1
|
Wang X, Cun J, Li S, Shi Y, Liu Y, Wei H, Zhang Y, Cong R, Yang T, Wang W, Xiao J, Song Y, Yan D, Yang Q, Sun Q, Ji T. Genotype F of Echovirus 25 with multiple recombination pattern have been persistently and extensively circulating in Chinese mainland. Sci Rep 2024; 14:3212. [PMID: 38332009 PMCID: PMC10853551 DOI: 10.1038/s41598-024-53513-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Echovirus 25 (E25), a member of the Enterovirus B (EV-B) species, can cause aseptic meningitis (AM), viral meningitis (VM), and acute flaccid paralysis (AFP). However, systematic studies on the molecular epidemiology of E25, especially those concerning its evolution and recombination, are lacking. In this study, 18 strains of E25, isolated from seven provinces of China between 2009 and 2018, were collected based on the Chinese hand, foot, and mouth disease (HFMD) surveillance network, and 95 sequences downloaded from GenBank were also screened. Based on the phylogenetic analysis of 113 full-length VP1 sequences worldwide, globally occurring E25 strains were classified into 9 genotypes (A-I), and genotype F was the dominant genotype in the Chinese mainland. The average nucleotide substitution rate of E25 was 6.08 × 10-3 substitutions/site/year, and six important transmission routes were identified worldwide. Seventeen recombination patterns were determined, of which genotype F can be divided into 9 recombination patterns. A positive selector site was found in the capsid protein region of genotype F. Recombination analysis and pressure selection analysis for genotype F showed multiple recombination patterns and evolution characteristics, which may be responsible for it being the dominant genotype in the Chinese mainland. This study provides a theoretical basis for the subsequent prevention and control of E25.
Collapse
Affiliation(s)
- Xiaoyi Wang
- Medical School, Anhui University of Science and Technology, Huainan, 232001, China
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianping Cun
- Yunnan Center for Disease Control and Prevention, Kunming, 650100, China
| | - Shikang Li
- Hunan Center for Disease Control and Prevention, Changsha, 410005, China
| | - Yong Shi
- Jiangxi Center for Disease Control and Prevention, Nanchang, 330006, China
| | - Yingying Liu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, 050000, China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, 450000, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ruyi Cong
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Tingting Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Wenhui Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| |
Collapse
|
2
|
Molecular Characteristics and Genetic Evolution of Echovirus 33 in Mainland of China. Pathogens 2022; 11:pathogens11111379. [PMID: 36422630 PMCID: PMC9697921 DOI: 10.3390/pathogens11111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Echovirus, a member of the Enterovirus B (EV-B) family, has led to numerous outbreaks and pandemics, causing a broad spectrum of diseases. Based on the national hand, foot, and mouth disease (HFMD) surveillance system, seven strains of echovirus 33 (E33) were isolated from Mainland of China between 2010 and 2018. The whole genomes of these strains were isolated and sequenced, and phylogenetic trees were constructed based on the gene sequences in different regions of the EV-B prototype strains. It was found that E33 may be recombined in the P2 and P3 regions. Five genotypes (A–E) were defined based on the entire VP1 region of E33, of which the C gene subtype was the dominant gene subtype at present. Recombinant analysis showed that genotype C strains likely recombined with EV-B80, EV-B85, E13, and CVA9 in the P2 and P3 regions, while genotype E had the possibility of recombination with CVB3, E3, E6, and E4. Results of Bayesian analysis indicated that E33 may have appeared around 1955 (95% confidence interval: 1945–1959), with a high evolutionary rate of 1.11 × 10−2 substitution/site/year (95% highest posterior density (HPD): 8.17 × 10−3 to 1.4 × 10−2 substitution/site/year). According to spatial transmission route analysis, two significant transmission routes were identified: from Australia to India and from Oman to Thailand, which the E33 strain in Mainland of China likely introduced from Mexico and India. In conclusion, our study fills the gaps in the evolutionary analysis of E33 and can provide important data for enterovirus surveillance.
Collapse
|
3
|
A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China. Sci Rep 2022; 12:593. [PMID: 35022489 PMCID: PMC8755819 DOI: 10.1038/s41598-021-04604-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.
Collapse
|
4
|
Xu B, Wang J, Yan B, Xu C, Yin Q, Yang D. Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 2019. Virus Evol 2021; 7:veab071. [PMID: 36819972 PMCID: PMC9927877 DOI: 10.1093/ve/veab071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 06/24/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Enterovirus 71 (EV71) can cause large outbreaks of hand, foot, and mouth disease (HFMD) and severe neurological diseases, which is regarded as a major threat to public health, especially in Asia-Pacific regions. However, the global spatiotemporal spread of this virus has not been identified. In this study, we used large sequence datasets and a Bayesian phylogenetic approach to compare the molecular epidemiology and geographical spread patterns of different EV71 subgroups globally. The study found that subgroups of HFMD presented global spatiotemporal variation, subgroups B0, B1, and B2 have caused early infections in Europe and America, and then subgroups C1, C2, C3, and C4 replaced B0-B2 as the predominant genotypes, especially in Asia-Pacific countries. The dispersal patterns of genotype B and subgroup C4 showed the complicated routes in Asia and the source might in some Asian countries, while subgroups C1 and C2 displayed more strongly supported pathways globally, especially in Europe. This study found the predominant subgroup of EV71 and its global spatiotemporal transmission patterns, which may be beneficial to reveal the long-term global spatiotemporal transmission patterns of human EV71 and carry out the HFMD vaccine development.
Collapse
Affiliation(s)
- Bing Xu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi’an Jiaotong University, 277, Yanta West Road, Xi’an, 710061, China
- The State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A, Datun Road, Chaoyang District, Beijing, 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100190, China
- Key Clinical Discipline by National Health Commission, 277, Yanta West Road, Xi’an, 710061, China
| | - Jinfeng Wang
- The State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A, Datun Road, Chaoyang District, Beijing, 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100190, China
| | - Bin Yan
- The State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A, Datun Road, Chaoyang District, Beijing, 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100190, China
| | - Chengdong Xu
- The State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Qian Yin
- The State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Deyan Yang
- College of Oceanography and Space Informatics, China University of Petroleum, 66 Changjiangxi Road, Huangdao District, Qingdao, 266580, China
| |
Collapse
|
5
|
Molecular epidemiology and recombination of Enterovirus A71 in mainland China from 1987 to 2017. Int Microbiol 2021; 24:291-299. [PMID: 33608776 PMCID: PMC7895512 DOI: 10.1007/s10123-021-00164-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 11/27/2022]
Abstract
Enterovirus A71 (EV-A71) is an important pathogen of severe hand, foot, and mouth disease (HFMD) in young children. This study aimed to retrospectively analyze the molecular epidemiology and recombination of EV-A71 in mainland China during 1987–2017. Phylogenetic tree showed that besides the previously reported subgenotypes A, B5, C0, C2, C3, and C4, a new subgenotype C6 emerged in mainland China. Recombination analysis indicated that C4 EV-A71 was derived from a common ancestor as a “double-recombinant” virus by intertypic recombination between C EV-A71 and CVA4, CVA5, CVA14, and CVA16 strains in P3 region and intratypic recombination between C and B EV-A71 strains in P2 region. The B5 EV-A71 shared high similarity with C EV-A71 in P1 region while it contained an unidentified sequence in P2 and P3 regions with two possible recombination patterns: one occurred between C4 EV-A71 and CVA3, CVA5, CVA6, CVA10, and CVA12 stains with one breakpoint in 3C, and the other occurred between C1, C2, C3, and C5 EV-A71 and CVA4, CVA5, CVA14, and CVA16 strains with two breakpoints in the 2A/2B junction and 3C. The C2 EV-A71 was probably a recombinant virus between C4 EV-A71 and CVA8 strains with two breakpoints located in the 5′UTR and 2A/2B junction. Moreover, an incredible recombination of C6 EV-A71 occurred between C4 and C2 EV-A71 with multiple breakpoints. Thus, continuous studies on EV-A71 genome characteristics are still useful and essential for monitoring emergence of new viruses and preventing HFMD outbreaks.
Collapse
|
6
|
Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, Wang J, Yang J, Yu Q, Yu D, Chen J, Huang W, Li J, Xie T, Lu H, Ji T, Yang Q, Yan D, Zhu S, Xu W. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol 2020; 6:veaa048. [PMID: 34804589 PMCID: PMC8597624 DOI: 10.1093/ve/veaa048] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Hand, foot, and mouth disease (HFMD) is a common global epidemic. From 2008
onwards, many HFMD outbreaks caused by coxsackievirus A6 (CV-A6) have been
reported worldwide. Since 2013, with a dramatically increasing number of
CV-A6-related HFMD cases, CV-A6 has become the predominant HFMD pathogen in
mainland China. Phylogenetic analysis based on the VP1 capsid
gene revealed that subtype D3 dominated the CV-A6 outbreaks. Here, we performed
a large-scale (near) full-length genetic analysis of global and Chinese CV-A6
variants, including 158 newly sequenced samples collected extensively in
mainland China between 2010 and 2018. During the global transmission of subtype
D3 of CV-A6, the noncapsid gene continued recombining, giving rise to a series
of viable recombinant hybrids designated evolutionary lineages, and each lineage
displayed internal consistency in both genetic and epidemiological features. The
emergence of lineage –A since 2005 has triggered CV-A6 outbreaks
worldwide, with a rate of evolution estimated at
4.17 × 10−3 substitutions
site-1 year−1 based on a
large number of monophyletic open reading frame sequences, and created a series
of lineages chronologically through varied noncapsid recombination events. In
mainland China, lineage –A has generated another two novel widespread
lineages (–J and –L) through recombination within the
enterovirus A gene pool, with robust estimates of occurrence time. Lineage
–A, –J, and –L infections presented dissimilar clinical
manifestations, indicating that the conservation of the CV-A6 capsid gene
resulted in high transmissibility, but the lineage-specific noncapsid gene might
influence pathogenicity. Potentially important amino acid substitutions were
further predicted among CV-A6 variants. The evolutionary phenomenon of noncapsid
polymorphism within the same subtype observed in CV-A6 was uncommon in other
leading HFMD pathogens; such frequent recombination happened in fast-spreading
CV-A6, indicating that the recovery of deleterious genomes may still be ongoing
within CV-A6 quasispecies. CV-A6-related HFMD outbreaks have caused a
significant public health burden and pose a great threat to children’s
health; therefore, further surveillance is greatly needed to understand the full
genetic diversity of CV-A6 in mainland China.
Collapse
Affiliation(s)
- Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Jianfang Yang
- Shanxi Center for Disease Control and Prevention, Taiyuan, Shanxi Province, China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Deshan Yu
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Jianhua Chen
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Wei Huang
- Chongqing Center for Disease Control and Prevention, Chongqing City, China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing City, China
| | - Tong Xie
- Tianjin Center for Disease Control and Prevention, Tianjin City, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, China.,Anhui University of Science and Technology, Anhui Province, China
| |
Collapse
|
7
|
Susi P. Special Issue "Human Picornaviruses". Viruses 2020; 12:v12010093. [PMID: 31941146 PMCID: PMC7019337 DOI: 10.3390/v12010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/02/2022] Open
Affiliation(s)
- Petri Susi
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| |
Collapse
|
8
|
The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019; 11:v11111032. [PMID: 31698764 PMCID: PMC6893659 DOI: 10.3390/v11111032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/05/2022] Open
Abstract
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.
Collapse
|