{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T17:02:35Z","timestamp":1778259755723,"version":"3.51.4"},"reference-count":45,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100005090","name":"Beijing Nova Program","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005090","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2022,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS\u2010CoV\u20102) plays an important role in COVID\u201019 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays that target SARS\u2010CoV\u20102 followed by either massively parallel or nanopore sequencing is a widely\u2010used strategy to obtain genome sequences from primary samples. However, multiplex PCR\u2010based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. Here we developed a two\u2010pool, long\u2010amplicon 36\u2010plex PCR primer panel with ~1000\u2010bp amplicon lengths for full\u2010genome sequencing of SARS\u2010CoV\u20102. We validated the panel by assessing nasopharyngeal swab samples with a\u2009&lt;30 quantitative reverse transcription PCR cycle threshold value and found that \u226590% of viral genomes could be covered with high sequencing depths (\u226520% mean depth). In comparison, the widely\u2010used ARTIC panel yielded 79%\u201388% high\u2010depth genome regions. We estimated that ~5 Mbp nanopore sequencing data may ensure a\u2009&gt;95% viral genome coverage with a\u2009\u226510\u2010fold depth and may generate reliable genomes at consensus sequence levels. Nanopore sequencing yielded false\u2010positive variations with frequencies of supporting reads &lt;0.8, and the sequencing errors mostly occurred on the 5\u2032 or 3\u2032 ends of reads. Thus, nanopore sequencing could not elucidate intra\u2010host viral diversity.<\/jats:p>","DOI":"10.1002\/jmv.27336","type":"journal-article","created":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T15:31:58Z","timestamp":1631719918000},"page":"327-334","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Assessment of two\u2010pool multiplex long\u2010amplicon nanopore sequencing of SARS\u2010CoV\u20102"],"prefix":"10.1002","volume":"94","author":[{"given":"Hongjie","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biotechnology Beijing Institute of Radiation Medicine Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinhui","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bio\u2010security Chinese PLA Center for Disease Control and Prevention Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanfeng","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Bio\u2010security Chinese PLA Center for Disease Control and Prevention Beijing China"},{"name":"Graduate School Academy of Military Medical Sciences Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaochen","family":"Bo","sequence":"additional","affiliation":[{"name":"Department of Biotechnology Beijing Institute of Radiation Medicine Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongbin","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Bio\u2010security Chinese PLA Center for Disease Control and Prevention Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kuibiao","family":"Li","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Microbiology Guangzhou Center for Disease Control and Prevention Guangzhou Guangdong China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bio\u2010security Chinese PLA Center for Disease Control and Prevention Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9465-2787","authenticated-orcid":false,"given":"Ming","family":"Ni","sequence":"additional","affiliation":[{"name":"Department of Biotechnology Beijing Institute of Radiation Medicine Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2021,9,23]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2008-3"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abc0523"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaa027"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.26.2001200"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty407"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-0997-y"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-0770-5"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/nsr\/nwaa036"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMcibr2032888"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.043"},{"key":"e_1_2_10_13_1","unstructured":"WHO. 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