lungs and liver. It seems likely that pleural effusion disease virus infection also results in a significant percentage of animals dying from heart failure, since degeneration and necrosis of myocytes, pulmonary edema, pleural effusion, dilated ventricles, and congestion of the lungs, liver, and spleen are common [18, 26] . doi = 10.1093/infdis/165.1.134 id = cord-286596-p10t0dta author = Erard, Veronique title = Airflow Decline after Myeloablative Allogeneic Hematopoietic Cell Transplantation: The Role of Community Respiratory Viruses date = 2006-06-15 keywords = FEV; HCT; LRT summary = We conducted a 12-year retrospective study to determine the effects that the community respiratory-virus species and the localization of respiratory-tract virus infection have on severe airflow decline, a serious and fatal complication occurring after hematopoietic cell transplantation (HCT). Lower-respiratory-tract infection with parainfluenza (odds ratio [OR], 17.9 [95% confidence interval {CI}, 2.0–160]; P=.01) and respiratory syncytial virus (OR, 3.6 [95% CI, 1.0–13]; P=.05) independently increased the risk of development of airflow decline ⩽1 year after HCT. This analysis also identified community respiratory-virus infections during the initial 100 days after HCT as being a significant risk factor for development of severe airflow decline but did not differentiate between specific viral infections or between infection localization in the upper respiratory tract (URT) or lower respiratory tract (LRT) [1] . Respiratory syncitial virus (RSV) infection in hematopoietic stem cell transplant (HCT) recipients: risks factor for acquisition and lower respiratory tract disease, and impact on mortality doi = 10.1086/504268 id = cord-289745-qtorq2qq author = Esper, Frank title = Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children date = 2005-02-15 keywords = HCoV; PCR summary = doi = 10.1086/428138 id = cord-313344-rqvi2ksc author = Farcas, Gabriella A. title = Fatal Severe Acute Respiratory Syndrome Is Associated with Multiorgan Involvement by Coronavirus date = 2005-01-15 keywords = CoV; SARS summary = doi = 10.1086/426870 id = cord-312552-udky2ko7 author = Fouque, Florence title = Introduction to a Landscape Analysis of Multisectoral Approaches for Prevention and Control of Infectious and Vector-Borne Diseases date = 2020-10-29 keywords = Development; MSA; control summary = doi = 10.1093/infdis/jiaa489 id = cord-011708-naezfola author = Frank, Gregory M. title = Infectious Diseases Society of America and Gain-of-Function Experiments With Pathogens Having Pandemic Potential date = 2016-05-01 keywords = GOF; NSABB summary = To that end, we highlight below 6 key recommendations that the IDSA recently shared with the NSABB as we discuss how best to assess the benefits and risk of GOF research of concern. The IDSA strongly urges the NSABB to narrow its definition of GOF research to be considered for risk-benefit assessment (RBA), to avoid this inadvertent capture of low-risk research, which is not mentioned in the White House Office of Science and Technology Policy''s original description of the types of research that should be included in the deliberative process. The IDSA strongly supports these actions and also urges the NSABB to consider seeking additional perspectives to inform the RBA process, including those of a range of experts in vaccine development, microbial risk assessment, and public health response; physicians whose work is primarily clinical; and the public. Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion doi = 10.1093/infdis/jiv474 id = cord-320445-pdvkyzci author = Fry, Alicia M. title = Human Bocavirus: A Novel Parvovirus Epidemiologically Associated with Pneumonia Requiring Hospitalization in Thailand date = 2007-04-01 keywords = RSV; patient summary = doi = 10.1086/512163 id = cord-011718-hcyluzkx author = Gaglani, Manjusha title = Antibody Response to Influenza A(H1N1)pdm09 Among Healthcare Personnel Receiving Trivalent Inactivated Vaccine: Effect of Prior Monovalent Inactivated Vaccine date = 2014-06-01 keywords = HCP; MIIV; TIV summary = For the 3 primary analyses, we examined HCP characteristics: demographics, health status, vaccination history, timing of serum sampling, site, proxies for influenza exposure, and HI titer preseason. We thus compared the proportion of HCP with HI ≥ 40 for preseason, post-TIV, and end-of-season serum samples by vaccination history. When compared with HCP included preseason (Table 1) , those post-TIV were more likely to be aged 50-65 years, have high-risk conditions, and receive 2009-2010 seasonal vaccines, and less likely to work in the emergency department. The proportion of HCP who had prior-season MIIV was similar among those providing preseason (42%) and end-of-season (43%) serum samples, but higher among those providing post-TIV sera (57%) ( Table 1 ). Among these 834 vaccinated HCP, history of receipt of MIIV was associated with lower HI GMTs for post-TIV and end-of-season regardless of preseason HI GMTs ( Figure 1 ). doi = 10.1093/infdis/jit825 id = cord-352433-sts48u9i author = Galanti, Marta title = Direct Observation of Repeated Infections With Endemic Coronaviruses date = 2020-07-07 keywords = OC43; SARS; infection summary = BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. However, in Korea, as reported by the Korean Centers for Disease Control and Prevention, viable SARS-CoV-2 was not isolated in cell culture of respiratory samples from potentially reinfected individuals [5] ; thus, these subsequent positive results may have been due to inactive genetic material detected by molecular testing. doi = 10.1093/infdis/jiaa392 id = cord-317232-qk72i0gv author = Gierer, Stefanie title = Inhibition of Proprotein Convertases Abrogates Processing of the Middle Eastern Respiratory Syndrome Coronavirus Spike Protein in Infected Cells but Does Not Reduce Viral Infectivity date = 2015-03-15 keywords = MERS; cell; figure summary = title: Inhibition of Proprotein Convertases Abrogates Processing of the Middle Eastern Respiratory Syndrome Coronavirus Spike Protein in Infected Cells but Does Not Reduce Viral Infectivity However, activation of viral glycoproteins, including activation of the S protein of certain strains of the coronavirus infectious bronchitis virus (IBV) [18] , may also proceed in the constitutive secretory pathway of infected cells and is often accomplished by furin and other proprotein convertases [19] [20] [21] [22] . Treatment of MERS-CoV-infected cells with a proprotein convertase inhibitor (PCI) abrogated S protein cleavage but did not alter viral infectivity, indicating that S protein processing in infected cells is dispensable for MERS-S activation. In sum, our results identify MERS-S as a substrate of proprotein convertases but indicate that the activity of these enzymes is dispensable for MERS-CoV spread in target cell lines and potentially also in the infected human host. doi = 10.1093/infdis/jiu407 id = cord-262840-fhfxnr76 author = Gorse, Geoffrey J. title = Human Coronavirus and Acute Respiratory Illness in Older Adults with Chronic Obstructive Pulmonary Disease date = 2009-03-15 keywords = HCoV; LDI; NL63; OC43 summary = doi = 10.1086/597122 id = cord-321580-3ru92tra author = Hadler, James L title = Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? date = 2020-09-07 keywords = SARS summary = The initial country-level responses to SARS-CoV-2 have provided substantial evidence of their collective impact on the COVID-19 pandemic and, incidentally, on seasonal influenza epidemics. As a country, it has perhaps the largest influenza sentinel surveillance system in the world, including active testing for influenza, and it was the first country to implement highly successful NPIs against SARS-CoV-2, giving it the best opportunity to see a possible change in influenza before the expected seasonal decline. To know what might happen with influenza this coming fall and winter, we need to know what has happened prospectively in southern hemisphere countries, especially those that like the US have used fewer NPI''s and used them with less rigor and, correspondingly, been less successful in controlling SARS-CoV-2 transmission. Nonpharmaceutical interventions used to control COVID-19 reduced seasonal influenza transmission in China doi = 10.1093/infdis/jiaa571 id = cord-278260-3o91v72a author = Halstead, Scott B title = COVID 19 Vaccines: Should we fear ADE? date = 2020-08-12 keywords = ADE; DENV; SARS summary = Within months large numbers of vaccinated children developed a severe breakthrough disease, called "atypical measles." [6] A similar outcome, "vaccine associated enhanced respiratory disease (VAERD)," was observed in infants, 4 -12 months of age, who were given formalininactivated respiratory syncytial virus (RSV) and a few months later infected by RSV. The biological behavior of some coronaviruses in non-human species together with evidence that human coronavirus antibodies enhanced infection of SARS or MERS CoVs in Fc receptor-bearing cells, in vitro, have led to speculations that ADE contributes to disease severity in humans. [11] It has been reported that high levels of SARS CoV-1 IgG antibodies circulated in severe SARS cases and that anti-S IgG neutralizing antibody (NAb) responses developed significantly faster after the onset of clinical symptoms in fatal compared with recovered cases leading some to attribute enhanced tissue damage to ADE. With others, we conclude that the differences in clinical, epidemiological and pathological features of SARS and DENV diseases suggest that iADE does not contribute to the severity of natural human coronavirus infections. doi = 10.1093/infdis/jiaa518 id = cord-007190-x1v4jpl4 author = Hardison, Jenny L. title = Chemokine CC Receptor 2 Is Important for Acute Control of Cardiac Parasitism but Does Not Contribute to Cardiac Inflammation after Infection with Trypanosoma cruzi date = 2006-06-01 keywords = CCR2; Ϫ/Ϫ summary = doi = 10.1086/503812 id = cord-270709-jahnjvyk author = Hasford, Joerg title = Large Simple Double-Blind Randomized Trials for the Rapid Assessment of the Effectiveness of COVID-19 Vaccines date = 2020-08-26 keywords = vaccine summary = doi = 10.1093/infdis/jiaa456 id = cord-344954-gpb25fga author = Hashem, Anwar M title = A Highly Immunogenic, Protective, and Safe Adenovirus-Based Vaccine Expressing Middle East Respiratory Syndrome Coronavirus S1-CD40L Fusion Protein in a Transgenic Human Dipeptidyl Peptidase 4 Mouse Model date = 2019-11-15 keywords = East; MERS; cd40l summary = title: A Highly Immunogenic, Protective, and Safe Adenovirus-Based Vaccine Expressing Middle East Respiratory Syndrome Coronavirus S1-CD40L Fusion Protein in a Transgenic Human Dipeptidyl Peptidase 4 Mouse Model Given its critical role in viral replication, the S protein has been the focus for MERS-CoV vaccine development similar to severe acute respiratory syndrome coronavirus (SARS-CoV), where it has been the main target for vaccines that led to robust induction of neutralizing antibody (nAb)-mediated protection in immunized animals [6] [7] [8] . We showed in this study that although rAd5 expressing S1 or CD40-targeted S1 were both capable of inducing significant levels of IgG and nAbs specific to MERS-CoV in immunized mice, incorporation of CD40L substantially enhances the immunogenicity of S1, as demonstrated by the effectiveness of a single immunization dose, which was sufficient to elicit stronger and robust immune responses compared to control groups, consistent with our previous reports [37, 38] . doi = 10.1093/infdis/jiz137 id = cord-275355-4izc5jxs author = Hayden, Frederick title = Transmission of Avian Influenza Viruses to and between Humans date = 2005-10-15 keywords = H5N1; influenza summary = in this issue of the Journal of Infectious Diseases [1] , and the recent instances of cross-species transmission that caused human disease [2] raise fundamental questions regarding the routes of transmission of avian viruses to and between humans, possible differences in transmission patterns between human and avian influenza viruses, and implications for prevention in those occupationally exposed to infected animals and also in health care, household, and community settings. The findings that seropositivity occurs in small numbers of poultry workers exposed during outbreaks of illness in poultry caused by some avian strains (H7N7, H7N3, and H5N1) but not others (H7N1 and H5N2) argue for actual infection and support the notion that some avian influenza viruses are more likely than others to infect humans [1] . Most cases of human infection due to avian influenza viruses have involved close contact with infected poultry, particularly ill or dying chickens. doi = 10.1086/444399 id = cord-255927-0tp4ig4o author = Hayman, David T S title = African Primates: Likely Victims, Not Reservoirs, of Ebolaviruses date = 2019-11-15 keywords = Africa; Ebola summary = This experimental work is supported by field data from related Marburg viruses, first identified after African monkeys infected people in Europe [24] , which apparently persist within large colonies of cave-dwelling Egyptian fruit bats, and RESTV in Asian bats. Thus, together the evidence for bats being the true reservoir host for EVD causing viruses is convincing, but relies on serological evidence of infection rather than virus detection, and the role of nonhuman primates as reservoirs remains uncertain. In other systems, archived sample banks have helped identify Middle East respiratory syndrome coronavirus-seropositive camels in East Africa over 11-year (Kenya) and 30-year (Sudan and Somalia) periods, suggesting extensive virus circulation in camels prior to the first human outbreaks [35] [36] [37] [38] . All of these studies are limited by data, but Ayouba et al''s comprehensive study supports the assumption that bats, not primates, are likely reservoir hosts and that nonhuman primates may be viewed as both sentinels for human infection and victims of EVD [9, 15, 33, 51] . doi = 10.1093/infdis/jiz007 id = cord-285087-i3nz5bvs author = Heimdal, Inger title = Human Coronavirus in Hospitalized Children With Respiratory Tract Infections: A 9-Year Population-Based Study From Norway date = 2019-04-15 keywords = HKU1; NL63; OC43 summary = doi = 10.1093/infdis/jiy646 id = cord-007180-pho3miid author = Heine, J. title = Enteric Lesions and Diarrhea in Gnotobiotic Calves Monoinfected with Cryptosporidium Species date = 1984-11-17 keywords = calf; cell; cryptosporidium summary = Clinically affected calves have atrophy of villi and hyperplasia of crypt epithelium (apparently as a result of the destruction of villous epithelium); those areas of the small intestine that are heavily infected with the parasite become inflamed [7, 9, 10] . On the other hand, if confirmed, the reported occurrence of diarrhea and intestinal lesions in gnotobiotic pigs infected with an inoculum treated in a manner that destroys infectious agents other than Cryptosporidium [18] provides strong evidence that the parasite can act as a primary enteropathogen in the absence of other enteric flora. Gnotobiotic calves inoculated with oocysts of Cryptosporidium that had been treated with potassium dichromate and peracetic acid became infected with Cryptosporidium and developed clinical signs and enteric lesions. doi = 10.1093/infdis/150.5.768 id = cord-297432-2edncbgn author = Helleberg, Marie title = Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date = 2020-07-23 keywords = COVID-19; PCR; SARS summary = A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. doi = 10.1093/infdis/jiaa446 id = cord-257521-1amcsgmj author = Hirsilä, Maija title = Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date = 2001-04-15 keywords = PCR summary = All 7 patients had a significant increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. Only 1 of the 7 patients from whom these samples were obtained was still positive by PCR at the first control visit 1 week later, but a signal was detected only with the NS-1 primer pair. A у8-fold increase between acute-and convalescent-phase serum samples was found in all 7 individuals with PCR-positive results (table 2). All 7 individuals with PCR-positive results had a у8-fold increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. In addition, 1 study participant with PCR-negative results also had a significant increase in antibody titer (patient 160; table 2). NPAs obtained from the 7 patients with RT-PCR-positive results at the first control visit 1 week after study entry also were tested. doi = 10.1086/319675 id = cord-299835-92karhpl author = Ho, Khek Y. title = Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date = 2004-02-17 keywords = SARS; patient; respiratory summary = doi = 10.1086/381558 id = cord-001764-njzyu4mv author = Hofmann-Winkler, Heike title = Comparative Analysis of Host Cell Entry of Ebola Virus From Sierra Leone, 2014, and Zaire, 1976 date = 2015-10-01 keywords = EBOV; Ebola; cell summary = Here, we show that the GPs of the EBOVs circulating in 1976 and 2014 transduce the same spectrum of target cells, use the same cellular factors for host cell entry, and are comparably susceptible to blockade by antiviral interferon-induced transmembrane proteins and neutralizing antibody KZ52. However, EBOV-GP 2014 was less susceptible than EBOV-GP 1976 to blockade by a third inhibitor, CatL ( Figure 3B ), which inhibits catB and catL activity to similar extents [40] , suggesting subtle differences in the protease dependence of these GPs. HIV-derived particles rapidly lose infectivity when stored at room temperature [41] , and this loss might be due to inactivation of the viral envelope protein. Comparably Inhibited by IFITM Proteins and Neutralizing Antibody KZ52 IFITM proteins 1, 2, and 3 inhibit cellular entry of EBOV [42] and several other viral pathogens [42, 43] and might reduce EBOV amplification in the infected host, raising the question of whether viruses circulating in 2014 are less susceptible to IFITM protein inhibition than those responsible for the 1976 outbreak in Zaire. doi = 10.1093/infdis/jiv101 id = cord-351776-otx5qwyu author = Ibáñez-Samaniego, Luis title = Elevation of Liver Fibrosis Index FIB-4 Is Associated With Poor Clinical Outcomes in Patients With COVID-19 date = 2020-06-21 keywords = COVID-19; FIB-4; patient summary = In this study, we evaluated the association between FIB-4, a liver fibrosis index, and the risk of progression to critical illness in middle-aged patients with COVID-19. To overcome this problem, we analyzed our data in different ways: (1) we retrieved available information on blood test done within 6 months before COVID-19 diagnosis in a relatively small number of patients (15% of the total series): at the time of COVID-19 diagnosis, AST and ALT increased significantly while platelets remained stable as compared with previous values; however, there were no significant changes in FIB-4 categories; (2) we evaluated specifically the prognostic value of isolated baseline AST: in contrast to previous reports, AST was not an independent predictor either at univariate level or when adjusted by other clinical and laboratory covariates; and (3) finally, we evaluated specifically the association between the elevation of AST (ie, AST above the upper limit of normality) and the need for MV, which identified that AST elevation was an independent risk factor. doi = 10.1093/infdis/jiaa355 id = cord-007305-pkjfnhro author = Iosub, Silvia title = Leukonychia Partialis in Kawasaki Disease date = 1984-10-17 keywords = HCV; OC43 summary = COLLEAGUES -Some areas in the northern part of the Israel desert (Negev) are known to be endemic for Borrelia recurrentis infection [1] (tick-borne relapsing fever). None of them developed overt symptoms and signs of tick-borne relapsing fever as observed in the subjects from groups I and II. Our patients had nail abnormalities typical for leukonychia partialis of the acquired type, since color changes had not been noted before the present illness and were transient. We would welcome correspondence from others who have seen nail color abnormalities in Kawasaki disease. COLLEAGUES -We examined paired sera from 62 infants with acute non bacterial gastroenteritis and from 50 age-matched controls (admitted to the hospital for nondiarrheal diseases) for antibody to human coronavirus (HCV) OC43 and neonatal-calf diarrhea coronavirus (NCDCY). Convalescent-phase sera from all the patients positive for excretion of coronavirus-like particles in stools, and seronegative for previous HCV OC43 infections, reacted by IEM with HECY-24 and HECV-35 and, to a lesser extent, with HCY OC43. doi = 10.1093/infdis/150.4.617-a id = cord-007176-61e9obb3 author = Jackson, George Gee title = Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date = 1973-11-17 keywords = infection; respiratory; virus summary = RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture doi = 10.1093/infdis/128.5.674 id = cord-301340-lhh04pum author = Jamieson, Frances B. title = Human Torovirus: A New Nosocomial Gastrointestinal Pathogen date = 1998-11-17 keywords = gastroenteritis; patient; torovirus summary = Torovirus-like particles purified from stool specimens were further shown to be toroviruses on the basis of their morphology, immunospecific interactions with Breda virus antiserum, ability to elicit an immune response following infection, and the high degree of homology of the 3 end of their genome with that of the Berne and Breda viruses [19] . At a different time from that of study 1, patients whose stool specimens were positive for torovirus, rotavirus, or astrovirus by electron microscopy were enrolled in study 2. In torovirus-positive patients, stool specimens were examined daily by electron microscopy during the hospitalization and at follow-up. Nine additional torovirus-positive patients developed bloody diarrhea within 2-15 days after study enrollment and had no other pathogen in the stool sample. Stool specimens collected on a follow-up visit 2-6 months after study enrollment from 168 patients infected with torovirus showed that 14 were shedding the virus. doi = 10.1086/314434 id = cord-267458-uofy7jyx author = Jiang, Xiao-Lin title = Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China date = 2020-04-22 keywords = CoV-2; SARS summary = title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China We report a three-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Herein, we report a 3-family cluster study of eight patients associated with asymptomatic and pauciasymptomatic (one mild symptom only) SARS-CoV-2 transmission in Shandong Province, China. The first positive SARS-CoV-2 patients in this cluster were identified on January 21, 2020 triggering an epidemiological investigation by the local center for disease control and prevention. Our findings show that the transmission of SARS-CoV-2 by individuals with asymptomatic or paucisymptomatic infections is possible. Patient 5 (asymptomatic) was identified to be infected with SARS-CoV-2 after frequent contact with Patients 3 and 4 during work and home visits. In this study, we detected SARS-CoV-2 in two environmental swabs from the household of Patient 3. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period doi = 10.1093/infdis/jiaa206 id = cord-293299-gdew0ueo author = Jordan, William S. title = Influenza Research in the Soviet Union—1974 date = 1974-12-17 keywords = Institute; Soviet; Union; influenza summary = A long historical tradition for the use of livevirus vaccines in the Soviet Union dates from Smorodintsev''s experimental infection of volunteers with influenza virus in 1937 [2] . Since registered morbidity rather than a more direct measure of real influenza-ARD morbidity is used, the model probably has more applicability for health planners, who need to anticipate increased requirements for delivery of health care associated with epidemics, and for industrial organizations that face future production losses, than for those concerned with anticipating changes in the health status of the population per se. Although data from the morbidity registration system in the Soviet Union provide the basic information for this model, data from the 52 All-Union reporting centers appear to be used as well, particularly for obtaining early warning of the location of the initial epidemic outbreak in the country. doi = 10.1093/infdis/130.6.686 id = cord-345727-bcxkycjh author = Karimata, Yosuke title = Clinical Features of Human Metapneumovirus Pneumonia in Non-Immunocompromised Patients: An Investigation of Three Long-Term Care Facility Outbreaks date = 2018-09-15 keywords = hmpv; outbreak; patient summary = title: Clinical Features of Human Metapneumovirus Pneumonia in Non-Immunocompromised Patients: An Investigation of Three Long-Term Care Facility Outbreaks BACKGROUND: Several studies have reported outbreaks due to human metapneumovirus (hMPV) in long-term care facilities (LTCF) for the elderly. Even though it is usually a mild and self-limiting disease, hMPV can potentially cause severe lower respiratory infections, especially in young children, the elderly, and immunocompromised patients [3] [4] [5] [12] [13] [14] . Several studies have reported outbreaks due to hMPV in long-term care facilities (LTCF) for the elderly and described the high incidence of pneumonia [3] [4] [5] [14] [15] [16] [17] . In conclusion, we report the clinical and radiological features of hMPV pneumonia in non-immunocompromised patients collected from 3 outbreaks in LTCF in Okinawa, Japan. An outbreak of severe respiratory tract infection due to human metapneumovirus in a long-term care facility for the elderly in Oregon doi = 10.1093/infdis/jiy261 id = cord-309786-8zyf9e3k author = Karron, Ruth A title = Safety and Immunogenicity of the Respiratory Syncytial Virus Vaccine RSV/ΔNS2/Δ1313/I1314L in RSV-Seronegative Children date = 2019-10-12 keywords = RSV; pfu; Δ1313 summary = RESULTS: In RSV-seronegative children, the 10(5) PFU dose was overattenuated, but the 10(6) PFU dose was well tolerated, infectious (RSV/ΔNS2/Δ1313/I1314L replication detected in 90% of vaccinees), and immunogenic (geometric mean serum RSV plaque-reduction neutralizing antibody titer, 1:64). b A >4 fold-rise in serum RSV neutralizing antibody was detected in a placebo recipient in the 10 5 PFU dose cohort, probably indicating infection with wild-type RSV between study days 28 and 56. b A >4 fold-rise in serum RSV neutralizing antibody was detected in a placebo recipient in the 10 5 PFU dose cohort, probably indicating infection with wild-type RSV between study days 28 and 56. Live respiratory syncytial virus (RSV) vaccine candidate containing stabilized temperature-sensitivity mutations is highly attenuated in RSV-seronegative infants and children doi = 10.1093/infdis/jiz408 id = cord-011722-82qzf8ht author = Keitel, Wendy A. title = Influenza A(H5N1) Vaccines: Are We Better Prepared for the Next Pandemic? date = 2014-01-01 keywords = A(H5N1; influenza summary = doi = 10.1093/infdis/jit573 id = cord-007277-86lynlxn author = Kenneth, McIntosh title = Coronaviruses in the Limelight date = 2005-02-15 keywords = Esper; Kawasaki summary = started their work), but rather that, in some of the earliest work on CoVs during the 1960s, viruses were reported that were then forgotten-viruses that came from adults with respiratory illness, that grew only in human embryonic tracheal organ culture, that caused illness in volunteers, and that were not, or were only distantly, antigenically related to the 2 HCoV species that were subsequently the best studied, HCoV-229E and HCoV-OC43. However, the details from Esper et al.''s study-the seasonal distribution, the percentage of positive samples, the associated respiratory syndromes, and the numbers of infected children at various ages, for example-were heavily influenced by both the particular population that was investigated and the clinical setting, so it is essentially impossible to draw conclusions on the epidemiology, pathogenicity, and relative importance of HCoV-NH in relation to other respiratory viruses. Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children doi = 10.1086/428510 id = cord-285527-1mceq6v0 author = Kinloch, Natalie N title = Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date = 2020-06-28 keywords = PCR; SARS summary = doi = 10.1093/infdis/jiaa370 id = cord-291486-5h96msv1 author = Kistler, Amy title = Pan-Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity date = 2007-09-15 keywords = HRV; HRV'X; PCR; Virochip summary = The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger-scale studies will be necessary to determine whether particular substrains of viruses confer an elevated risk of asthma exacerbation. Each NatURI specimen was analyzed independently in a blinded manner by 3 distinct viral detection methods: Virochip analysis and culture isolation for 9 common respiratory pathogens (HRV; RSV; influenza viruses A and B; human parainfluenza viruses 1, 2, and 3; adenovirus; and human enterovirus) and PCR for HRV. This diversity indicates that future studies that seek to link a particular virus or set of viruses to a discrete clinical outcome, such as exacerbation of asthma symptoms, will need to include large numbers of subjects and use pan-viral detection methods (such as the Virochip) that can differentiate among such isolates. doi = 10.1086/520816 id = cord-324001-m7ys95z7 author = Kobinger, Gary P. title = Assessment of the Efficacy of Commercially Available and Candidate Vaccines against a Pandemic H1N1 2009 Virus date = 2010-04-01 keywords = H1N1; influenza; vaccine summary = Groups of five 16-to 20-weekold ferrets without antibodies against circulating influenza strains were immunized with one of the 2008 seasonal inactivated split vaccines (Fluviral; GlaxoSmithKline) or the cold-adapted live attenuated vaccine (FluMist; MedImmune), a swine influenza vaccine (FluSure; Pfizer), or a matched laboratory-produced inactivated vaccine (pH1N1inact). HAI antibody titers against the pandemic H1N1 2009 MX10 isolate were detected at day 7 in ferrets receiving the laboratory-produced matched vaccine pH1N1inact or the swine influenza vaccine FluSure, reaching titers 140 on day 7 or 10, respectively. Toward this end, we compared the antibody and cellular responses elicited by 2 seasonal vaccines (Fluviral and FluMist), the commercial swine vaccine FluSure, and a laboratory-produced matched inactivated whole-virus preparation. A curious observation is the more severe cases of disease and the higher mortality rate noted for animals vaccinated with FluMist, which correlated with slightly more infectious virus in the nasal washes of this group at day 3. doi = 10.1086/651171 id = cord-345101-h0i5o0do author = Koo, Bon-Sang title = Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date = 2020-08-03 keywords = SARS; figure summary = Using a reliable primate model is critical for developing therapeutic advances to treat humans infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The absence of a reliable preclinical animal model that recapitulates patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection poses a major limitation to the development of improved diagnostics and therapeutics. Studies reported that SARS-CoV-2 developed no severe clinical signs, but pulmonary pneumonia in 50% of cynomolgus macaques, recapitulating mild symptoms in humans [6] . The viral RNA was highest in the upper respiratory swab samples and lung tissues at the earliest phase of infection, and the viral antigen was present in the lungs ( Figure 1C and D) , suggesting the predominant site of the virus. Using a high viral titre administered through combined routes, virus assays, and histopathological changes suggests that both cynomolgus and rhesus macaques are permissive to infection of SARS-CoV-2 and recapitulate COVID-19-like disease in human. doi = 10.1093/infdis/jiaa486 id = cord-007295-lq8h1pc6 author = Koudstaal, Wouter title = Pre- and Postexposure Use of Human Monoclonal Antibody against H5N1 and H1N1 Influenza Virus in Mice: Viable Alternative to Oseltamivir date = 2009-12-15 keywords = CR6261 summary = doi = 10.1086/648378 id = cord-350201-tluc2ck7 author = Kuiken, Thijs title = Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia date = 2018-10-01 keywords = New; PPMV-1; dutch; pigeon summary = The impetus for the current study was the identification of a virus related to avian paramyxovirus type 1 (APMV-1) from a fatal human case of unknown cause in the Netherlands by viral metagenomics analysis [8] . In this study, we fully characterized the Dutch clinical isolate of APMV-1-like virus, determined its phylogenetic relationship to other APMV-1 strains, and correlated presence of this virus with lesions in tissues obtained from the patient at autopsy. Domestic pigeons were inoculated intratracheally with the Dutch clinical virus isolate to determine infectivity and transmissibility, clinical signs, and pathological changes (Supplementary Methods). This is consistent with the New York case, where evidence of PPMV-1 infection in feces and urine also suggested extrarespiratory Pigeon Paramyxovirus-Linked Pneumonia • JID 2018:218 (1 October) • 1041 Table 1 spread [11] . It is relevant for these PPMV-1 cases that the risk of 2 pigeon-associated diseases-chlamydiosis and cryptococcosis-was largely a function of the immune status of patients, rather than contact with infected birds [32, 33] . doi = 10.1093/infdis/jiy036 id = cord-269383-1tyorrb0 author = Lai, Christopher K C title = Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date = 2020-08-01 keywords = DTS; SARS summary = doi = 10.1093/infdis/jiaa487 id = cord-288485-m3g88fl2 author = Lam, Katherine W title = Continued In-Hospital Angiotensin-Converting Enzyme Inhibitor and Angiotensin II Receptor Blocker Use in Hypertensive COVID-19 Patients Is Associated With Positive Clinical Outcome date = 2020-07-23 keywords = COVID-19; arb summary = title: Continued In-Hospital Angiotensin-Converting Enzyme Inhibitor and Angiotensin II Receptor Blocker Use in Hypertensive COVID-19 Patients Is Associated With Positive Clinical Outcome BACKGROUND: This study investigated continued and discontinued use of angiotensin-converting enzyme inhibitors (ACEi) or angiotensin II receptor blockers (ARB) during hospitalization of 614 hypertensive laboratory-confirmed COVID-19 patients. Because the widely used antihypertensive medications angiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB) may upregulate ACE2 receptors [7] [8] [9] , through which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the host cells [10] , concerns have been raised as to whether their use may result in increased morbidity and mortality [4, [11] [12] [13] . The goal of this study was to investigate the effects of in-hospital continuation and discontinuation of ACEi/ARBs on the clinical outcomes of hypertensive COVID-19 patients, controlling for newly developed hypotension or AKI during hospitalization. doi = 10.1093/infdis/jiaa447 id = cord-266573-vfl08i2p author = Largent, Emily A title = Paying Participants in COVID-19 Trials date = 2020-05-29 keywords = COVID-19; research; trial summary = Given increased risk of undue influence against pandemic background conditions, incentive payment should be avoided unless essential to recruitment and retention in important trials whose social value outweighs this risk. Given the pandemic''s devastating economic effects, as well as the fact that risks may be higher or more uncertain in COVID-19 trials than in nonpandemic research, there is an increased likelihood of undue influence stemming from incentive payments. Rather, in light of pandemic circumstances-similar features of which may be replicated in other contexts, including research conducted in low-and middle-income countries or with participants whose nonresearch options are limited even in the absence of a pandemic-offers of compensation may raise ethical concerns akin to incentives [14] . Acknowledging this challenge, the best IRBs can do is to minimize the possibility of undue influence for trial participants on the whole by making it unlikely for research participation to constitute an objectively unreasonable choice for members of the target study population. doi = 10.1093/infdis/jiaa284 id = cord-304766-h9kuytuf author = Lei, Hao title = Non-pharmaceutical interventions used to control COVID-19 reduced seasonal influenza transmission in China date = 2020-09-08 keywords = China; covid-19 summary = To suppress the COVID-19 pandemic, from January 23-25, 2020, 30 provinces began a 1-level response and implemented a set of non-pharmaceutical interventions (NPIs), including not only the classical isolation of the confirmed/suspected cases and quarantine of their close contacts in special facilities, but also unprecedented measures like strict community containments with social distancing, such as the Wuhan city travel ban to prevent the exportation of cases from Wuhan and other priority areas of Hubei Province, extension of the Spring Festival holiday, suspension of traffic and transportation, closure of school and entertainment venues, banning of mass gathering activities, compulsory community use of facemasks in public areas, and information about the epidemic and prevention measures widely disseminated, public risk communications and health education strengthened, new hospital built to ensure that all cases could be treated [2] . doi = 10.1093/infdis/jiaa570 id = cord-277735-a9gkath5 author = Leung, Danny Tze Ming title = Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date = 2004-07-15 keywords = ELISA; SARS summary = doi = 10.1086/422040 id = cord-321132-xdpb3ukt author = Lhomme, Sebastien title = Influence of Polyproline Region and Macro Domain Genetic Heterogeneity on HEV Persistence in Immunocompromised Patients date = 2014-01-15 keywords = HEV; infection summary = We investigated the association between the genetic heterogeneity of HEV quasispecies in ORF1 and the outcome of infection in solid-organ transplant patients. Both sequence entropy and genetic distances during the hepatitis E acute phase were higher in patients whose infection became chronic than in those who cleared the virus. Both sequence entropy and genetic distances during the hepatitis E acute phase were higher in patients whose infection became chronic than in those who cleared the virus. We therefore analysed the characteristics of HEV quasispecies at the acute phase of hepatitis E in 2 groups of SOT patients, one whose infection became chronic and the other who cleared the virus. Both the complexity and diversity of the PPR and the macro domain were higher in viral population of the patients whose infection became chronic than in those who cleared the virus. doi = 10.1093/infdis/jit438 id = cord-350302-xmyqqgn5 author = Li, Pengfei title = Estimating Global Epidemiology of Low-Pathogenic Human Coronaviruses in Relation to the COVID-19 Context date = 2020-08-15 keywords = LPH summary = title: Estimating Global Epidemiology of Low-Pathogenic Human Coronaviruses in Relation to the COVID-19 Context Studies were included and data extracted only if they reported participants with symptoms of acute respiratory tract infections or influenza like illness. Australia 74 125 30 30 149 1876 9 35 251 68 47 81 7 26 198 175 40 580 21 35 28 30 116 26 230 303 25 367 11 3 5 23 81 6 60 66 1652 48 71 20 131 80 29 18 1231 12 523 514 2277 526 561 6221 70 988 277 739 6064 1041 665 593 244 300 1910 4259 1059 7158 450 417 309 311 2060 1404 2693 3899 407 3910 172 411 114 369 2370 67 972 1528 40 150 686 1166 112 8462 372 2428 369 24 [2, 3] , our included studies only detected LPH-CoV in individuals with respiratory illness or symptoms. doi = 10.1093/infdis/jiaa321 id = cord-007187-gb1txu1o author = Lindner, Juha title = CD4(+) T Helper Cell Responses against Human Bocavirus Viral Protein 2 Viruslike Particles in Healthy Adults date = 2008-12-01 keywords = B19V; HBoV; VP2 summary = To date, HBoV genomes have been detected worldwide in respiratory tract samples obtained from children with pulmonary diseases, whereas only limited data on virus-specific immunity are available, mainly because of the lack of recombinant viral antigens. seronegative individuals have been described and were found predominantly among infants and young children (those 2 years of age) [20, 27, 28, 29] , serum samples obtained from 10 healthy infants (mean age, 11.8 months [range, 6 -45 months]) without detectable virus-specific antibodies (median OD 450 value, 0.056 [range, 0.017-0.104]) were selected and representatively included in the study, to ensure the specificity of the serologic analysis performed. By use of viral protein 2 (VP2) viruslike particles (VLPs), all 69 healthy adults who were studied were found to be positive (seropositive) for HBoV-specific IgG antibodies by ELISA. Using HBoV VLPs, we observed frequent VP2-specific humoral immune responses in healthy adults, whereas seronegative status was predominantly detected in young children (age, 2 years) [27, 37] . doi = 10.1086/592985 id = cord-351571-gwtkrt5u author = Mackay, Ian M. title = Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date = 2013-05-01 keywords = HRV; virus summary = Human rhinovirus (HRV) infections trigger exacerbations of asthma and chronic obstructive pulmonary disease and the majority of acute respiratory illnesses (ARIs), some of which meet criteria for influenza-like illness. Nevertheless, each available majority sequence of an HRV-C type has to date represented a genetically unique, phylogenetically distinct, and globally distributed virus detected in patients with ARIs. There are specific seasonal and annual variations in respiratory virus circulation and interactions [11] [12] [13] . We sought to quantify the genetic diversity, epidemiology, and impact of HRV and enterovirus species, conjointly referred to hereafter as picornaviruses, circulating among a community cohort of preschool-aged children who provided respiratory samples over a 1-year period. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children doi = 10.1093/infdis/jis476 id = cord-002333-90f9vr0a author = Madan, Anuradha title = Immunogenicity and Safety of an AS03-Adjuvanted H7N9 Pandemic Influenza Vaccine in a Randomized Trial in Healthy Adults date = 2016-12-01 keywords = AS03; H7N9; vaccine summary = The coprimary immunogenicity objective determined whether adjuvanted vaccines elicited an immune response against the vaccine-homologous virus, 21 days after the second vaccine dose per US and European licensure criteria in the per-protocol cohort (n = 389). The coprimary immunogenicity objective was to evaluate whether the adjuvanted A/Shanghai/2/2013 (H7N9) vaccines elicited an immune response against the vaccine-homologous virus that met US CBER and European Committee for Medicinal Products for Human Use (CHMP) immunogenicity targets at day 42 (21 days after the second vaccine dose). In a sub-analysis of the homologous immune response by age, the adjuvanted vaccine was immunogenic in both age groups, with SPRs ≥80.0% in participants 41-64 years of age, despite lower GMTs (Table 3 ). The results of this phase I/II randomized, placebo-controlled trial showed that 2 doses of the H7N9 AS03-adjuvanted vaccine elicited a robust immune response in healthy adults up to 64 years of age, with an acceptable safety profile. doi = 10.1093/infdis/jiw414 id = cord-342996-honeavwj author = Mair-Jenkins, John title = The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date = 2015-01-01 keywords = CFR; SARS; convalescent summary = title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . doi = 10.1093/infdis/jiu396 id = cord-007237-8y7218oj author = Manning, Ashleigh title = Comparison of Tissue Distribution, Persistence, and Molecular Epidemiology of Parvovirus B19 and Novel Human Parvoviruses PARV4 and Human Bocavirus date = 2007-05-01 keywords = B19; HIV; PARV4 summary = At autopsy, bone marrow, lymphoid tissue, and brain tissue from human immunodeficiency virus (HIV)—infected individuals with acquired immunodeficiency syndrome (AIDS) and those without AIDS and from HIV-uninfected individuals were screened for parvovirus B19, PARV4, and HBoV DNA by means of quantitative polymerase chain reaction analyses. In the current study, we examined a series of samples of different tissues, collected at autopsy, for the presence of HBoV and PARV4 DNA sequences and compared the frequencies of detection, viral loads, and genetic variability with those for B19. Samples from HIV-infected individuals who did not have AIDS (hereafter referred to as "pre-AIDS study subjects") and those with terminal AIDS at time of death were compared with corresponding samples from HIV-uninfected individuals, to investigate the relationship between viral load and immunosuppression and, thus, the role of the immune system in controlling virus replication. Among the HIV-infected study subjects, a similar difference was found in PARV4 viral loads in bone marrow versus lymphoid tissue (median values of 220 and 46 DNA copies/10 6 cells, respectively; ) (figure 1B). doi = 10.1086/513280 id = cord-288072-42sx52tn author = Monto, Arnold S. title = The Tecumseh Study of Respiratory Illness. VI. Frequency of and Relationship between Outbreaks of Coronavims Infection date = 1974-03-17 keywords = OC43 summary = Specimens of blood collected in Tecumseh, Michigan over a four-year period were studied for rise in antibody titer against coronavirus OC43. As part of the study of respiratory infections in Tecumseh, Michigan, specimens of blood were collected on a regular basis from families under surveillance [10] . By testing of specimens collected in early 1967, a large-scale outbreak of infection with coronavirus 229E was detected [11] . All specimens of serum collected from members of 269 families were studied by CF and HAl for rise in titer of antibody to coronavirus OC43. The specimens with rises in CF or HAl titer both showed 66.7% agreement with the neutralization test. Neutralization tests confirmed the difference, and indicated that in the individual case during a period of prevalence of agents related to OC43, even if CF and HAl do not agree, it is likely that an infection with the agent actually did occur. doi = 10.1093/infdis/129.3.271 id = cord-002921-i5jxn1vj author = Morens, David M title = Pandemic Zika: A Formidable Challenge to Medicine and Public Health date = 2017-12-15 keywords = Zika; virus summary = Because of the pandemic''s uniqueness and the insidious ability of Zika virus to harm unborn children, the pandemic has captured the attention of infectious disease researchers and practitioners of clinical and public health medicine around the world, as well as the attention of allied colleagues working in entomology, vector control, informatics, teratology, immunology, and a host of other disciplines [3] [4] [5] . Furthermore, some studies have suggested that preexisting flavivirus immunity (eg, from prior dengue virus infection) might potentiate Zika [16] via antibody-dependent infection enhancement in some circumstances [17] , while other research has countered this view [18] . As with most flaviviruses, small-animal models of Zika virus infection and disease have been problematic, but considerable progress has nonetheless been made, including important new information bearing on teratogenicity and vaccine design strategy [20] . Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes doi = 10.1093/infdis/jix383 id = cord-268490-e8jub01m author = Moscona, Anne title = CSI Microbiology: Emerging Pathogens and a Staged Strategy for Detection and Discovery date = 2007-12-15 keywords = York; respiratory summary = [2] in this issue of the Journal makes 2 unique contributions to this field: it demonstrates the need to consider and identify rhinoviruses as a cause of serious acute respiratory disease in children, and it establishes the MassTag polymerase-chainreaction (PCR) multiplex platform as a practical tool for microbial surveillance. [4] , in the same group, went on to report the use of the method to investigate both undiagnosed influenza-like illness in New York State and the discovery of a novel genetic clade within the picornaviruses; "human rhinovirus New York" was the first new agent to be detected by use of MassTag PCR. [2] report clear evidence that links these viruses to severe respiratory disease: 75% of viruses detected among 97 nasopharyngeal aspirates from children hospitalized with acute respiratory infection-with no pathogen identified by routine methods-were rhinoviruses. MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during doi = 10.1086/524313 id = cord-269324-zh1a3gwh author = Mubareka, Samira title = Human Genes and Influenza date = 2008-01-01 keywords = influenza; virus summary = doi = 10.1086/524067 id = cord-000842-kff3gig0 author = Nayak, Jennifer L. title = CD4(+) T-Cell Expansion Predicts Neutralizing Antibody Responses to Monovalent, Inactivated 2009 Pandemic Influenza A(H1N1) Virus Subtype H1N1 Vaccine date = 2013-01-15 keywords = CD4; cell summary = Knowledge of the relationship between CD4 + T cells and the development of a neutralizing antibody response following administration of TIV is even more limited, with the few studies addressing this question failing to find a correlation between these parameters [12, 20] , except when an adjuvanted influenza A virus subtype H5N1 vaccine was used [29] . In this study, we used an experimental approach designed to maximally detect antigen-specific CD4 + T cells by using cytokine enzyme-linked immunosorbent spot (ELISPOT) assays with pools of overlapping synthetic peptides as recall antigens to quantify responses to conserved and novel epitopes following vaccination of adults with monovalent inactivated A (H1N1)pdm09 vaccine. We conclude from this that expansion of CD4 + T cells rather than the baseline number of influenza virus-reactive cells correlates with and predicts the development of a neutralizing antibody response following A (H1N1)pdm09 vaccination, a result that is consistent with the idea that CD4 + T-cell help may limit the antibody response to pandemic influenza vaccines. doi = 10.1093/infdis/jis684 id = cord-001401-f29y8vh5 author = Nelson, Martha I. title = Multiyear Persistence of 2 Pandemic A/H1N1 Influenza Virus Lineages in West Africa date = 2014-07-01 keywords = Africa; West summary = Increased genetic sequencing of African A/H1N1 pandemic influenza viruses during 2009-2013 revealed multiyear persistence of 2 viral lineages within West Africa, raising questions about the roles of reduced air traffic and the asynchrony of seasonal influenza epidemics among West African countries in the evolution of independent lineages. Increased genetic sequencing of African A/H1N1 pandemic influenza viruses during 2009-2013 revealed multiyear persistence of 2 viral lineages within West Africa, raising questions about the roles of reduced air traffic and the asynchrony of seasonal influenza epidemics among West African countries in the evolution of independent lineages. To elucidate the evolution of influenza viruses in Africa, we conducted a large-scale phylogenetic analysis of global pH1N1 influenza virus diversity during 2009-2013, including 299 pH1N1 HA sequences collected in 18 African countries. Our analysis identified 2 well-supported clades of pH1N1 viruses that each persisted for >1.5 years in West Africa, highlighting the need to further understand the ecology and evolution of IAVs in this understudied and relatively geographically isolated region. doi = 10.1093/infdis/jiu047 id = cord-307918-8y89p11a author = Onyango, Clayton O. title = Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date = 2012-12-15 keywords = Kenya; influenza; virus summary = Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. The following clinical and laboratory features obtained on admission or that relate to discharge outcome were compared between influenza-positive and influenza-negative children: duration of hospitalization >14 days, very severe pneumonia, wheezing, hypoxia (oxygen saturation level <90%, by fingertip pulse oximetry), circulatory shock (capillary refill time ≥3 seconds), severe anemia (hemoglobin level <5 g/dL), prematurity, congenital heart disease, positivity for HIV antibody (by 2 rapid tests), severe underweight (weight for age Z score ≤3), slide positivity for Plasmodium species, bacteremia, concurrent viral infection diagnosis, and death before discharge [2] . Our study identified all 3 influenza viruses in circulation in this rural coastal Kenya location among patients hospitalized with severe or very severe pneumonia and among outpatients with URTI. doi = 10.1093/infdis/jis536 id = cord-339271-t7cxqkp1 author = Pan, Yanfeng title = Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date = 2020-04-22 keywords = SARS summary = The median period from diagnosis to negative nucleic acid test was significantly different between patients with normal or atypical chest computed tomography (CT) findings (n=16, 61.5%; 7.5 days [2–20 days]) and patients with typical ground-glass or patchy opacities on CT(n=10, 38.5%; 12.5 days[8–22 days]; P<0.01). Here, we identified a total of 26 persistently asymptomatic patients with positive test results for SARS-CoV-2 nucleic acid to determine the clinical characteristics and asymptomatic carrier transmission of COVID-19 infection. A total of 26 hospitalized patients with a SARS-CoV-2 epidemiological history and positive SARS-CoV-2 nucleic acid test results were identified to analyze the epidemiological and clinical characteristics of COVID-19infected asymptomatic carriers. Discharge criteria for COVID-19 were as follows: 1) normal body temperature for more than 3 days; 2) significantly improved respiratory symptoms; 3) significantly improved chest radiography; and 4) two consecutive negative SARS-CoV-2 nucleic acid test results (sampling interval at least 1 day). doi = 10.1093/infdis/jiaa205 id = cord-350749-ihkxouz8 author = Panda, Aditya K title = Plasmodium falciparum Infection May Protect a Population from Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-07-29 keywords = infection summary = title: Plasmodium falciparum Infection May Protect a Population from Severe Acute Respiratory Syndrome Coronavirus 2 Infection The authors have suggested that prior exposure of children to coronavirus OC43 offers protection against severe COVID-19 phenotype by possible crossimmunity. These observations encouraged us to investigate the possible role of Plasmodium infection on coronavirus disease 2019 (COVID-19) infection or severity. Based on these observations on Plasmodium infection and positive-strand RNA viruses, we hypothesized that there could be a possible association between malaria and SARS-CoV-2 infection. To validate our observation, we investigated the prevalence of COVID-19 in the Plasmodium falciparum-endemic area of Odisha, India, Odisha is highly endemic for P. falciparum for the last 10 years (2010-2019) from the National Vector Borne Disease Control Program and COVID-19 infection status in Odisha from the government of Odisha website (see https://health. Naturally-occurring anti-alphagalactosyl antibodies in human Plasmodium falciparum infections-a possible role for autoantibodies in malaria doi = 10.1093/infdis/jiaa455 id = cord-007288-lzxi6q1p author = Pazin, George J. title = Leukocyte Interferon for Treating First Episodes of Genital Herpes in Women date = 1987-12-17 keywords = HSV; day; interferon summary = Women experiencing their first episodes of genital herpes were treated, beginning within three days of the onset of lesions, with 5 × 10(4) units of human leukocyte interferon/kg of body weight for 12 doses over 14 days (total, ∼3.6 × 10(7) units) or with placebo in equivalent volumes. We clinically and virologically assessed the effect of early treatmentwith leukocyte interferon (Cantellvariety) [13] on the initial episode of'' genital herpes.Weindirectly evaluated the effect of .interferon on latency by determining the incidence and frequency of both asymptomatic reactivations and symptomatic recurrences during an intensive one-year follow-up period. Overall, interferon treatment at rv3 x 10 6 U/day had an ameliorative effect on both shedding of virus and the time to healing of initial episodes of genital herpes, but had no significant effect on the associated pain. doi = 10.1093/infdis/156.6.891 id = cord-315476-7rdiesav author = Peret, Teresa C. T. title = Characterization of Human Metapneumoviruses Isolated from Patients in North America date = 2002-06-01 keywords = HMPV; PCR summary = In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In the present article, we describe polymerase chain reaction (PCR) and sequencing studies done on 11 isolates from respiratory specimens from 10 Canadian patients with acute respiratory tract illness. Published nucleocapsid (N) and fusion (F) gene sequences of HMPV and avian pneumovirus were used to develop primers for detection and sequencing of HMPV at the Respiratory Virus Section (Centers for Disease Control and Prevention, Atlanta). We detected virus in isolates from children with acute respiratory tract infection, as described in the first report of HMPV [1] . doi = 10.1086/340518 id = cord-352526-t8odetzw author = Pinto, Bruna G G title = ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date = 2020-06-11 keywords = ACE2; SARS; covid-19 summary = Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. The molecular mechanism responsible for the increased disease severity in patients with these comorbidities is not fully understood, but previous studies suggest a role for angiotensin-converting enzyme 2 (ACE2) (5) . Here, we showed that the expression of the gene encoding the ACE2 receptor in lung tissue is upregulated by diseases representing comorbidities along with COVID-19. doi = 10.1093/infdis/jiaa332 id = cord-007255-jmjolo9p author = Pulliam, Juliet R. C. title = Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses date = 2009-02-15 keywords = model; viral summary = The database contains information on the 3 molecular characteristics hypothesized to influence the potential of a virus to cross host species: site of replication (X SR ; whether replication is completed in the cytoplasm or requires nuclear entry), genomic material (X GM ; RNA or DNA), and segmentation of the viral genome (X Seg ; segmented or nonsegmented). Hypothesis testing allowed us to determine how likely it was that the observed patterns were due to chance, whereas model-based prediction allowed us to determine what trait or set of traits was the best predictor of a livestock virus''s ability to infect humans and to estimate the probability that a particular virus species would be able to jump host species, given knowledge of the traits of interest. To examine the magnitude and relative importance of the effects that the 3 molecular characteristics of interest have on the ability of the viral species in the database to infect humans, we developed a set of logistic regression models. doi = 10.1086/596510 id = cord-327673-3uem0e22 author = Qin, Gang title = Phosphoantigen-Expanded Human γδ T Cells Display Potent Cytotoxicity against Monocyte-Derived Macrophages Infected with Human and Avian Influenza Viruses date = 2009-09-01 keywords = Vg9Vd2; nkg2d summary = doi = 10.1086/605413 id = cord-007234-hcpa8ej5 author = Renwick, Neil title = A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date = 2007-12-15 keywords = HRV; PCR; respiratory summary = title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. In an attempt to gather additional information on the potential pathogenicity, as well as temporal and geographic distribution, of rhinoviruses, including the recently identified genotype, we evaluated specimens collected, during the 2003-2006 seasons in Bad Kreuznach, Germany, from children hospitalized because of severe LRTI. In this study of samples collected, during a 3-year interval, from hospitalized children with severe undiagnosed respiratory infection, MassTag PCR allowed us to detect viral pathogens in 49 (51%) of 97 cases. Although we did not have samples to test for the presence of HRV in the lower respiratory tract, the high frequency at which HRV was identified as being the sole virus detected suggests a correlation between the agent and the observed LRTI symptoms. doi = 10.1086/524312 id = cord-012509-887xlllb author = Roy-Ghanta, Sumita title = Responses to A(H1N1)pdm09 Influenza Vaccines in Participants Previously Vaccinated With Seasonal Influenza Vaccine: A Randomized, Observer-Blind, Controlled Study date = 2014-11-01 keywords = TIV summary = We investigated the effect of TIV priming on humoral responses to AS03-adjuvanted and nonadjuvanted A(H1N1)pdm09 vaccines, the role of AS03 on cell-mediated immune (CMI) responses, and vaccine safety. Healthy adults (aged 19–40 years) were randomized 1:1:1:1 to receive TIV or saline followed 4 months later by 2 doses, 3 weeks apart, of adjuvanted or nonadjuvanted A(H1N1)pdm09 vaccine and followed up to study end (day 507). Assessment of HI responses was based on the European Medicines Agency, Committee for Medicinal Products for Human Use (CHMP) guidance targets for pandemic influenza vaccines in adults [32] (point estimates, SCR >40%; SPR >70%; GMFR >2.5) and the Center for Biologics Evaluation and Research (CBER) licensure criteria [33] [lower limits of 95% confidence interval (CI) ≥40% for SCR and ≥70% for SPR]. After TIV or placebo administration (dose 1; days 0-122), GMTs of A(H1N1)pdm09-specific HI responses in both groups remained low (ranges, 12.5-19.9 and 13.3-13.9, respectively), and CHMP or CBER criteria were not met (Supplementary Table 1) . doi = 10.1093/infdis/jiu284 id = cord-273356-1ius4ksa author = Sauceda, John A title = Findings From a Probability-Based Survey of United States Households About Prevention Measures Based on Race, Ethnicity, and Age in Response to Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-08-29 keywords = COVID-19; Latinos summary = doi = 10.1093/infdis/jiaa554 id = cord-317421-xzf723w2 author = Schieffelin, John S title = Infectious Disease Outbreaks: The Need For an All-in Approach date = 2020-04-08 keywords = Ebola summary = As of March 29, 2020, the 2018 to 2020 outbreak of Ebola virus disease (EVD) in the Democratic Republic of Congo (DRC) has led to 3453 cases and 2264 deaths [1] . In their article entitled "Identifying mechanisms of violence that impact Ebola virus disease transmission during the 2018-2019 outbreak in the Democratic Republic of the Congo, " Kelly et al [7] test the hypothesis that violent events directly targeting the Ebola response result in greater transmission than violence that does not directly target the Ebola response. These goals can only be accomplished through social mobilization and risk communication, highly specialized medical care and infection control practices, support for safe burial practices, and vaccination of those most at risk [10, 11] . Identifying mechanisms of violence that impact Ebola virus disease transmission during the 2018-2019 outbreak in the Democratic Republic of the Congo doi = 10.1093/infdis/jiaa167 id = cord-332303-0bbw64p5 author = Schuit, Michael title = Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date = 2020-06-11 keywords = SARS summary = This study examined the effect of simulated sunlight, relative humidity, and suspension matrix on the stability of SARS-CoV-2 in aerosols. Therefore, the present study examined the influence of both simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in different liquid matrices. Two different environmentally controlled rotating drum aerosol chambers, with volumes of 16-L and 208-L, were used in the present study to expose aerosols containing SARS-CoV-2 to controlled levels of temperature, relative humidity, and simulated sunlight. The present study examined the influence of simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in either simulated saliva or culture medium at 20°C. The half-lives estimated from the mean decay constants across all relative humidity levels without simulated sunlight present were 55 and 86 minutes for aerosols generated from virus suspended in culture medium and simulated saliva, respectively. doi = 10.1093/infdis/jiaa334 id = cord-327501-8s6dvanf author = Schwaiger, Julia title = No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date = 2020-09-17 keywords = IVIG; SARS summary = Testing 54 intravenous immunoglobulin preparations, produced from plasma collected in Europe and the United States, confirmed highly potent neutralization of a seasonal coronavirus; however, no cross-neutralization of the new SARS-CoV-2 was seen. The question is of significant clinical relevance, as SARS-CoV-2 cross-neutralizing antibodies in IVIGs, if they were present, might afford some protection to people with immune deficiencies and may even represent a treatment option for coronavirus disease 2019 (COVID-19) patients. The current study tested a representative number of IVIG lots for nAbs against SARS-CoV-2 and the longer-circulating HCoV-229E, to establish clarity about cross-neutralization of the pandemic virus by antibodies induced by earlier circulating seasonal coronaviruses. SARS-CoV-2 nAb titers were below the limit of detection for all 54 IVIG lots tested, irrespective of geographic origin of the plasma (Europe vs United States) and plasma collection modality (recovered vs source) ( Figure 1A) . doi = 10.1093/infdis/jiaa593 id = cord-270335-8vqi9c68 author = Seifert, Stephanie N title = Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date = 2019-11-04 keywords = EFB; Nipah; bat; virus summary = Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Studies of wild caught Pteropus spp suggest potential for viral recrudescence [16, 23] ; however, the hypothesis that NiV may persist in an individual bat and re-emerge under times of stress has yet to be confirmed experimentally. In contrast, the Egyptian fruit bat (EFB), Rousettus aegyptiacus, belongs to the same taxonomic family as Pteropus spp, Pteropodidae, and has been successfully used to model Marburg virus transmission [24, 25] and serological cross-reactivity after filovirus challenge [26] . Previous studies have demonstrated that EFB cells are permissive to Ebola virus, but experimentally challenged bats did not shed virus or support productive replication [38, 39] despite compatibility between the Ebola virus glycoprotein and the host receptor, NPC1 [40] . doi = 10.1093/infdis/jiz429 id = cord-289255-qwzg7prx author = Seligman, Stephen J. title = Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date = 2007-02-15 keywords = SARS summary = title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants have reported data on a 386-nt deletion in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) [1] . Because 1 patient had both the L386del variant and the wild-type variant in the same specimen, they raised the possibility that SARS-CoV exists as a quasi species, at least in some patients. Previous authors studying single-nucleotide variants from Beijing-area isolates in 2003 [2] and from the Singapore 2004 outbreak [3] have also found multiple viral sequences in the same sample that they attributed to quasi species. Although these 3 studies clearly establish the presence of a diversity of SARS-CoV genomes in individual patients, the issue of whether SARS-CoV quasi species exists remains open, particularly with respect to the 386-nt deletion. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? SARS-associated coronavirus quasispecies in individual patients doi = 10.1086/510917 id = cord-324280-e8mj6ecl author = Shaman, Jeffrey title = Asymptomatic Summertime Shedding of Respiratory Viruses date = 2018-04-01 keywords = virus summary = Here, we explore respiratory virus infection rates in a segment of this population through a convenience survey and sampling study of adult visitors to a New York City tourist attraction during spring and summer 2016. Among all participants there was a statistically significant positive association between reporting a greater tendency to get sick and total self-reported symptom score (P < .0001 by the Tukey test); however, there was no significant association between reporting a greater tendency to get sick and actual detection of respiratory virus shedding (P = .10 by χ 2 analysis). The best-fit logistic regression model supported an association between an increased likelihood of testing positive for respiratory virus infection and a higher total symptom score (P < .0001) and being Hispanic (P < .005). doi = 10.1093/infdis/jix685 id = cord-333429-bq7kfpby author = Shi, Ding title = Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date = 2020-07-02 keywords = RNA; SARS; patient summary = title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. doi = 10.1093/infdis/jiaa388 id = cord-300019-8vxqr3mc author = Shi, Ting title = The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date = 2019-03-08 keywords = ARI; adult; respiratory summary = doi = 10.1093/infdis/jiy662 id = cord-315457-w1nx9g91 author = Siedner, Mark J title = Desperate times call for temperate measures: practicing infectious diseases during a novel pandemic date = 2020-04-21 keywords = covid-19 summary = authors: Siedner, Mark J; Gandhi, Rajesh T; Kim, Arthur Y Of the thousands of peer-reviewed articles indexed in Pubmed, exactly one has reported the results of a randomized controlled trial; a single-centered study with approximately 200 COVID-19 infected individuals, investigating a drug developed for another virus, and resulting in a null finding. And although we agree with ethical obligations that compel medical researchers to make their data publicly available so it can inform the epidemic response, we also remain acutely aware that there has been a corresponding pandemic of COVID-19 misinformation. In the coming months, there will be results from well-designed and peer-reviewed trials that we hope will reveal therapeutic options for the treatment and prevention of COVID-19. In the meantime, we will be asked countless times to help decide which ones are which, often by trusted colleagues in search of a miracle for patients in extremis. doi = 10.1093/infdis/jiaa209 id = cord-013049-7d436sqg author = Sobhanie, Mahdee title = Evaluation of the Safety and Immunogenicity of a Candidate Pandemic Live Attenuated Influenza Vaccine (pLAIV) Against Influenza A(H7N9) date = 2016-03-15 keywords = A(H7N9; HAI; dose summary = We evaluated a candidate A/Anhui/2013(H7N9) pandemic live attenuated influenza vaccine (pLAIV) in healthy adults, and assessed the ability of 1 or 2 doses to induce immune memory. All subjects received a single 30-µg dose of unadjuvanted, antigenically matched A/Shanghai2/2013(H7N9) pandemic inactivated influenza vaccine (pIIV) 12 weeks after their first dose of pLAIV. Vaccines for control of influenza viruses with pandemic potential are under development, and results of clinical trials have suggested that these vaccines will require the use of adjuvants and multiple doses to induce substantial serum antibody responses [4, 5] . If vaccine virus infection is defined as detection of the virus in culture or by real-time RT-PCR at any time after day 1 or as development of a ≥4-fold increased HAI antibody response, then approximately 20%-30% of subjects were infected after each dose of pLAIV. doi = 10.1093/infdis/jiv526 id = cord-253768-y35m3vh1 author = Springer, Sandra A title = Federal and State Action Needed to End the Infectious Complications of Illicit Drug Use in the United States: IDSA and HIVMA’s Advocacy Agenda date = 2020-10-01 keywords = HCV; HIV; OUD; SUD summary = doi = 10.1093/infdis/jiz673 id = cord-281158-vjh9z7l4 author = Storch, Gregory A title = Respiratory Viruses in Babies: Important Insights From Down Under date = 2018-02-01 keywords = HRV; virus summary = Impressive study attributes include large size, community base, enrollment from birth, scheduled frequent longitudinal sampling with or without illness, high percentage of specimen acquisition rate, even enrollment of subjects throughout the year to account for virus seasonality, and testing of samples with an extensive panel of real-time polymerase chain reaction (PCR) assays. This intensive prospective study of respiratory viruses in infants finds that human rhinovirus (HRV) is by far the most frequent virus detected in the infant respiratory tract. Of the 152 infants followed, 81% experienced a first infection with HRV by 6 months of age, compared to 8.5% for RSV, and 0.7%-9.4% for the other respiratory viruses. Timing of first respiratory virus detection in infants: a community-based birth cohort study Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study Etiology of acute respiratory infections in infants: a prospective birth cohort study doi = 10.1093/infdis/jix600 id = cord-279725-d82sj80v author = Ströher, Ute title = Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date = 2004-04-01 keywords = IFN; SARS summary = We evaluated the susceptibility of the SARS-related coronavirus (SARS CoV) to ribavirin and interferon (IFN)-α in vitro by use of cytopathic effect, plaque assay, and immunoblot analysis. To support the search for effective antiviral treatments, we evaluated the susceptibility of SARS CoV isolates (detailed studies were performed with the Tor2 isolate [Toronto, Canada]) to ribavirin and interferon (IFN)-a-2b in vitro. Our data indicate that ribavirin does not inhibit the virus at concentrations attainable in human serum but that IFN-a-2b may be useful and deserves further evaluation as a therapeutic agent. To quantify the effect of IFN-a-2b on the replication of the SARS CoV, Vero E6 cells were infected at an MOI of 0.001 and were incubated in the presence IFN-a-2b (0-5000 IU/mL), as described above. Whether combined therapy with IFN-a-2b and ribavirin would inhibit the replication of the SARS CoV in vitro has not yet been evaluated; the combination is more effective than either agent used alone for the treatment of HCV infection in humans. doi = 10.1086/382597 id = cord-308979-qhlvd2mt author = Sumino, Kaharu C. title = Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date = 2005-09-15 keywords = PCR; patient; respiratory summary = doi = 10.1086/432728 id = cord-007009-4wbvdg1r author = Takahashi, Toru title = The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan date = 2014-03-15 keywords = Japan; RNA; SFTSV; figure; patient summary = Severe fever with thrombocytopenia syndrome (SFTS), an infectious disease with a high case-fatality rate, is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic to central and northeastern parts of China [1, 2] . Vero cells were inoculated with RT-PCR-positive patient sera for virus isolation, cultured for 4-7 days, and examined for SFTSV antigen detection by indirect immunofluorescence assay (IFA) with a polyclonal antibody raised against SFTSV recombinant NP (rNP; rabbit anti-SFTSV rNP serum), which was produced as follows. Physicians were asked to volunteer information if they had treated patients who satisfied the following case definition: (1) fever of >38°C; (2) gastrointestinal tract symptoms, such as nausea, vomiting, abdominal pain, diarrhea, and melena; (3) thrombocytopenia, with <100 × 10 9 platelets/L; (4) leukopenia, with <4 × 10 9 white blood cells/L; (5) elevated levels of aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase; (6) absence of other causes; and (7) death or admission to an intensive care unit because of the severity symptoms. Detection of severe fever with thrombocytopenia syndrome virus (SFTSV) RNA in the right cervical lymph node by the in situ hybridization ATtailing method. doi = 10.1093/infdis/jit603 id = cord-333411-hqtb4a2c author = Tan, Tina Q title = Location Matters: Geographic Disparities and Impact of Coronavirus Disease 2019 (COVID-19) date = 2020-09-17 keywords = COVID-19; United summary = doi = 10.1093/infdis/jiaa583 id = cord-007375-hqmyund4 author = Tang, Yi-Wei title = Host Single-Nucleotide Polymorphisms and Altered Responses to Inactivated Influenza Vaccine date = 2007-10-01 keywords = IL-10; MBL-2; response summary = We analyzed the relationship between host gene polymorphisms and responses in recipients of inactivated influenza vaccine, who were classified into poor, normal, or adverse response groups. The frequency of the mannose-binding lectin-2 codon 54 allele was significantly different among the 3 types of responders, with a decreased odds ratio for the development of poor or adverse responses (P = .033). The present study explored the possibility that host gene polymorphisms influence inactivated influenza vaccineinduced immune responses by comparing the frequencies of 8 SNPs in the MBL-2 gene and in the TNF-a and IL-10 promoter regions among different groups. We found a significant difference in allele frequency in the MBL-2 codon 54 among the poor, normal, and adverse responders, suggesting that the allele polymorphism is independently associated with poor and adverse responses to influenza vaccination. These findings support the present data by suggesting that the Ϫ1082 allele polymorphism in the IL-10 promoter region may be associated with adverse responses induced by influenza vaccine. doi = 10.1086/521370 id = cord-334242-m5dr19v4 author = Teran, Luis M. title = RANTES, Macrophage-Inhibitory Protein 1α, and the Eosinophil Product Major Basic Protein Are Released into Upper Respiratory Secretions during Virus-Induced Asthma Exacerbations in Children date = 1999-03-01 keywords = MBP; RANTES summary = doi = 10.1086/314618 id = cord-332537-rtdu4jae author = Tong, Tommy R. title = Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date = 2005-05-01 keywords = SARS summary = Airborne transmission of the severe acute respiratory syndrome (SARS) coronavirus (CoV) has been the favored explanation for its transmission on an aircraft [1] and appeared to explain a large community outbreak of SARS in the Amoy Gardens in Hong Kong [2] . in this issue of the Journal of Infectious Diseases [3] suggests that airborne dissemination of SARS-CoV may also occur in the health-care setting. However, if SARS-CoV is naturally airborne (produced by breathing and coughing), as was shown by Booth et al., then there is sufficient concern that it can be transmitted successfully by air. Acknowledgment of the fact that SARS-CoV can be aerosolized justifies the actions of those who have already committed resources for providing a safer environment in terms of preventing airborne transmission of infectious diseases and might provide the needed pressure for others to follow suit. Evidence of airborne transmission of the severe acute respiratory syndrome virus doi = 10.1086/429637 id = cord-334988-brumg6jh author = Traugott, Marianna title = Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in Different Stages of Infection: Comparison of Commercial Enzyme-Linked Immunosorbent Assays and Rapid Tests date = 2020-05-30 keywords = SARS; Wantai summary = We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction–confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. In the current study, we compared the diagnostic ability of 4 enzyme-linked immunosorbent assays (ELISAs), which assess SARS-CoV-2-specific antibodies of different immunoglobulin (Ig) classes (Euroimmun SARS-CoV-2 IgA and IgG and Wantai SARS-CoV-2 IgM and total antibody), and 2 rapid tests (Wantai SARS-CoV-2 Ab Rapid Test and Hangzhou AllTest Biotech 2019-nCoV IgG/IgM Rapid Test) in 77 patients with symptomatic SARS-CoV-2 infection. Of the 77 patients with PCR-confirmed SARS-CoV-2 infection, 30 individuals (12 female, 18 male; median age, 58 years; age range, 15-83 years) provided serum/plasma samples that were obtained at symptom onset or 1-5 days after the onset of disease (group 1). doi = 10.1093/infdis/jiaa305 id = cord-007264-r1w9a6gc author = Turner, Ronald B. title = Rhinovirus Infection of Human Embryonic Lung Fibroblasts Induces the Production of a Chemoattractant for Polymorphonuclear Leukocytes date = 1988-02-17 keywords = cell; chemoattractant summary = This study describes a chemoattractant for PMNLs that is elaborated by human embryonic lung fibroblast cells infected with rhinovirus. Chemotaxis assays were done in a 48-well microchemotaxis chamber with normal adult PMNLs. Medium supernatants from rhinovirus-infected cellculture attracted 87 ± 6 (mean ± SE) PMNLs/10 high-power fields (×450) compared with 38 ± 6 PMNLs/10 highpower fields attracted by medium from uninfected cell cultures (P < .0001). Human embryonic lung fibroblast cellsinfected with rhinovirus produced a chemoattractant for PMNLs. Media from R39-infected and uninfected cells attracted 87 ± 6 (mean ± SE) and 38 ± 6 PMNLs/ 10 hpf, respectively (P = .0001). Similarly, medium from uninfected cells disrupted by freezing and thawing attracted a mean of 6 ± 1 PMNLs/lO hpf (P < .0001 compared with Discussion These experiments indicate that attachment of rhinovirus to human embryonic lung fibroblast cells results in the elaboration of a chemoattractant for human PMNLs. This chemoattractant activity is not dependent upon the presence of complement. doi = 10.1093/infdis/157.2.346 id = cord-007201-m87jid5l author = Tzipori, Saul title = Diarrhea in Young Red Deer Associated with Infection with Cryptosporidium date = 1981-08-17 keywords = cryptosporidium; diarrhea summary = In the present communication, an association between severe diarrhea in artificially reared red deer calves and infection with Cryptosporidium is described. Cryostat-cut sections obtained from a specific pathogen-free lamb that was heavily infected with Cryptosporidium derived originally from calves [14] were reacted with 12 convalescent-phase sera from red deer that were recovering from diarrhea. The results of the present communication demonstrate, on the basis of the excretion of typical oocysts in the feces and the attachment of typical stages of the organism to the brush borders of enterocytes, that these artificially reared red deer were infected with Cryptosporidium, There is thus strong circumstantial evidence to incriminate Cryptosporidium as the cause of diarrhea and mortality in the outbreak. The clinical disease was similar to that observed in field outbreaks of diarrhea associated with Cryptosporidium in calves [14] , lambs [9A] , and experimentally infected, specific pathogen-free lambs [13] . doi = 10.1093/infdis/144.2.170 id = cord-341667-ayl71jpc author = Van Reeth, Kristien title = Bronchoalveolar Interferon-α, Tumor Necrosis Factor-α, Interleukin-1, and Inflammation during Acute Influenza in Pigs: A Possible Model for Humans? date = 1998-04-17 keywords = IL-1; TNF summary = doi = 10.1086/517398 id = cord-011712-fyrbe8tw author = Venkatesan, Sudhir title = Neuraminidase Inhibitors and Hospital Length of Stay: A Meta-analysis of Individual Participant Data to Determine Treatment Effectiveness Among Patients Hospitalized With Nonfatal 2009 Pandemic Influenza A(H1N1) Virus Infection date = 2020-02-01 keywords = NAI; influenza; patient; treatment summary = doi = 10.1093/infdis/jiz152 id = cord-330645-46qaljq1 author = Waghmare, Alpana title = Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics date = 2020-07-25 keywords = Fig; RSV summary = Using longitudinal home-based self-sampling, we demonstrate nasal cytokine levels correlate and cluster according to immune cell of origin. Nasal foam swab self-sampling at home provides a precise, mechanistic readout of respiratory virus shedding and local immune responses. Here we demonstrate that home self-sampling with nasal foam swabs is well-tolerated and provides reliable results for monitoring viral load and molecular immune responses to respiratory virus infection. We have previously demonstrated increased sensitivity of self-collected foam nasal swabs compared to nasal washes in immunocompetent adults with respiratory viral infections [21] , and in longitudinal studies in solid organ transplant recipients [22] , with good compliance and participants reporting no issues with swab discomfort. M a n u s c r i p t In summary, we establish a foam swab-based sampling method that is optimal for patient selftesting, both at home and in the clinical setting, permits serial therapeutic monitoring, and is suitable for tracking the natural virologic and immunologic course of respiratory virus infections. doi = 10.1093/infdis/jiaa451 id = cord-279311-msh9wvsh author = Wang, Fan title = Characteristics of Peripheral Lymphocyte Subset Alteration in COVID-19 Pneumonia date = 2020-03-30 keywords = CD8 summary = METHODS: The levels of peripheral lymphocyte subsets were measured by flow cytometry in 60 hospitalized COVID-19 patients before and after treatment, and their association with clinical characteristics and treatment efficacy was analyzed. In this study, we aimed to clarify the characteristics and clinical significance of peripheral lymphocyte subset alteration in COVID-19, which might help elucidate the pathogenesis and develop novel biomarkers and therapeutic strategies for COVID-19. In multivariate analysis, posttreatment decrease in CD8 + T cells (P = .011) and B cells (P = .010) and increase in CD4 + / CD8 + ratio (P = .032) indicated a poor efficacy when considering the factors of age, sex, disease severity on admission, oxygen inhalation, antiviral treatment, and use of corticosteroid and immune enhancer ( Table 2) . Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets doi = 10.1093/infdis/jiaa150 id = cord-306983-6w2fvtfy author = Wang, Siye title = Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date = 2010-10-01 keywords = TNF; figure; influenza; virus summary = Influenza A virus infection resulted in significant increases in TNF-α, IL-6, IL-1β, viral hemagglutininprocessing protease trypsin levels, and viral replication with vascular hyperpermeability in lung and brain in the first 6 days of infection. The present study reports several new observations: (1) proinflammatory cytokines, TNF-a, IL-1b, and IL-6, when upregulated by influenza A virus infection, induce trypsin expression in various organs and human endothelial cells; (2) the upregulated trypsin induces [Ca 2+ ] i mobilization via activation of the PAR-2, followed by loss of zonula occludens-1 and vascular hyperpermeability; (3) inhibitors of NF-kB and activator protein 1 effectively suppress the upregulation of proinflammatory cytokines and trypsin and improve the survival rates of infected mice. The present results allow us to propose a new mechanism of junctional permeability regulation: upregulated trypsin by influenza A virus and/or proinflammatory cytokines induces increase in [Ca 2+ ] i and loss of zonula occludens-1 in endothelial cells via PAR-2 signaling. doi = 10.1086/656044 id = cord-287210-sars5dmi author = Woo, Patrick C. Y. title = Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia date = 2005-12-01 keywords = HKU1; SARS; patient summary = However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. All prospectively collected NPAs from patients with community-acquired pneumonia that were sent to the clinical microbiology laboratories of 4 hospitals in Hong Kong during a 12-month period (22 March 2003 [the beginning of the SARS epidemic in Hong Kong] to 21 March 2004) for detection of SARS-CoV and were found to be negative for SARS-CoV RNA, by reverse-transcription polymerase chain reaction (RT-PCR) [20] , were included in the study. Sequence analysis revealed 0%-2% nucleotide differences between the sequences of the fragments and the sequence of the pol gene from The epidemiological, clinical, and radiological characteristics of the 10 patients with CoV-HKU1-associated community-acquired pneumonia are summarized in table 2. doi = 10.1086/497151 id = cord-288756-r96izsyq author = Wu, Zhiqiang title = ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date = 2016-02-15 keywords = SARS summary = doi = 10.1093/infdis/jiv476 id = cord-353495-c3s5n5vo author = Yao, Yanfeng title = An Animal Model of MERS Produced by Infection of Rhesus Macaques With MERS Coronavirus date = 2014-01-15 keywords = EMC; MERS summary = In 2012, a novel coronavirus (CoV) associated with severe respiratory disease, Middle East respiratory syndrome (MERS-CoV; previously known as human coronavirus–Erasmus Medical Center or hCoV-EMC), emerged in the Arabian Peninsula. The infected monkeys showed clinical signs of disease, virus replication, histological lesions, and neutralizing antibody production, indicating that this monkey model is suitable for studies of MERS-CoV infection. The development of animal models for MERS-CoV infection of humans is of utmost importance to study the pathogenesis of this virus and to test the efficacy of potential therapeutic or prophylactic intervention strategies. Therefore, in the present study, we explored the suitability of the rhesus monkey as an animal model for MERS-CoV isolate human coronavirus-Erasmus Medical Center (hCoV-EMC) infection or disease. Rhesus macaques can be infected by MERS-CoV in the laboratory, but we recognize that it is necessary to search for more suitable animal model that will have similar disease presentations as that observed among those laboratoryconfirmed human cases. doi = 10.1093/infdis/jit590 id = cord-261472-qcu73sdu author = Yao, Yong Xiu title = Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date = 2004-07-01 keywords = SARS; protein summary = Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. The possible use of insect cell-displayed S protein for diagnostic application was assessed by examining fragment reactivity with serum samples from patients infected with human CoV 229E and also with serum from a patient with suspected but clinically unconfirmed SARS (serum sample 3118). Of the 2 assay formats we used, nondenatured S protein present on the cell surface provided the most sensitive detection of antibodies, with clear shifts in fluorescence for serum samples from patients with suspected but clinically unconfirmed SARS. doi = 10.1086/421280 id = cord-002926-7ereip3x author = Yoon, Sun-Woo title = Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus date = 2018-02-01 keywords = ferret; pregnant summary = title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. To determine whether a similar phenotype is present in pregnant ferrets, we measured the expression levels of inflammatory cytokines and chemokines by quantitative real-time polymerase chain reaction in the trachea (representative of the upper respiratory tract), lungs (representative of the lower respiratory tract), and bronchoalveolar lavage to evaluate responses in resident or infiltrating immune cells lining the airways [6] of pregnant and nonpregnant animals following infection. doi = 10.1093/infdis/jix328 id = cord-338776-2wa30218 author = Zhao, Xiaoyu title = Activation of C-Type Lectin Receptor and (RIG)-I-Like Receptors Contributes to Proinflammatory Response in Middle East Respiratory Syndrome Coronavirus-Infected Macrophages date = 2020-02-15 keywords = CLR; MERS; Mincle; RLR summary = The cytokine and/or chemokine induction was significantly attenuated by siRNA depletion of retinoic acid-inducible-I-like receptors (RLR) or adaptor, indicating that RLR signaling also contributed to MERS-CoV-induced proinflammatory response. We first used the inhibitors of RLR and CLR signaling pathway to evaluate their potential contribution for mediating the proinflammatory response in MERS-CoV-infected macrophages. To assess the contribution of RLR or CLR pathway to induce proinflammatory response, we measured the expression levels of a series of key proinflammatory cytokines and/or chemokines in MERS-CoV-infected MDMs in the presence of these inhibitors ( Figure 1B ). Overall, the above results suggested that RLR and CLR signaling might be involved in viral recognition and trigger the proinflammatory response upon MERS-CoV infection in macrophages. Our results indicate that CLR and RLR signaling may be involved in mediating the immune activation in MERS-CoV-infected human macrophages. doi = 10.1093/infdis/jiz483 id = cord-267015-mprsdi2e author = Zhu, Zhongyu title = Exceptionally Potent Cross-Reactive Neutralization of Nipah and Hendra Viruses by a Human Monoclonal Antibody date = 2008-03-15 keywords = antibody; hev summary = One of these antibodies, m102, which exhibited the highest level of cross-reactive neutralization of both NiV and HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavy-chain variable domain and panning against sG(HeV). We have previously identified neutralizing human monoclonal antibodies against Nipah virus (NiV) and Hendra virus (HeV) by panning a large nonimmune antibody library against a soluble form of the HeV attachment-envelope glycoprotein G (sG HeV ). One of these antibodies, m102, which exhibited the highest level of cross-reactive neutralization of both NiV and HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavychain variable domain and panning against sG HeV . To demonstrate that m102.4 measured in plasma was biologically active, serum collected on days 1, 4, and 8 was evaluated using virus neutralization assays, as described above (data not shown). Receptor binding, fusion inhibition, and induction of cross-reactive neutralizing antibodies by a soluble G glycoprotein of Hendra virus doi = 10.1086/528801 id = cord-276005-ifn88mjd author = da Silva Filho, Luiz Vicente Ribeiro Ferreira title = The Differential Clinical Impact of Human Coronavirus Species in Children With Cystic Fibrosis date = 2012-08-01 keywords = NL63; respiratory summary = We investigated the clinical impact of human coronaviruses (HCoV) OC43, 229E, HKU1 and NL63 in pediatric patients with cystic fibrosis (CF) during routine and exacerbation visits. The proportion of cases with acute respiratory exacerbation among patients infected with different HCoV species was compared by χ 2 or Fisher exact tests. The identification of new species of HCoV [7, 8] and the emergence of SARS HCoV [6] highlighted the potential role of these viruses as causative agents of severe lower respiratory tract infections. However, most of the studies on the clinical impact of different HCoV species were only performed among children who were hospitalized for acute respiratory tract infections, with small sample sizes and short periods of sample collection [10] . New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia doi = 10.1093/infdis/jis274 id = cord-344271-5aynmdsk author = de Souza Luna, Luciano Kleber title = Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection date = 2007-03-01 keywords = patient; respiratory summary = title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. These assays were used to determine a point prevalence of the full spectrum of respiratory viruses and atypical bacteria in SARS-compatible patients. Inf and PIV were clearly the most prevalent agents in flight patients, at 14.2% and 15.5%, respectively, without significant differences between age groups (1-way analysis of variance [ANOVA], 95% significance level). Baseline data on the prevalence of respiratory viruses and atypical bacteria after air travel are not currently available. It cannot be told whether the high prevalence and diversity of respiratory viruses seen in our study is specific to patients with recent intercontinental air travel. doi = 10.1086/511432 id = cord-329392-fufattj8 author = den Hartog, Gerco title = SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date = 2020-08-08 keywords = RBD; SARS summary = doi = 10.1093/infdis/jiaa479 id = cord-261241-eqf6ame6 author = van Beek, Josine title = Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date = 2017-08-15 keywords = ILI; influenza; virus summary = doi = 10.1093/infdis/jix268 id = cord-259004-plst2wno author = van Elden, Leontine J. R. title = Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction date = 2004-02-17 keywords = PCR summary = doi = 10.1086/381207