{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:51Z","timestamp":1740135171990,"version":"3.37.3"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Rapid analysis of <jats:italic>SARS-CoV-2<\/jats:italic> genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous <jats:italic>SARS-CoV-2<\/jats:italic> sequence data generated at an unprecedented rate.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We present an updated version of the <jats:italic>SARS-CoV-2<\/jats:italic> analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.0, to perform genomic analysis to understand the variability and dynamics of the virus. It adopts the recent clade nomenclature and demonstrates the clade prediction accuracy of 92.8%. IPD 2.0 also contains a <jats:italic>SARS-CoV-2<\/jats:italic> updater module, allowing automatic upgrading of the variant database using genome sequences from GISAID. As a proof of principle, analyzing 208,911 <jats:italic>SARS-CoV-2<\/jats:italic> genome sequences, we generate an extensive database of 2.58 million sample-wise variants. A comparative account of lineage-specific mutations in the newer <jats:italic>SARS-CoV-2<\/jats:italic> strains emerging in the UK, South Africa and Brazil and data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>A novel and dynamic feature of the <jats:italic>SARS-CoV-2<\/jats:italic> module of IPD 2.0 makes it a contemporary tool to analyze the diverse and growing genomic strains of the virus and serve as a vital tool to help facilitate rapid genomic surveillance in a population to identify variants involved in breakthrough infections. IPD 2.0 is freely available from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.actrec.gov.in\/pi-webpages\/AmitDutt\/IPD\/IPD.html\">http:\/\/www.actrec.gov.in\/pi-webpages\/AmitDutt\/IPD\/IPD.html<\/jats:ext-link> and the web-application is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ipd.actrec.gov.in\/ipdweb\/\">http:\/\/ipd.actrec.gov.in\/ipdweb\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04172-x","type":"journal-article","created":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T18:03:03Z","timestamp":1620928983000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome"],"prefix":"10.1186","volume":"22","author":[{"given":"Sanket","family":"Desai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aishwarya","family":"Rane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asim","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1119-4774","authenticated-orcid":false,"given":"Amit","family":"Dutt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,5,13]]},"reference":[{"key":"4172_CR1","doi-asserted-by":"crossref","unstructured":"Jaroszewski L, Iyer M, Alisoltani A, Sedova M, Godzik A. The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins. bioRxiv. 2020;2020.08.10.244756.","DOI":"10.1101\/2020.08.10.244756"},{"issue":"7842","key":"4172_CR2","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/d41586-021-00065-4","volume":"589","author":"D Cyranoski","year":"2021","unstructured":"Cyranoski D. Alarming COVID variants show vital role of genomic surveillance. Nature. 2021;589(7842):337\u20138.","journal-title":"Nature"},{"key":"4172_CR3","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1093\/bib\/bbaa437","volume":"22","author":"S Desai","year":"2021","unstructured":"Desai S, Rashmi S, Rane A, Dharavath B, Sawant A, Dutt A. An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. 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