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?' ---------------------------------------------------------- 40 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 3332 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 55 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 6 PEDV 6 PCR 5 SARS 5 China 3 RNA 3 COVID-19 2 piglet 2 cpv 2 covid-19 2 MERS 2 Lee 2 IBV 2 Coronavirus 2 Bat 1 vulnificus 1 turkey 1 score 1 relative 1 porcine 1 negligible 1 infection 1 gene 1 disease 1 country 1 case 1 canine 1 Vibrio 1 SPF 1 SL2 1 SDPP 1 SDG 1 SADS 1 Portugal 1 PRDC 1 PCV3 1 Mexico 1 Korea 1 Italy 1 IHR 1 IDTE 1 Health 1 HLJBY 1 GII 1 East 1 ELISA 1 DEL 1 CoV-2 1 CSFV 1 Brazil 1 Belgium Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 920 virus 556 strain 489 disease 423 sequence 401 study 394 sample 392 gene 376 coronavirus 356 % 312 infection 290 analysis 271 case 268 piglet 244 epidemic 242 protein 231 group 216 animal 211 assay 207 pig 199 genome 188 c 187 detection 180 time 175 diarrhea 174 ° 170 day 169 result 165 outbreak 156 cell 149 country 147 pathogen 146 acid 143 temperature 142 transmission 140 swine 137 control 137 antibody 134 coronaviruse 133 type 124 datum 119 region 117 diarrhoea 116 number 113 primer 109 tree 107 score 107 method 107 farm 104 field 102 characterization Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 926 al 815 . 724 et 384 PEDV 334 PCR 269 SARS 216 China 200 S 192 RNA 173 RT 158 CoV-2 137 IBV 114 CoV 105 COVID-19 101 MERS 86 Table 86 Korea 85 S1 72 South 70 USA 70 BCoV 69 Belgium 68 Lee 66 Health 63 United 63 SDPP 61 States 61 M. 58 Italy 54 vulnificus 54 Europe 53 Coronavirus 52 N 50 aa 49 V. 48 GenBank 48 FeKoV 48 C 48 Bat 47 TGEV 46 Wang 44 East 43 HLJBY 43 CoV-1 41 Middle 40 BVDV 39 Transbound 39 Li 39 Emerg 38 January Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 189 we 179 it 60 they 17 them 14 i 7 us 6 itself 5 he 2 you 2 themselves 2 one 1 re-)emerge 1 mtlabc 1 http://endmemo.com/bio/dnacopynum 1 clustalx 1 af1004 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 3658 be 598 have 529 use 222 show 207 detect 162 report 158 identify 158 base 153 include 151 associate 143 isolate 126 describe 124 follow 111 test 110 collect 109 find 106 contain 99 inoculate 98 cause 97 do 94 obtain 94 infect 93 suggest 92 indicate 90 perform 90 emerge 90 confirm 83 increase 82 determine 77 observe 76 compare 71 provide 66 reveal 64 relate 63 analyse 59 support 58 spread 57 result 57 occur 57 accord 56 reduce 54 circulate 53 take 53 protect 52 affect 51 sequence 51 know 50 remain 49 extract 49 demonstrate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 377 porcine 238 not 221 respiratory 208 high 204 positive 200 - 196 other 192 viral 186 also 184 infectious 149 different 141 low 137 canine 133 first 131 genetic 116 however 111 bovine 106 human 104 such 104 novel 104 clinical 102 real 102 negative 101 more 99 specific 99 only 97 phylogenetic 97 molecular 96 complete 92 nucleotide 88 further 82 new 81 then 80 same 80 previously 78 well 76 avian 75 non 75 early 72 most 68 respectively 67 acute 65 severe 65 available 62 several 58 diagnostic 57 potential 55 single 55 global 55 current Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 22 high 18 most 18 least 9 good 9 close 8 low 8 Most 4 large 3 early 2 late 2 deadly 1 strong 1 strict 1 small 1 near 1 great 1 furth Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 54 most 16 least 5 well Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 25 orcid.org 2 doi.org 1 www.who.int 1 www.viprb 1 www.pymol.org 1 www.news.gov.hk 1 www.ncbi.nlm.nih.gov 1 www.ncbi.nlm.nih 1 www.iipcr.com 1 www.cbs.dtu.dk 1 www.cbs.dtu 1 viro60.tiho-hannover.de 1 swissmodel.expasy.org 1 orcid 1 mfold.rna.albany.edu 1 itol.e 1 faostat.fao.org 1 endmemo.com 1 cran.r-proje Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://orcid.org/0000-0002-5930-5461 1 http://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ 1 http://www.viprb 1 http://www.pymol.org/ 1 http://www.news.gov.hk/eng/2020/02/20200 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.ncbi.nlm.nih 1 http://www.iipcr.com/eweb/ 1 http://www.cbs.dtu.dk/services/BepiPred/ 1 http://www.cbs.dtu 1 http://viro60.tiho-hannover.de/eg/csf/ 1 http://swissmodel.expasy.org/ 1 http://orcid.org/0000-0003-4651-9433 1 http://orcid.org/0000-0003-4123-0892 1 http://orcid.org/0000-0003-3672-6471 1 http://orcid.org/0000-0003-3394-3702 1 http://orcid.org/0000-0003-2680-0519 1 http://orcid.org/0000-0002-8413-7260Cheng 1 http://orcid.org/0000-0002-8233-2353 1 http://orcid.org/0000-0002-7781-3080 1 http://orcid.org/0000-0002-7566-8158 1 http://orcid.org/0000-0002-6697-7688 1 http://orcid.org/0000-0002-5634-1360 1 http://orcid.org/0000-0002-4969-1768 1 http://orcid.org/0000-0002-4625-874X 1 http://orcid.org/0000-0002-3274-4296 1 http://orcid.org/0000-0002-2453-1821 1 http://orcid.org/0000-0002-0280-4964Zeng 1 http://orcid.org/0000-0001-9844-1573 1 http://orcid.org/0000-0001-8392-4919José 1 http://orcid.org/0000-0001-7431-2523 1 http://orcid.org/0000-0001-6422-4730 1 http://orcid.org/0000-0001-6285-312X 1 http://orcid.org/0000-0001-6283-4172 1 http://orcid.org/0000-0001-5362-1415 1 http://orcid 1 http://mfold.rna.albany.edu/ 1 http://itol.e 1 http://faostat.fao.org 1 http://endmemo.com/bio/dnacopynum 1 http://doi.org/10.3201/eid2309 1 http://doi.org/ 1 http://cran.r-proje Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 5 rna was then 5 study are available 4 samples were positive 2 assay described here 2 coronavirus indicating person 2 disease was initially 2 pcr described here 2 pcr using primers 2 piglets were randomly 2 pigs did not 2 rna was reverse 2 samples did not 2 samples were also 2 samples were infective 2 strain were positive 2 strain were rt 2 strains were also 2 strains were primarily 2 study describes clusters 2 viruses do not 1 . detected idv 1 analyses are scarce 1 analyses using different 1 analyses were then 1 analysis indicated fekov 1 analysis using custom 1 analysis was not 1 animal use protocol 1 animals including dogs 1 animals including guinea 1 animals including pangolin 1 animals including pet 1 animals showed acute 1 animals using elisa 1 animals was also 1 animals were negative 1 assay detected p. 1 assay detected rna 1 assay had comparable 1 assay had detectable 1 assay has broader 1 assay uses lyophilized 1 assay using pulmonary 1 assay was most 1 assays using lyophilized 1 assays using wet 1 assays were more 1 case did not 1 case report cooperative 1 case were successively Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 analysis was not possible 1 infection does not significantly 1 piglets had no deaths 1 piglets were no longer 1 piglets were not available 1 protein does not clearly 1 samples were not available 1 study found no difference A rudimentary bibliography -------------------------- id = cord-284398-rhfwbyav author = Aboubakr, Hamada A. title = Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date = 2020-07-14 keywords = SARS; covid-19 summary = In another study, aerosolized SARS-CoV-2 retained its infectivity for a period of 16h at room temperature and the authors concluded that the virus can be considered as an airborne pathogen (Fears et al., 2020 and was infectious after 72 hr of aerosolization (Ijaz, Brunner, Sattar, Nair, & Johnson-Lussenburg, 1985) . In the first study, SARS-CoV-2 retained its infectivity for 4 days but was completely decayed after 7 days on plastic surface at room temperature and 65% RH (Chin et al., 2020) . Although this study reported longer virus survival, it has been shown that the survivability of SARS-CoV-1 on plastic surface is drastically affected by increases in temperature and RH as described below. In another study, a this virus with a higher initial load (5.5 log TCID 50 ) retained its infectivity for 4 days and was completely inactivated after 7 days on stainless steel at room temperature and RH of 65% (Chin et al., 2020) . doi = 10.1111/tbed.13707 id = cord-283316-a8jewy2h author = Bianchini, Juana title = Prioritization of livestock transboundary diseases in Belgium using a multicriteria decision analysis tool based on drivers of emergence date = 2019-10-09 keywords = Belgium; disease; negligible; score summary = Score 2 Low: increased (il)legal imports of animal subproducts such as skin, meat and edible products from EU member states have a low influence on the pathogen/disease (re)emergence in Belgium. Score 0 Score 1 Negligible: increased (il)legal imports of NON-animal products such as tires, wood, furniture from EU member states have a negligible influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: increased (il)legal imports of NON-animal products such as tires, wood, furniture from EU member states have a low influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: Increased imports of animal subproducts such as skin, meat and edible products from Third countries have a low influence on the pathogen/disease (re)emergence in Belgium. Score 2 Low: increased (il)legal imports of NON-animal products such as tires, wood, furniture from Third countries have a low influence on the pathogen/disease (re)emergence in Belgium. doi = 10.1111/tbed.13356 id = cord-317455-6qx0v28w author = Brown, Paul A. title = Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date = 2018-09-10 keywords = RNA; SPF; turkey summary = Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission. doi = 10.1111/tbed.13006 id = cord-326596-8ux1q9xw author = Chen, Yanyu title = Biological and phylogenetic characterization of a novel hemagglutination‐negative avian avulavirus 6 isolated from wild waterfowl in China date = 2018-09-08 keywords = China; PCR summary = To better further explore the relationships among above factors, an AAvV‐6 epidemiological surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter‐species transmission and being intercontinental flyways during the year 2013–2017 was conducted. Despite this, knowledge about the regularities of transmission, genetic and biological characteristics of AAvV-6 viruses in commercial poultry and wild birds in the China recent years remains limited. Therefore, in this study, an AAvV-6 surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter-species transmission and being intercontinental flyways from December 2013 to June 2017 was conducted. Complete genome sequence of a novel avian paramyxovirus isolated from wild birds in South Korea Complete nucleotide sequence of avian paramyxovirus type 6 strain JL isolated from mallard ducks in China Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan doi = 10.1111/tbed.13005 id = cord-281081-rifr5uub author = Deng, Junhua title = Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date = 2020-05-07 keywords = ELISA; SARS summary = In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. The results showed that no SARS-CoV-2-specific antibodies were detected in above species of animals including pangolin which has been reported as an intermediate host of SARS-CoV-2 (Kangpeng Xiao, 2020) . After confirming the specificity, sensitivity and suitability of SARS-CoV-2 ELISA kit for different species of experimental animals, clinical serum samples from domestic livestock (pig, cow, sheep, horse), poultry (chicken, duck, goose), experimental animal (mice, rat and rhesus monkey), companion animal (dog and cat) and wild animals (camel, fox, mink, alpaca, ferret, bamboo rat, peacock, eagle, tiger rhinoceros, pangolin, leopard cat, jackal, giant panda, masked civet, porcupine, bear, yellow-throated marten, weasel, red pandas and wild boar) were used for antibody detection. doi = 10.1111/tbed.13577 id = cord-279794-hn5vmic0 author = Guo, Jiahui title = Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains date = 2018-08-27 keywords = GII; PEDV summary = Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Consistent with our previous research (Wang, Fang, & Xiao, 2016a) , the phylogenetic tree indicated that the complete PEDV genomes evolved into two separate genogroups, GI (classical) and GII (variant), as presented in Figure 1a . Genetic variation of nucleocapsid genes of porcine epidemic diarrhea virus field strains in China Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand doi = 10.1111/tbed.12991 id = cord-303289-qoukiqr7 author = Hemida, M. G. title = Coronavirus infections in horses in Saudi Arabia and Oman date = 2017-03-13 keywords = MERS; PCR summary = We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. RNA extracts were tested for evidence of conserved coronavirus nucleic acid genetic sequences using previously reported RT-PCR assays (Chu et al., 2014) , RTqPCR assay for MERS-CoV upE gene (Corman et al., 2012) , RTqPCR assay for ECoV (Miszczak et al., 2014) , and a RTqPCR assay for HKU23 reported below. T A B L E 5 Cross-neutralization titres (denoted as reciprocal titres) for Middle East respiratory coronavirus (MERS-CoV), bovine coronavirus (BCoV) and equine coronavirus (ECoV) in hyperimmune or naturally infected sera known to be positive for different coronaviruses NR460pig antiserum to porcine respiratory coronavirus 1,200 a <20 <20 <20 <20 Similarly, a BCoV immune serum from an experimentally infected gnotobiotic calf showed detectable, but 16-fold reduced antibody titre with ECoV but no cross-reaction with MERS-CoV. doi = 10.1111/tbed.12630 id = cord-354729-dpaz01np author = Huan, Changchao title = Characterization and evolution of the coronavirus porcine epidemic diarrhoea virus HLJBY isolated in China date = 2019-08-22 keywords = HLJBY; PEDV summary = doi = 10.1111/tbed.13321 id = cord-331740-yjt3q9ph author = Jones, R. M. title = Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date = 2011-04-07 keywords = IBV; PCR summary = This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls'' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes. doi = 10.1111/j.1865-1682.2011.01222.x id = cord-294468-0v4grqa7 author = Kasilingam, Dharun title = Exploring the Growth of COVID‐19 Cases using Exponential Modelling Across 42 Countries and Predicting Signs of Early Containment using Machine Learning date = 2020-08-04 keywords = COVID-19; Coronavirus; country; infection summary = This research uses exponential growth modelling studies to understand the spreading patterns of the COVID‐19 virus and identifies countries that have shown early signs of containment until 26(th) March 2020. Machine learning models based on logistic regression, decision tree, random forest, and support vector machines are developed and show accuracies between 76.2% to 92.9% to predict early signs of infection containment. The objective of the research is to develop a mathematical model using exponential growth analysis coupled with machine learning, to predict worldwide COVID-19 early containment signs. Secondly, the research aims at building supervised machine learning models with high accuracies for predicting signs of early containment with infrastructure availability, environmental factors, infection severity factors, and government policies of countries as independent variables. The research presents machine learning models based on variables such as infrastructure, environment, policies, and the infection itself, to predict early signs of containment in the country. doi = 10.1111/tbed.13764 id = cord-294698-mtfrbn87 author = Kim, H. K. title = Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date = 2016-05-23 keywords = B15; Bat; SARS summary = In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential. doi = 10.1111/tbed.12515 id = cord-316006-t080mykk author = Kong, Dechuan title = Clusters of 2019 coronavirus disease (COVID‐19) cases in Chinese tour groups date = 2020-07-27 keywords = COVID-19; China; case summary = Our study describes clusters of COVID-19 cases within tour groups travelling in European countries from January 16 through 28. Tour group transmission may have occurred in the following sceParis-Shanghai, all of the confirmed and suspected cases had seats within two rows ( Figure 3 ). We reported three clusters of COVID-19 confirmed cases in three tour groups travelling in European countries and one cluster of suspected cases on one flight in late January 2020. In group A, the cluster was initiated by a familial transmission, followed by spread of disease to 13 out of 34 members in the 12-day tour. In conclusion, we reported a cluster of 13 COVID-19 cases, which was initiated by within-family transmission followed by propagative transmission into tour groups travelling in European countries. The study findings show that clustered cases in tour groups may be more propagative than simple familial transmission. Clusters of 2019 coronavirus disease (COVID-19) cases in Chinese tour groups doi = 10.1111/tbed.13729 id = cord-342766-ndzhlf3k author = Ku, X. title = Identification and genetic characterization of porcine circovirus type 3 in China date = 2017-03-19 keywords = PCV3 summary = title: Identification and genetic characterization of porcine circovirus type 3 in China This study reports on the first identification, widely epidemic, different phylogenetic clusters, potential role in sow reproductive failure and possible origins of PCV3 in China. PCV3 is associated with porcine dermatitis, nephropathy syndrome and reproductive failure (Palinski et al., 2016) and cardiac and multisystemic inflammation (Phan et al., 2016) . To better understand the infection status, epidemic status, geographical distribution, potential pathogenicity and genetic characteristics of PCV3 in China, a total of 222 samples (i.e., stillborn, tissues, semen and serum) were collected from 35 farms in 11 provinces or districts (i.e., Anhui, Chongqing, Fujian, Hebei, Henan, Hunan, Jiangsu, Jiangxi, Liaoning, Shenyang and Zhejiang) in China. Genetic variability of porcine circovirus 2 (PCV2) field isolates from vaccinated and nonvaccinated pig herds in Germany Similarity plot of the whole genome of 10 PCV3 isolates with 5 Bat circovirus isolates. doi = 10.1111/tbed.12638 id = cord-260212-m80dkzm4 author = Lee, J. H. title = Detection and Phylogenetic Analysis of Porcine Deltacoronavirus in Korean Swine Farms, 2015 date = 2016-03-10 keywords = SL2 summary = In this study, faecal samples of pigs showing signs of diarrhoea (n = 681) collected from January 2013 to March 2015 were screened for the presence of porcine deltacoronavirus (PDCoV). The phylogenetic trees showed that Korean PCDoV isolates in 2014 (KNU14.04) and in 2015 (SL2, SL5) were grouped within US PDCoV cluster, but they located at different branches (highlights). For the genetic characterization, the maximum likelihood phylogenetic trees reconstructed from the S and N genes (Fig. 1a, b) showed a clear separation between Chinese and US strains of PDCoV and is similar to the previous studies (Marthaler et al., 2014; Wang et al., 2016) . Based on the S gene, the inferred ancestral amino acid changes along the nodes of the phylogeny (Fig. 2a) showed that the branches leading to Korean PDCoV isolates in 2014 and in 2015 shared 1 back substitution (node #40: Q106L, node #37: L106Q) and four unique substitutions (node #39: S697A, node #38: V550A, I669L and node #37: I1014V). doi = 10.1111/tbed.12490 id = cord-010053-kniq2mbw author = Lee, Sunhee title = Molecular characteristics and pathogenic assessment of porcine epidemic diarrhoea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea date = 2019-05-20 keywords = DEL; Lee; PEDV summary = doi = 10.1111/tbed.13219 id = cord-339871-jso21mbx author = Lee, Sunhee title = Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 date = 2018-05-16 keywords = Korea; Lee; PEDV summary = To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea doi = 10.1111/tbed.12904 id = cord-284377-hsju2shr author = Li, Meng title = Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health date = 2018-07-26 keywords = Vibrio; vulnificus summary = title: Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health vulnificus is frequently distributed in aquariums, thus constituting a threat to captive marine mammals and to public health. Several known viral pathogens that have been reported to infect marine mammals were also detected by virus-specific PCR, including type A influenza virus (IAV), phocine distemper virus (PDV), coronavirus, and rotavirus. In this analysis, we successfully collected 54 samples from six aquariums in northern China ( genotypes based on its virulence-correlated gene (vcg) (Warner & Oliver, 2008) ; our analysis showed that 11 of the 12 isolated V. vulnificus strains display a potential threat to mammals, including marine animals and humans. vulnificus is not the only threat to marine animals and public health in aquariums. Wound infections caused by Vibrio vulnificus and other marine bacteria Vibrio vulnificus in aquariums is a novel threat to marine mammals and public health doi = 10.1111/tbed.12967 id = cord-291026-99cit4ig author = Lung, O. title = Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date = 2015-01-27 keywords = CSFV; PCR; RNA summary = In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock. doi = 10.1111/tbed.12318 id = cord-331932-oujdl459 author = Lung, O. title = Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date = 2015-12-12 keywords = PCR; PRDC summary = doi = 10.1111/tbed.12449 id = cord-352211-3ps5o8ji author = Mai, K. title = The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China date = 2017-03-27 keywords = China summary = A previous study (Zhai et al., 2016) reported that the current prevalence in Southern China was 1.54% (5/390), and three of the five detected strains were from Guangdong Province, revealing that the information regarding the molecular epidemiology of PDCoVs in Guangdong was still limited. T A B L E 3 Detection of porcine enteric pathogens from 13 tissue cultured purified PDCoV-positive samples from 11 swine farms in Guangdong Two pairs of strains 07 and 08 from farm G and 10 and 11 from farm I were isolated from the same commercial swine farms, but at different times. Complete genome sequence of strain SDCV/USA/Illinois121/2014, a porcine deltacoronavirus from the United States Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from Mainland China doi = 10.1111/tbed.12644 id = cord-347475-ttmactz0 author = Mesquita, J. R. title = Outbreak of Porcine Epidemic Diarrhea Virus in Portugal, 2015 date = 2015-09-07 keywords = PEDV; Portugal summary = An outbreak of porcine epidemic diarrhea virus (PEDV) in the South of Portugal in January 2015 and the spread of PEDV northwards in the territory are described. Comparative analysis of the amplified sequences showed a very high (99.0%) identity with the PEDV variant most recently reported in the United States and also show complete (100%) identity to the strains recently reported in Germany, supporting the hypothesis that a unique strain is currently circulating in Europe. Typical clinical symptoms of PED include watery diarrhea, vomiting, dehydration, and Porcine epidemic diarrhea virus (PEDV; family Coronaviridae, subfamily Coronavirinae, genus Alphacoronavirus) is a highly contagious virus responsible for enteric disease in swine characterized by an acute onset of symptoms including severe watery diarrhea, vomiting, dehydration, and high mortality in suckling piglets (ICTV, 2012; Song and Park, 2012) . 2013: Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences doi = 10.1111/tbed.12409 id = cord-318237-22s13v2y author = Mira, Francesco title = Spreading of canine parvovirus type 2c mutants of Asian origin in southern Italy date = 2019-07-14 keywords = Italy; cpv summary = Although to date CPV‐2 is circulating in all continents, most of the current studies have analysed the amino acid changes accounted in the VP2 gene sequence, with limited information on virus introductions from other countries. The aim of this study was the detection and molecular analysis of CPV strains displaying genetic features of Asian viruses spreading in southern Italy. More recently, a CPV-2c strain displaying genetic signatures typical of Asian viruses was detected in southern Italy (Mira, Purpari, Lorusso, et al., 2018) , thus suggesting the introduction of the virus from other countries, as reported for other canine viruses (Decaro, Campolo, et al., 2007; Martella et al., 2006; . doi = 10.1111/tbed.13283 id = cord-269287-vbuepdm4 author = Ogbu, Kenneth Ikejiofor title = Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria date = 2019-10-16 keywords = canine; cpv summary = doi = 10.1111/tbed.13379 id = cord-011411-hufxjf5p author = Oliveira, Thalita Evani Silva title = Mycoplasma bovis and viral agents associated with the development of bovine respiratory disease in adult dairy cows date = 2019-06-24 keywords = BRD; BVDV; Brazil summary = doi = 10.1111/tbed.13223 id = cord-302819-oj33i2ma author = Pasick, J title = Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada date = 2014-08-07 keywords = PCR; PEDV; SDPP; piglet summary = On the SDPP sample that was tested, the following N gene rRT-PCR results were observed: C t of 35.84 for PBS supernatant after 10 000 g, C t of 36.74 for the PBS pellet after 10 000 g, C t of 38.83 for the PBS + Nonidet P-40 Comparison of S protein gene sequences obtained from bioassay piglets versus those of field cases. No significant difference was observed in the kinetics of N gene rRT-PCR positivity in animals that were inoculated with the three SDPP samples that were tested, suggesting that each contained infectious virus. Negative contrast staining electron microscopy of fecal samples collected at 4 dpi from the SDPP-inoculated piglets and the positive control group piglets showed the presence of virus-like particles consistent with coronavirus virions. Similar virus-like particles were also found in the content of the small intestine of a SDPP-inoculated piglet at 7 dpi and a positive control group contact piglet at 5 days post-contact. doi = 10.1111/tbed.12269 id = cord-294021-x8avmtef author = Pérez‐Rivera, Claudia title = First report and phylogenetic analysis of porcine deltacoronavirus in Mexico date = 2019-04-16 keywords = Mexico; porcine summary = Subsequently, in early 2014, PDCoV was reported from the United States of America (USA) and Canada, and it caused heavy economic losses to the swine industry due to the presentation of a clinical enteric disease Song et al., 2015; Wang et al., 2014) . The authors note that PDCoV infections are common in pigs and that coinfections are frequent, especially with the porcine epidemic diarrhoea virus and rotavirus C (Hu et al., 2015; Marthaler, Raymond, et al., 2014; Song et al., 2015) . The most common coinfection was PDCoV/PEDV, found in 54.1% of the total deltacoronavirus-positive cases (46/85), a result that coincides with that reported by other authors (Song et al., 2015; Zhang, 2016 Figure 1 ). Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis First report and phylogenetic analysis of porcine deltacoronavirus in Mexico doi = 10.1111/tbed.13193 id = cord-330364-ye02hwhy author = Semenza, Jan C. title = Systemic resilience to cross‐border infectious disease threat events in Europe date = 2019-05-17 keywords = Health; IDTE; IHR summary = doi = 10.1111/tbed.13211 id = cord-309734-m8miwtha author = Vergara‐Alert, J. title = Middle East respiratory syndrome coronavirus experimental transmission using a pig model date = 2017-06-26 keywords = East; MERS summary = Dromedary camels are the main reservoir of Middle East respiratory syndrome coronavirus (MERS‐CoV), but other livestock species (i.e., alpacas, llamas, and pigs) are also susceptible to infection with MERS‐CoV. Virus was present in nasal swabs of infected animals, and limited amounts of viral RNA, but no infectious virus were detected in the direct contact pigs. However, other animal species such as non-human primates (rhesus macaques and common marmosets), members of the family Camelidae (alpacas and llamas), rabbits and pigs have been demonstrated to be susceptible to MERS-CoV infection (Crameri et al., 2016; Falzarano et al., 2014; Haagmans et al., 2015; Vergara-Alert, van den Brand, et al., 2017; de Wit et al., 2013 de Wit et al., , 2017 . To study whether MERS-CoV might be transmitted between pigs, an experimental transmission study in this animal model was designed and performed under direct and indirect contact settings. doi = 10.1111/tbed.12668 id = cord-280328-16fpiuc2 author = Villanueva‐Cabezas, JP title = One Health needs a vision beyond zoonoses date = 2020-08-12 keywords = SDG summary = We propose that the United Nation''s sustainable development goals provide an adequate multidimensional set of targets that can help researchers and policymakers contextualise emerging diseases, and guide One Health long‐term solutions that are equitable, efficacious, and sustainable. All rights reserved farming supports food security (SDG 2), and underpins peri-urban and urban sustainability (SDG 11) (Costard et al., 2009) , smallholders respond to ASF outbreaks by selling or consuming infected pigs (Chenais et al., 2017) . All rights reserved If after COVID-19 the community resumes the trade of wildlife, positive SDG effects associated with the trading ban will be lost (C  B) to improved human population wellbeing (C  C). If in contrast, the systems lack resilience and ASF outbreaks result in pathogen-centric approaches (for example, culling of animals with minimum or no compensation), the positive SDGs effects associated with the pig value chain are severely undermined (E  D). doi = 10.1111/tbed.13782 id = cord-316617-8cqxz3wi author = Ward, Michael P. title = SARS‐CoV‐2, where to now? date = 2020-06-19 keywords = COVID-19; SARS summary = (2020) present the results of a SARS-CoV-2 serological survey in 35 animal species in China, including the dog of a COVID-19 patient and an additional two in-contact dogs. Tests available for the detection of SARS-CoV-2 are comprehensively described in this issue of Transboundary and Emerging Diseases (Li & Ren, 2020) . In addition to the publication of new knowledge about SARS-CoV-2 in this issue of Transboundary and Emerging Diseases, new ideas are also presented. A key enabler of such a shift in our thinking and approach to disease emergence and spread is a One Health workforce capable of undertaking integrated monitoring, surveillance, risk assessment and response activities. The COVID-19 pandemic could be a catalyst for such a seismic shift in how we approach emerging infectious diseases and One Health. We can be sure, even when the current COVID-19 pandemic is resolved, that the need for surveillance, response and prevention of transboundary and emerging diseases will remain. doi = 10.1111/tbed.13654 id = cord-351584-380s4j70 author = Ward, Michael P. title = The role of climate during the COVID‐19 epidemic in New South Wales, Australia date = 2020-06-01 keywords = covid-19; relative summary = doi = 10.1111/tbed.13631 id = cord-293082-fw7deem8 author = Zhang, Guangzhi title = Animal coronaviruses and SARS‐CoV‐2 date = 2020-08-16 keywords = CoV-2; Coronavirus; SARS summary = As of April 7, just four months since its first outbreak, more 48 than 3.4 million confirmed cases and 238,000 deaths have been recorded in 215 countries, areas, 49 and territories, and moreover it seems that severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2) that causes COVID-19 will probably continue to circulate around the globe 51 (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/). The health 52 authorities and governments of affected countries have paid attention to current pandemic and 53 have taken immediate measures to block COVID-19 transmission, including utilization of personal 54 protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis 55 and sharing, public health education, maintaining social distance, the creation of diagnostics, 56 therapeutics, and vaccines, etc (Xiao and Torok 2020) . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain doi = 10.1111/tbed.13791 id = cord-274773-3jhka8wl author = Zhang, Jialin title = Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date = 2019-09-30 keywords = RNA; piglet summary = title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge doi = 10.1111/tbed.13369 id = cord-351564-nikcd44o author = Zhang, Xiaozhan title = Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes date = 2020-01-24 keywords = China; IBV summary = doi = 10.1111/tbed.13477 id = cord-289584-rbp7p8s9 author = Zhou, Ling title = Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date = 2019-01-09 keywords = Bat; SADS summary = So far, six coronaviruses have been identified from pigs, which include porcine epidemic diarrhoea virus (PEDV), porcine respiratory coronavirus (PRCV), SADS-CoV and transmissible gastroenteritis virus (TGEV) that all belong to the Alphacoronavirus genus, as well as one betacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) and one deltacoronavirus, porcine deltacoronavirus (PDCoV) (Lin, Saif, Marthaler, & Wang, 2016; Wesley, Woods, & Cheung, 1991; Woo et al., 2010) . Our results also indicated that both the complete genomes, N genes and S genes of all SADS-CoV strains shared the highest nucleotides identifies with those corresponding sequences of four bat coronavirus HKU2 strains. In this work, The phylogenetic trees of full length genomes and S genes of SADS-CoV sequences showed that the SADS-CoV branch clustered with these four HKU2 strains, which is same to previous results (Gong et al., 2017; Pan et al., 2017; Zhou et al., 2018) . doi = 10.1111/tbed.13008 id = cord-253450-k7p510p4 author = keha, Abi title = Prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/esterase gene in dairy calves in China date = 2019-05-31 keywords = China; gene summary = doi = 10.1111/tbed.13228