{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T12:33:30Z","timestamp":1777984410963,"version":"3.51.4"},"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T00:00:00Z","timestamp":1777334400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2019-67015-29918"],"award-info":[{"award-number":["2019-67015-29918"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["2023-67021-40018"],"award-info":[{"award-number":["2023-67021-40018"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The concept of viral quasispecies refers to a constantly mutating viral population occurring within hosts, which is essential for grasping the micro-evolutionary patterns of viruses. Despite its high error rate, long-read sequencing holds potential for advancing viral quasispecies research by resolving coverage limitations in next-generation sequencing. We introduce a refined workflow, QoALa, implemented in the\n                    <jats:italic>longreadvqs<\/jats:italic>\n                    R package. This workflow begins with nucleotide position-wise noise minimization of read alignments and sample size standardization, and extends to viral quasispecies comparison across related samples with integrated visualization capabilities. Benchmarking on simulated SARS-CoV-2 and HIV-1 datasets demonstrated that QoALa consistently outperformed existing error-correction methods in recovering quasispecies composition, particularly in preserving nucleotide diversity and hierarchical population structure. Real raw read samples from five studies of different viruses (HCV, HBV, HIV-1, SARS-CoV-2, and IAV), sequenced by major long-read platforms, were also used to evaluate these approaches. The comparative results provide novel insights into intra- and inter-host diversity dynamics in various scenarios and unveil rare haplotypes not reported in the original studies, underscoring the versatility and practicality of our methodology.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1014208","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T17:34:28Z","timestamp":1777397668000},"page":"e1014208","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0378-0316","authenticated-orcid":true,"given":"Nakarin","family":"Pamornchainavakul","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Declan C.","family":"Schroeder","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimberly","family":"VanderWaal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,4,28]]},"reference":[{"issue":"3","key":"pcbi.1014208.ref001","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/ilar\/ilx026","article-title":"Are RNA Viruses Candidate Agents for the Next Global Pandemic? 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