{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T00:36:27Z","timestamp":1793061387659,"version":"4.5.0"},"reference-count":29,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2020,2,8]],"date-time":"2020-02-08T00:00:00Z","timestamp":1581120000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["MOST 106\u20102923\u2010B\u2010195\u2010001\u2010MY3"],"award-info":[{"award-number":["MOST 106\u20102923\u2010B\u2010195\u2010001\u2010MY3"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004861","name":"Mackay Memorial Hospital","doi-asserted-by":"publisher","award":["MMH-108-22"],"award-info":[{"award-number":["MMH-108-22"]}],"id":[{"id":"10.13039\/501100004861","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centers for Diseases Control, Taiwan","award":["MOHW108-CDC-C-315-134510"],"award-info":[{"award-number":["MOHW108-CDC-C-315-134510"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Human bocavirus (HBoV) is a causative agent of respiratory and gastrointestinal diseases worldwide. Four HBoV species (HBoV1-4) have been identified so far. Although a previous report has documented the HBoV association with acute gastroenteritis (AGE) in Taiwan, their epidemiology, genetic diversity, and phylogenetic relationships remain unclear. In this study, we focused on an investigation of these unsolved issues, which will help to reveal molecular epidemiology and phylogeny of the circulating HBoV2 in Taiwan. A total of 176 stool samples were collected from children with AGE for this study. PCR amplification and sequencing on the VP1 gene region were used to identify species. Phylogenetic analysis was conducted by maximum-likelihood and neighbor-joining methods. Selection pressure was also estimated to obtain HBoV evolutionary information. Our results showed the prevalence of HBoV in AGE children was 8.5%, of which HBoV1 was the predominant species (6.3%), followed by HBoV2 (2.3%). Phylogenetic analysis showed those Taiwanese HBoV2 strains have significant genetic variability and can be divided into two clusters. One belongs to HBoV2 genotype A and the other forms an independent unclassified cluster. The nucleotide distance between that independent cluster and the known HBoV2 genotypes was more than 5%, suggesting a new HBoV2 genotype. No positive selection site was found and the virus was under purifying selection. This is the first report to reveal HBoV2 genetic diversity and phylogenetic relationships among AGE children in Taiwan. We find that HBoV2 may have been introduced into the country by multiple origins, and a potential new HBoV2 genotype is proposed.<\/jats:p>","DOI":"10.3390\/ijerph17031086","type":"journal-article","created":{"date-parts":[[2020,2,10]],"date-time":"2020-02-10T11:48:51Z","timestamp":1581335331000},"page":"1086","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genetic Diversity and Phylogenetic Analysis of Human Bocavirus 2 in Pediatric Patients with Acute Gastroenteritis in Taiwan"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3672-3000","authenticated-orcid":false,"given":"Marco Yung-Cheng","family":"Lin","sequence":"first","affiliation":[{"name":"Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan"},{"name":"Department of Nursing, Shu-Zen junior College of Medicine and Management, Kaohsiung 82144, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiu-Chuan","family":"Chan","sequence":"additional","affiliation":[{"name":"Lipid Science and Aging Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2385-344X","authenticated-orcid":false,"given":"Hsin","family":"Chi","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MacKay Children\u2019s Hospital and MacKay Memorial Hospital, Taipei 10449, Taiwan"},{"name":"Department of Medicine, MacKay Medical College, New Taipei 25245, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu-Chun","family":"Chiu","sequence":"additional","affiliation":[{"name":"Center of Diagnostics and Vaccine Development, Centers for Disease Control, Taipei 11561, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0594-1091","authenticated-orcid":false,"given":"Zaiga","family":"Nora-Krukle","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Virology, Riga Stradins University, LV-1067 Riga, Latvia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6519-7121","authenticated-orcid":false,"given":"Santa","family":"Rasa-Dzelzkaleja","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Virology, Riga Stradins University, LV-1067 Riga, Latvia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1738-013X","authenticated-orcid":false,"given":"Anda","family":"Vilmane","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Virology, Riga Stradins University, LV-1067 Riga, Latvia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0971-1784","authenticated-orcid":false,"given":"Modra","family":"Murovska","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Virology, Riga Stradins University, LV-1067 Riga, Latvia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jih-Hui","family":"Lin","sequence":"additional","affiliation":[{"name":"Center of Diagnostics and Vaccine Development, Centers for Disease Control, Taipei 11561, Taiwan"},{"name":"Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0082-2269","authenticated-orcid":false,"given":"Hsin-Fu","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan"},{"name":"Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,2,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"12891","DOI":"10.1073\/pnas.0504666102","article-title":"Cloning of a human parvovirus by molecular screening of respiratory tract samples","volume":"102","author":"Allander","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1086\/652416","article-title":"Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections","volume":"201","author":"Kapoor","year":"2010","journal-title":"J. Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1086\/595831","article-title":"A newly identified bocavirus species in human stool","volume":"199","author":"Kapoor","year":"2009","journal-title":"J. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Arthur, J.L., Higgins, G.D., Davidson, G.P., Givney, R.C., and Ratcliff, R.M. (2009). A novel bocavirus associated with acute gastroenteritis in Australian children. PLoS Pathog., 5.","DOI":"10.1371\/journal.ppat.1000391"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.meegid.2012.01.025","article-title":"Circulating of human bocavirus 1, 2, 3, and 4 in pediatric patients with acute gastroenteritis in Thailand","volume":"12","author":"Khamrin","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.jcv.2008.12.018","article-title":"Clinical and genetic analysis of Human Bocavirus in children with lower respiratory tract infection in Taiwan","volume":"44","author":"Lin","year":"2009","journal-title":"J. Clin. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/cid\/cir957","article-title":"Detection of human bocavirus in the cerebrospinal fluid of children with encephalitis","volume":"54","author":"Mitui","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.3201\/eid1911.121548","article-title":"Human bocavirus in patients with encephalitis, Sri Lanka, 2009\u20132010","volume":"19","author":"Mori","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Nora-Krukle, Z., Vilmane, A., Xu, M., Rasa, S., Ziemele, I., Silina, E., Soderlund-Venermo, M., Gardovska, D., and Murovska, M. (2018). Human Bocavirus Infection Markers in Peripheral Blood and Stool Samples of Children with Acute Gastroenteritis. Viruses, 10.","DOI":"10.3390\/v10110639"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/S2352-4642(19)30057-4","article-title":"Human bocaviruses and paediatric infections","volume":"3","author":"Christensen","year":"2019","journal-title":"Lancet Child Adolesc. Health"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.meegid.2013.03.040","article-title":"Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4","volume":"17","author":"Khamrin","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.meegid.2014.08.022","article-title":"Prevalence analysis of different human bocavirus genotypes in pediatric patients revealed intra-genotype recombination","volume":"27","author":"Zhao","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1097\/00001432-200410000-00011","article-title":"A review of viral gastroenteritis","volume":"17","author":"Clark","year":"2004","journal-title":"Curr. Opin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1128\/JCM.01519-06","article-title":"Molecular epidemiology and clinical manifestations of viral gastroenteritis in hospitalized pediatric patients in Northern Taiwan","volume":"45","author":"Chen","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Chen, C.J., Wu, F.T., Huang, Y.C., Chang, W.C., Wu, H.S., Wu, C.Y., Lin, J.S., Huang, F.C., and Hsiung, C.A. (2015). Clinical and Epidemiologic Features of Severe Viral Gastroenteritis in Children: A 3-Year Surveillance, Multicentered Study in Taiwan With Partial Rotavirus Immunization. Medicine, 94.","DOI":"10.1097\/MD.0000000000001372"},{"key":"ref_16","first-page":"1005","article-title":"Molecular Detection of Human Bocavirus 1 and 2 in Children with Acute Gastroenteritis in Taiwan","volume":"46","author":"Tang","year":"2015","journal-title":"Southeast Asian J. Trop. Med. Public Health"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.1093\/molbev\/msx149","article-title":"SMS: Smart Model Selection in PhyML","volume":"34","author":"Lefort","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: A comparison of methods for detecting amino acid sites under selection","volume":"22","author":"Frost","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: A fast, unconstrained bayesian approximation for inferring selection","volume":"30","author":"Murrell","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Weaver, S., Shank, S.D., Spielman, S.J., Li, M., Muse, S.V., and Kosakovsky Pond, S.L. (2018). Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Mol. Biol. Evol.","DOI":"10.1093\/molbev\/msx335"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Rambaut, A., Lam, T.T., Max Carvalho, L., and Pybus, O.G. (2016). Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol., 2.","DOI":"10.1093\/ve\/vew007"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.jcv.2009.11.030","article-title":"Newly recognized bocaviruses (HBoV, HBoV2) in children and adults with gastrointestinal illness in the United States","volume":"47","author":"Chow","year":"2010","journal-title":"J. Clin. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1002\/jmv.24593","article-title":"Molecular epidemiology and clinical severity of Human Bocavirus (HBoV) 1-4 in children with acute gastroenteritis from Pune, Western India","volume":"89","author":"Lasure","year":"2017","journal-title":"J. Med. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1002\/jmv.23744","article-title":"Detection and molecular characterization of diarrhea causing viruses in single and mixed infections in children: A comparative study between Bangladesh and Turkey","volume":"86","author":"Mitui","year":"2014","journal-title":"J. Med. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Cheng, W., Chen, J., Xu, Z., Yu, J., Huang, C., Jin, M., Li, H., Zhang, M., Jin, Y., and Duan, Z.J. (2011). Phylogenetic and recombination analysis of human bocavirus 2. BMC Infect. Dis., 11.","DOI":"10.1186\/1471-2334-11-50"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.meegid.2018.11.006","article-title":"Changing pattern of prevalence and genetic diversity of rotavirus, norovirus, astrovirus, and bocavirus associated with childhood diarrhea in Asian Russia, 2009\u20132012","volume":"67","author":"Zhirakovskaia","year":"2019","journal-title":"Infect. Genet. Evol."}],"container-title":["International Journal of Environmental Research and Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1660-4601\/17\/3\/1086\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:56:04Z","timestamp":1760172964000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1660-4601\/17\/3\/1086"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,2,8]]},"references-count":29,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,2]]}},"alternative-id":["ijerph17031086"],"URL":"https:\/\/doi.org\/10.3390\/ijerph17031086","relation":{},"ISSN":["1660-4601"],"issn-type":[{"value":"1660-4601","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,8]]}}}