{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:59:44Z","timestamp":1740146384247,"version":"3.37.3"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2018,5,24]],"date-time":"2018-05-24T00:00:00Z","timestamp":1527120000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["5U19GH000622"],"award-info":[{"award-number":["5U19GH000622"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["5U51IP000528"],"award-info":[{"award-number":["5U51IP000528"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0198101","type":"journal-article","created":{"date-parts":[[2018,5,24]],"date-time":"2018-05-24T17:59:49Z","timestamp":1527184789000},"page":"e0198101","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Intra-host and intra-household diversity of influenza A viruses during household transmissions in the 2013 season in 2 peri-urban communities of South Africa"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4804-3774","authenticated-orcid":true,"given":"Ziyaad","family":"Valley-Omar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Preetha","family":"Iyengar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claire","family":"von Mollendorf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefano","family":"Tempia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra","family":"Moerdyk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Orienka","family":"Hellferscee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neil","family":"Martinson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meredith","family":"McMorrow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ebrahim","family":"Variava","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katlego","family":"Masonoke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam L.","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheryl","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florette K.","family":"Treurnicht","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,5,24]]},"reference":[{"issue":"2","key":"ref1","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.jcv.2011.06.022","article-title":"Viral genetic sequence variations in pandemic H1N1\/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community","volume":"52","author":"LL Poon","year":"2011","journal-title":"Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology"},{"issue":"4","key":"ref2","doi-asserted-by":"crossref","first-page":"e18956","DOI":"10.1371\/journal.pone.0018956","article-title":"Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic","volume":"6","author":"JE Morlighem","year":"2011","journal-title":"PloS one"},{"issue":"3","key":"ref3","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1086\/658671","article-title":"Molecular characteristics of outbreaks of nosocomial infection with influenza A\/H3N2 virus variants","volume":"32","author":"T Oguma","year":"2011","journal-title":"Infection control and hospital epidemiology"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1111\/j.1750-2659.2011.00322.x","article-title":"An outbreak of the 2009 influenza a (H1N1) virus in a children&apos;s hospital","volume":"6","author":"A Bearden","year":"2012","journal-title":"Influenza and other respiratory viruses"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"16178","DOI":"10.1038\/srep16178","article-title":"Emergence of Hemagglutinin Mutations During the Course of Influenza Infection","volume":"5","author":"A Cushing","year":"2015","journal-title":"Scientific reports"},{"issue":"10","key":"ref6","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1093\/infdis\/jis571","article-title":"Presence of oseltamivir-resistant pandemic A\/H1N1 minor variants before drug therapy with subsequent selection and transmission","volume":"206","author":"E Ghedin","year":"2012","journal-title":"The Journal of infectious diseases"},{"issue":"11","key":"ref7","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1086\/345372","article-title":"Assessment of hemagglutinin sequence heterogeneity during influenza virus transmission in families","volume":"186","author":"LV Gubareva","year":"2002","journal-title":"The Journal of infectious diseases"},{"issue":"2","key":"ref8","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/ng.3479","article-title":"Quantifying influenza virus diversity and transmission in humans","volume":"48","author":"LL Poon","year":"2016","journal-title":"Nature genetics"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1097\/INF.0b013e3180616cfb","article-title":"Transmission of influenza A in families","volume":"26","author":"SS Teo","year":"2007","journal-title":"The Pediatric infectious disease journal"},{"issue":"Suppl 4","key":"ref10","first-page":"6","article-title":"Viral evolution from one generation of human influenza infection to the next","volume":"19","author":"S Riley","year":"2013","journal-title":"Hong Kong medical journal = Xianggang yi xue za zhi"},{"issue":"9","key":"ref11","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1097\/QAD.0000000000000267","article-title":"Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure","volume":"28","author":"S Mohamed","year":"2014","journal-title":"Aids"},{"issue":"24","key":"ref12","doi-asserted-by":"crossref","first-page":"11247","DOI":"10.1128\/JVI.01657-16","article-title":"Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification","volume":"90","author":"A Sobel Leonard","year":"2016","journal-title":"Journal of virology"},{"issue":"5","key":"ref13","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.jinf.2015.09.001","article-title":"Case-ascertained study of household transmission of seasonal influenza\u2014South Africa, 2013","volume":"71","author":"P Iyengar","year":"2015","journal-title":"The Journal of infection"},{"key":"ref14","first-page":"1","article-title":"CDC real time RT-PCR (rRT-PCR) protocol for detection and characterization of influenza 2009 A(H1N1)pdm virus","volume":"2010","journal-title":"RUO International"},{"issue":"50","key":"ref15","doi-asserted-by":"crossref","first-page":"20248","DOI":"10.1073\/pnas.1320524110","article-title":"Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins","volume":"110","author":"NS Heaton","year":"2013","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"19","key":"ref16","doi-asserted-by":"crossref","first-page":"10309","DOI":"10.1128\/JVI.01109-09","article-title":"Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses","volume":"83","author":"B Zhou","year":"2009","journal-title":"Journal of virology"},{"key":"ref17","unstructured":"Organisation WH. WHO information for molecular diagnosis of influenza virus\u2014update 2014 [updated March 2014]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/influenza\/gisrs_laboratory\/molecular_diagnosis_influenza_virus_humans_update_201403.pdf\" xlink:type=\"simple\">http:\/\/www.who.int\/influenza\/gisrs_laboratory\/molecular_diagnosis_influenza_virus_humans_update_201403.pdf<\/ext-link>."},{"issue":"5","key":"ref18","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":"RC Edgar","year":"2004","journal-title":"Nucleic acids research"},{"issue":"3","key":"ref19","doi-asserted-by":"crossref","first-page":"e0120226","DOI":"10.1371\/journal.pone.0120226","article-title":"Evaluation of two influenza surveillance systems in South Africa","volume":"10","author":"E Budgell","year":"2015","journal-title":"PloS one"},{"issue":"9","key":"ref20","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref21","unstructured":"Shisana O, Rehle, T, Simbayi LC, Zuma, K, Jooste, S, Zungu N, Labadarios, D, Onoya, D. South African National HIV Prevalence, Incidence and Behaviour Survey, 2012 HSRC Press. 2012."},{"key":"ref22","unstructured":"diseases NIfc. Respiratory virus surveillance report, South Africa, 2013 [Bulletin\/Report]. 2014 [updated April 2014; cited 12 1]. April 2014:[9\u201310]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.nicd.ac.za\/assets\/files\/CommDisBull%2012(1)-April%202014_Fin.pdf\" xlink:type=\"simple\">http:\/\/www.nicd.ac.za\/assets\/files\/CommDisBull%2012(1)-April%202014_Fin.pdf<\/ext-link>."},{"issue":"44","key":"ref23","first-page":"7","article-title":"Review of the 2011 winter influenza season, southern hemisphere","volume":"86","year":"2011","journal-title":"WHO Weekly Epidemiological Report"},{"issue":"13","key":"ref24","doi-asserted-by":"crossref","first-page":"7130","DOI":"10.1128\/JVI.00420-14","article-title":"Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses","volume":"88","author":"Y Iba","year":"2014","journal-title":"Journal of virology"},{"issue":"46","key":"ref25","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1016\/j.vaccine.2016.09.011","article-title":"Risk factors associated with hospitalisation for influenza-associated severe acute respiratory illness in South Africa: A case-population study","volume":"34","author":"TR Abadom","year":"2016","journal-title":"Vaccine"},{"issue":"9","key":"ref26","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1093\/cid\/ciu095","article-title":"Mortality associated with seasonal and pandemic influenza and respiratory syncytial virus among children &lt;5 years of age in a high HIV prevalence setting\u2014South Africa, 1998\u20132009","volume":"58","author":"S Tempia","year":"2014","journal-title":"Clinical infectious diseases: an official publication of the Infectious Diseases Society of America"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0198101","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T11:52:58Z","timestamp":1589025178000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0198101"}},"subtitle":[],"editor":[{"given":"Florian","family":"Krammer","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,24]]},"references-count":26,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2018,5,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0198101","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2018,5,24]]}}}