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1. Molecular epidemiology and histopathological study of a natural infection with decapod iridescent virus 1 in farmed white leg shrimp, Penaeus vannamei

Author:
Qiu, Liang; Chen, Xing; Gao, Wen; Li, Chen; Guo, Xiao-Meng; Zhang, Qing-Li; Yang, Bing; Huang, Jie
Source:
Aquaculture 2021 v.533 pp. 736105
ISSN:
0044-8486
Subject:
molecular epidemiology,   etc   ; Iridoviridae; Litopenaeus vannamei; Pomacea canaliculata; atrophy; coat proteins; color; crayfish; die-off; epithelium; farms; genes; hemocytes; histopathology; loop-mediated isothermal amplification; lymphatic system; microbial detection; new genus; pathogens; pigmentation; polymerase chain reaction; sequence alignment; shrimp; stomach; transmission electron microscopy; viruses; China;     Show all 27 Subjects
Abstract:
... As the only species of the new genus Decapodiridovirus within the family Iridoviridae, Decapod iridescent virus 1 (DIV1) has been proved to be the aetiological agent of the new disease, which causes mass die-offs of shrimp, prawn and crayfish. Samples of Penaeus vannamei were collected from three farms in Guangdong Province of China. Diseased P. vannamei exhibited the symptoms of hepatopancreatic ...
DOI:
10.1016/j.aquaculture.2020.736105

2. Analysis of reassortant and intragenic recombination in Cypovirus

Author:
Zhang, Zhendong; Li, Ning; Hou, Chengxiang; Gao, Kun; Tang, Xudong; Guo, Xijie
Source:
Virology journal 2020 v.17 no.1 pp. 48
ISSN:
1743-422X
Subject:
molecular epidemiology,   etc   ; Cypovirus; crops; forests; genome; host range; insect pests; intragenic recombination; pathogens; silkworms; virulence; viruses;     Show all 12 Subjects
Abstract:
... Cypoviruses (CPVs) are RNA viruses with segmented double-stranded genome and major pathogens of various insects, including economic insects like silkworms and pest insects for agricultural crops and forests. Genome reassortment and recombination are common phenomenon for viruses as a mechanism to expand host range and increase virulence. In the present study, we analyzed the reassortant and recomb ...
DOI:
10.1186/s12985-020-01321-1
PubMed:
32248835
PubMed Central:
PMC7132967

3. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Author:
Lu, Jing; du Plessis, Louis; Liu, Zhe; Hill, Verity; Kang, Min; Lin, Huifang; Sun, Jiufeng; François, Sarah; Kraemer, Moritz U.G.; Faria, Nuno R.; McCrone, John T.; Peng, Jinju; Xiong, Qianling; Yuan, Runyu; Zeng, Lilian; Zhou, Pingping; Liang, Chumin; Yi, Lina; Liu, Jun; Xiao, Jianpeng; Hu, Jianxiong; Liu, Tao; Ma, Wenjun; Li, Wei; Su, Juan; Zheng, Huanying; Peng, Bo; Fang, Shisong; Su, Wenzhe; Li, Kuibiao; Sun, Ruilin; Bai, Ru; Tang, Xi; Liang, Minfeng; Quick, Josh; Song, Tie; Rambaut, Andrew; Loman, Nick; Raghwani, Jayna; Pybus, Oliver G.; Ke, Changwen
Source:
Cell 2020 v.181 no.5 pp. 997-1003.e9
ISSN:
0092-8674
Subject:
molecular epidemiology,   etc   ; Coronavirinae; Coronavirus infections; genetic variation; genome; metagenomics; monitoring; pandemic; phylogeny; travel; viruses; China;     Show all 12 Subjects
Abstract:
... Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China’s most populous province, during early 2020 resulted in 1,388 reported RNA-positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China, we genera ...
DOI:
10.1016/j.cell.2020.04.023
PubMed:
32359424
PubMed Central:
PMC7192124

4. Genotypes, carbapenemase carriage, integron diversity and oprD alterations among carbapenem-resistant Pseudomonas aeruginosa from Russia

Author:
Bocharova, Yuliya; Savinova, Tatiana; Lazareva, Anna; Polikarpova, Svetlana; Gordinskaya, Nataliya; Mayanskiy, Nikolay; Chebotar, Igor
Source:
International journal of antimicrobial agents 2020 v.55 no.4 pp. 105899
ISSN:
0924-8579
Subject:
molecular epidemiology,   etc   ; Pseudomonas aeruginosa; antibiotic resistance; beta-lactamase; carbapenems; evolution; genes; genotype; secondary infection; transposons; Russia;     Show all 11 Subjects
Abstract:
... Pseudomonas aeruginosa is a serious opportunistic pathogen demonstrating a high level of resistance to many groups of antibiotics, including carbapenems. This study aimed to characterise the molecular epidemiology and prevalence of mobile genetic elements associated with resistance to carbapenems among P. aeruginosa (CRPA) clinical isolates. Among 145 carbapenem-resistant P. aeruginosa isolates, 3 ...
DOI:
10.1016/j.ijantimicag.2020.105899

5. Molecular epidemiology and intercontinental spread of cholera

Author:
Mutreja, Ankur; Dougan, Gordon
Source:
Vaccine 2020 v.38 pp. A46
ISSN:
0264-410X
Subject:
molecular epidemiology,   etc   ; Vibrio cholerae; cholera; databases; nucleotide sequences; pandemic; phylogeny; public health; sequence analysis; vaccines;     Show all 10 Subjects
Abstract:
... Whole genome sequence analysis has revealed the phylogenetic structure of Vibrio cholerae and has shown that the current seventh pandemic is highly clonal, emerging from a single source. Such analysis has the potential to become a powerful public health tool as we build public sequence databases, and as the speed of sequencing and analysis increases. Examples of such studies, as applied to differe ...
DOI:
10.1016/j.vaccine.2019.07.038

6. A database for ITS2 sequences from nematodes

Author:
Workentine, Matthew L.; Chen, Rebecca; Zhu, Shawna; Gavriliuc, Stefan; Shaw, Nicolette; Rijke, Jill de; Redman, Elizabeth M.; Avramenko, Russell W.; Wit, Janneke; Poissant, Jocelyn; Gilleard, John S.
Source:
BMC genetics 2020 v.21 no.1 pp. 74
ISSN:
1471-2156
Subject:
molecular epidemiology,   etc   ; Nematoda; computer software; databases; genes; genetic markers; population genetics; ribosomal DNA; ribosomal RNA; species identification; surveys;     Show all 11 Subjects
Abstract:
... BACKGROUND: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. RESULTS: Here we present an ITS2 rDNA database for marker gene sur ...
DOI:
10.1186/s12863-020-00880-0

7. Heteroresistance to cefepime in Pseudomonas aeruginosa bacteraemia

Author:
Jia, Xiaojiong; Ma, Weijia; He, Jianchun; Tian, Xiaolang; Liu, Hang; Zou, Hua; Cheng, Si
Source:
International journal of antimicrobial agents 2020 v.55 no.3 pp. 105832
ISSN:
0924-8579
Subject:
molecular epidemiology,   etc   ; Pseudomonas aeruginosa; bacteremia; central venous catheters; cephalosporins; elderly; patients; prognosis; rapid methods; risk factors; therapeutics; China;     Show all 12 Subjects
Abstract:
... Heteroresistance to antibiotic agents can lead to diagnostic and therapeutic failures; however, to date, cefepime heteroresistance (FEP-HR) in Pseudomonas aeruginosa (P. aeruginosa) bacteraemia has not been characterised. The primary goal of this study was to investigate the molecular epidemiology, mechanisms and risk factors for cefepime-heteroresistant P. aeruginosa bacteraemia over approximatel ...
DOI:
10.1016/j.ijantimicag.2019.10.013

8. Determining Ancestry between Rodent- and Human-Derived Virus Sequences in Endemic Foci: Towards a More Integral Molecular Epidemiology of Lassa Fever within West Africa

Author:
Olayemi, Ayodeji; Adesina, Adetunji Samuel; Strecker, Thomas; Magassouba, N’Faly; Fichet-Calvet, Elisabeth
Source:
Biology 2020 v.9 no.2
ISSN:
2079-7737
Subject:
molecular epidemiology,   etc   ; Bayesian theory; Lassa mammarenavirus; Lassa virus fever; ancestry; epidemiological studies; hosts; humans; phylogeny; rodents; viruses; Nigeria; Sierra Leone;     Show all 13 Subjects
Abstract:
... Lassa fever is a viral hemorrhagic illness responsible for thousands of human deaths in West Africa yearly. Rodents are known as natural reservoirs of the causative Lassa mammarenavirus (LASV) while humans are regarded as incidental, spill-over hosts. Analysis of genetic sequences continues to add to our understanding of the evolutionary history, emergence patterns, and the epidemiology of LASV. H ...
DOI:
10.3390/biology9020026
PubMed:
32046182
PubMed Central:
PMC7167862

9. Molecular epidemiology of toxigenic Clostridioides difficile isolates from hospitalized patients and the hospital environment in Dhaka, Bangladesh

Author:
Sofjan, Amelia K.; Islam, Mohammad Aminul; Halder, Kakali; Kabir, Nayel D.; Saleh, Ahmed Abu; Miranda, Julie; Lancaster, Chris; Begum, Khurshida; Alam, M. Jahangir; Garey, Kevin W.
Source:
Anaerobe 2020 v.61 pp. 102081
ISSN:
1075-9964
Subject:
molecular epidemiology,   etc   ; Clostridium difficile; adults; cohort studies; diarrhea; feces; hospitals; patients; pollution; ribotypes; risk; toxigenic strains; toxins; Bangladesh;     Show all 14 Subjects
Abstract:
... Epidemiology of Clostridioides difficile (syn. Clostridium difficile) infection (CDI) in Bangladesh is poorly understood. This study assessed the epidemiology of CDI in hospitalized patients and hospital environmental contamination of toxigenic C. difficile at two large urban Bangladesh hospitals. This 12-month prospective observational cohort study collected stool samples from adults with diarrhe ...
DOI:
10.1016/j.anaerobe.2019.102081

10. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018

Author:
Arana, Ainara; Jere, Khuzwayo C.; Chaguza, Chrispin; Montes, Milagrosa; Alkorta, Miriam; Iturriza-Gomara, Miren; Cilla, Gustavo
Source:
Infection, genetics, and evolution 2019 v.71 pp. 67-75
ISSN:
1567-1348
Subject:
molecular epidemiology,   etc   ; Rotavirus; genetic variation; genome; genotype; phylogeny; Spain;     Show all 7 Subjects
Abstract:
... G12 rotaviruses were first detected in Spain (Gipuzkoa province) in December 2004. After four years with no detections, G12 strains re-emerged in the 2010–2011 epidemic season, when the first European epidemic circulation of this genotype was observed in Gipuzkoa. G12 rotaviruses were also the dominant strains in 2011–2012, 2014–2015 and 2015–2016 epidemic seasons and were sporadically detected in ...
DOI:
10.1016/j.meegid.2019.03.016

11. Molecular detection and phylogenetic analysis of lumpy skin disease virus from outbreaks in Uganda 2017–2018

Author:
Ochwo, Sylvester; VanderWaal, Kimberly; Ndekezi, Christian; Nkamwesiga, Joseph; Munsey, Anna; Witto, Sarah Gift; Nantima, Noelina; Mayanja, Franklin; Okurut, Anna Rose Ademun; Atuhaire, David Kalenzi; Mwiine, Frank Norbert
Source:
BMC veterinary research 2020 v.16 no.1 pp. 66
ISSN:
1746-6148
Subject:
molecular epidemiology,   etc   ; G-protein coupled receptors; Lumpy skin disease virus; biopsy; blood sampling; cattle; genes; lumpy skin disease; nucleic acids; phylogeny; sequence diversity; vaccines; Eurasia; Europe; Uganda;     Show all 15 Subjects
Abstract:
... BACKGROUND: Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripoxvirus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecul ...
DOI:
10.1186/s12917-020-02288-5
PubMed:
32085763
PubMed Central:
PMC7035724

12. Molecular epidemiology and genetic variation analyses of porcine circovirus type 2 isolated from Yunnan Province in China from 2016-2019

Author:
Lv, Nianci; Zhu, Li; Li, Wengui; Li, Zhilan; Qian, Qisheng; Zhang, Tianyu; Liu, Lu; Hong, Jinmei; Zheng, Xiaolin; Wang, Yuan; Zhang, Yifang; Chai, Jun
Source:
BMC veterinary research 2020 v.16 no.1 pp. 96
ISSN:
1746-6148
Subject:
molecular epidemiology,   etc   ; Porcine circovirus-2; amino acids; animal viruses; epidemiological studies; evolution; genes; genetic variation; genotype; herds; immunosuppression; nucleotide sequences; polymerase chain reaction; pork industry; swine; vaccines; China;     Show all 17 Subjects
Abstract:
... BACKGROUND: Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated disease (PCVAD). Its prevalence in swine herds was first reported in China in 2000. PCV2 infection causes immunosuppression that leads to multiple diseases, causing serious economic problems for the swine industry in China. Since information on the genetic variation of PCV2 in Yunnan province is li ...
DOI:
10.1186/s12917-020-02304-8
PubMed:
32293447
PubMed Central:
PMC7087357

13. Molecular survey of duck circovirus infection in poultry in southern and southwestern China during 2018 and 2019

Author:
Liu, Hao; Li, Li Xia; Sun, Wen Chao; Shi, Ning; Sun, Xiu Tao; Jin, Ning Yi; Si, Xing Kui
Source:
BMC veterinary research 2020 v.16 no.1 pp. 80
ISSN:
1746-6148
Subject:
molecular epidemiology,   etc   ; Anas platyrhynchos; Cairina moschata; Circovirus; Muscovy; Pekin; disease susceptibility; ducks; epidemiological studies; farms; genetic variation; genome; genotype; immunosuppression; phylogeny; polymerase chain reaction; poultry diseases; viruses; China;     Show all 19 Subjects
Abstract:
... BACKGROUND: Duck circovirus (DuCV) is a potential immunosuppressive virus that causes feather disorders in young ducks. In this study, DuCV obtained from various species of ducks was investigated by polymerase chain reaction (PCR) in southern and southwestern China (Guangdong, Guangxi and Yunnan provinces) from 2018 to 2019. RESULTS: A total of 848 bursa samples were collected from dead Mulard, Ch ...
DOI:
10.1186/s12917-020-02301-x
PubMed:
32138728
PubMed Central:
PMC7059369

14. Phylogenetic analysis of porcine circovirus type 2 (PCV2) between 2015 and 2018 in Henan Province, China

Author:
Zheng, Guanmin; Lu, Qingxia; Wang, Fangyu; Xing, Guangxu; Feng, Hua; Jin, Qianyue; Guo, Zhenhua; Teng, Man; Hao, Huifang; Li, Dongliang; Wei, Xin; Zhang, Yuhang; Deng, Ruiguang; Zhang, Gaiping
Source:
BMC veterinary research 2020 v.16 no.1 pp. 6
ISSN:
1746-6148
Subject:
molecular epidemiology,   etc   ; Porcine circovirus; Porcine circovirus-2; amino acid sequences; amino acids; financial economics; genetic variation; genome; genotype; industry; mutation; pathogens; phylogeny; swine; China;     Show all 15 Subjects
Abstract:
... BACKGROUND: Porcine circovirus type 2 (PCV2) is the pathogen of porcine circovirus associated diseases (PCVAD) and one of the main pathogens in the global pig industry, which has brought huge economic losses to the pig industry. In recent years, there has been limited research on the prevalence of PCV2 in Henan Province. This study investigated the genotype and evolution of PCV2 in this area. RESU ...
DOI:
10.1186/s12917-019-2193-1
PubMed:
31910824
PubMed Central:
PMC6947828

15. Molecular epidemiology of fowl adenoviruses in Greece

Author:
Franzo, Giovanni; Prentza, Zoi; Paparounis, Thomas; Tsiouris, Vasilios; Centonze, Giovanni; Legnardi, Matteo; Catelli, Elena; Tucciarone, Claudia Maria; Koutoulis, Konstantinos; Cecchinato, Mattia
Source:
Poultry science 2020 v.99 no.11 pp. 5983-5990
ISSN:
0032-5791
Subject:
molecular epidemiology,   etc   ; Fowl aviadenovirus E; broiler breeders; control methods; economic impact; flocks; genetic similarity; gizzard; hepatitis; histopathology; immunologic techniques; mortality; phylogeny; polymerase chain reaction; sequence analysis; Greece;     Show all 16 Subjects
Abstract:
... Outbreaks of inclusion body hepatitis (IBH) and adenoviral gizzard erosion have been anecdotally reported in Greece since approximately 2011. However, a relevant increase in clinical outbreaks compatible with IBH has been described since 2014. Unfortunately, with limited exceptions, only serological assays were performed, and involved strains were not properly characterized. In the present study, ...
DOI:
10.1016/j.psj.2020.07.019

16. Genetic characterization of fowl aviadenovirus 4 isolates from Guangxi, China, during 2017–2019

Author:
Rashid, Farooq; Xie, Zhixun; Zhang, Lei; Luan, Yongjiao; Luo, Sisi; Deng, Xianwen; Xie, Liji; Xie, Zhiqin; Fan, Qing
Source:
Poultry science 2020 v.99 no.9 pp. 4166-4173
ISSN:
0032-5791
Subject:
molecular epidemiology,   etc   ; Aviadenovirus; arginine; aspartic acid; chickens; disease severity; etiology; genetic markers; genetic variation; mortality; mutation; phylogeny; poultry diseases; serine; serotypes; structural genes; tyrosine; virulence; China;     Show all 19 Subjects
Abstract:
... Hepatitis-hydropericardium syndrome (HHS) is a severe disease that causes 20 to 80% mortality in chickens aged 3 to 6 wk. Fowl aviadenovirus serotype 4 (FAdV-4) plays an important role in the etiology of HHS. Since 2015, outbreaks of HHS have been reported in several provinces of China; however, details regarding the FAdV-4 genome properties are lacking. In the present study, the complete genomes ...
DOI:
10.1016/j.psj.2020.06.003

17. The tcdA-negative and tcdB-positive Clostridium difficile ST81 clone exhibits a high level of resistance to fluoroquinolones: a multi-centre study in Beijing, China

Author:
Cheng, Jing-Wei; Liu, Chang; Kudinha, Timothy; Xiao, Meng; Fan, Xin; Yang, Chun-Xia; Wei, Ming; Liang, Guo-Wei; Shao, Dong-Hua; Xiong, Zhu-Jia; Hou, Xin; Yu, Shu-Ying; Wang, Yao; Yang, Qi-Wen; Su, Jian-Rong; Xu, Ying-Chun
Source:
International journal of antimicrobial agents 2020 v.56 no.1 pp. 105981
ISSN:
0924-8579
Subject:
molecular epidemiology,   etc   ; Clostridium difficile; amino acids; antibiotic resistance; ciprofloxacin; diarrhea; hospitals; levofloxacin; metronidazole; monitoring; moxifloxacin; mutation; mutation rate; resistance genes; sequence analysis; vancomycin; China;     Show all 17 Subjects
Abstract:
... Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhoea worldwide. In order to gain a better understanding about the molecular epidemiology of C. difficile in Beijing, China, molecular typing, antimicrobial susceptibility testing and drug resistance gene sequencing were performed on 174 strains of C. difficile collected from four large tertiary hospitals in Be ...
DOI:
10.1016/j.ijantimicag.2020.105981

18. Genetic characterization of bovine ephemeral fever virus in southern China, 2013–2017

Author:
Kun, Jia; Rongrong, Jia; Xiangbin, Wang; Yan, Zhao; Yiping, Dou; Gang, Lu; Pei, Zhou; Shoujun, Li
Source:
Virus genes 2020 v.56 no.3 pp. 390-395
ISSN:
0920-8569
Subject:
molecular epidemiology,   etc   ; Bovine ephemeral fever virus; amino acids; arboviruses; bovine ephemeral fever; cattle; genes; glycoproteins; glycosylation; inactivated vaccines; mutation; phylogeny; China; Japan; Taiwan; Thailand;     Show all 16 Subjects
Abstract:
... Bovine ephemeral fever virus (BEFV) can cause bovine ephemeral fever and is an economically important arbovirus of cattle. To expand the knowledge of the molecular epidemiology of BEFV in southern China, the complete surface glycoprotein G gene of BEFV was sequenced from samples collected in five restricted outbreaks from 2013 to 2017, namely 2013ZH, 2014HM, 2015GX, 11082-2016, and qy2017. It was ...
DOI:
10.1007/s11262-020-01740-w

19. The fowl adenovirus (Fadv-11) outbreak in Iranian broiler chicken farms: The first full genome characterization and phylogenetic analysis

Author:
Hosseini, Hossein; Langeroudi, Arash Ghalyanchi; FallahMehrabadi, Mohammad Hossein; Ziafati Kafi, Zahra; Dizaji, Reza Esmaeelzadeh; Ghafouri, Seyed Ali; Hamadan, Amir Modiri; Aghaiyan, Leila; Hajizamani, Niusha
Source:
Comparative immunology, microbiology, and infectious diseases 2020 v.70 pp. 101365
ISSN:
0147-9571
Subject:
molecular epidemiology,   etc   ; Adenoviridae; DNA; broiler chickens; etiological agents; farms; flocks; genes; hepatitis; liver; nucleotide sequences; phylogeny; polymerase chain reaction; sequence analysis; serotypes; Iran;     Show all 16 Subjects
Abstract:
... Fowl adenoviruses D and E (FAdV-D and E) can cause inclusion body hepatitis (IBH) in commercial chicken flocks. Recently, IBH outbreaks have been increasingly reported in different regions of Iran, particularly in broiler farms. The present study was conducted to perform, for the first time, a complete genome characterization of a FAdV isolate from an IBH outbreak in Iran. Briefly, liver samples w ...
DOI:
10.1016/j.cimid.2019.101365

20. Co-infection status of porcine circoviruses (PCV2 and PCV3) and porcine epidemic diarrhea virus (PEDV) in pigs with watery diarrhea in Henan province, central China

Author:
Guo, Zhenhua; Ruan, Haiyu; Qiao, Songlin; Deng, Ruiguang; Zhang, Gaiping
Source:
Microbial pathogenesis 2020 v.142 pp. 104047
ISSN:
0882-4010
Subject:
molecular epidemiology,   etc   ; Circoviridae; Porcine epidemic diarrhea virus; amino acid substitution; diarrhea; genes; genetic variation; genotype; mixed infection; piglets; pork industry; reverse transcriptase polymerase chain reaction; viruses; China;     Show all 14 Subjects
Abstract:
... Porcine circoviruses (PCV2 and PCV3) and porcine epidemic diarrhea virus (PEDV) are important swine viruses that threaten the swine industry worldwide. Here, we evaluated the co-infection status of PCV2, PCV3 and PEDV in 76 enteric samples from piglets with severe diarrhea disease in Henan, China. All samples were tested by PCR/RT-PCR. Our results showed that the infection rate of PCV2, PCV3 and P ...
DOI:
10.1016/j.micpath.2020.104047