{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:42:26Z","timestamp":1785422546224,"version":"3.56.0"},"reference-count":10,"publisher":"Cambridge University Press (CUP)","license":[{"start":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T00:00:00Z","timestamp":1755216000000},"content-version":"unspecified","delay-in-days":226,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2025]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The rapid evolution of SARS-CoV-2 has led to the emergence of variants of concern (VOCs) characterized by increased transmissibility, pathogenicity, and resistance to neutralizing antibodies. Identifying these variants is essential for guiding public health efforts to control COVID-19. Although whole genome sequencing (WGS) is the gold standard for variant identification, its implementation is often limited in developing countries due to resource constraints. In Bolivia, genomic surveillance is a challenge due to its limited technological infrastructure and resources. An RT-qPCR-based strategy was designed to address these limitations and detect the mutations associated with VOCs and variants of interest (VOIs). The multiplex RT-qPCR commercial kits Allplex\n                    <jats:sup>TM<\/jats:sup>\n                    Master and Variants I (Seegene\u00ae) and the ValuPanel\n                    <jats:sup>TM<\/jats:sup>\n                    (Biosearch\u00ae) were used to target mutations such as HV69\/70del, E484K, N501Y, P681H, and K417N\/T. They are characteristic of the Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621), and Zeta (P.2) variants. A total of 157 samples collected in Cochabamba from January to November 2021 were evaluated, identifying 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron were identified. The strategy\u2019s effectiveness was validated against WGS data generated with Oxford Nanopore\n                    <jats:sup>TM<\/jats:sup>\n                    technology, showing a concordance rate of 0.96. This highlights the value of the RT-qPCR strategy in guiding the selection of samples for WGS, enabling broader detection of new variants that cannot be identified by RT-qPCR alone.\n                  <\/jats:p>","DOI":"10.1017\/s095026882510037x","type":"journal-article","created":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T01:49:39Z","timestamp":1755222579000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":1,"title":["Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience"],"prefix":"10.1017","volume":"153","author":[{"given":"Rudy","family":"Parrado","sequence":"first","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"},{"id":[{"id":"https:\/\/ror.org\/03z27es23","id-type":"ROR","asserted-by":"publisher"}],"name":"Universidad Mayor de San Sim\u00f3n"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina X.","family":"Cuba-Grandy","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugenia","family":"Fuentes-Luppichini","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04teye511","id-type":"ROR","asserted-by":"publisher"}],"name":"Pontificia Universidad Cat\u00f3lica de Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nattaly Grecia","family":"Torrico Villarroel","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03z27es23","id-type":"ROR","asserted-by":"publisher"}],"name":"Universidad Mayor de San Sim\u00f3n"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yercin","family":"Mamani-Ortiz","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaqueline","family":"Mendez","sequence":"additional","affiliation":[{"name":"Departmental Health Service of Cochabamba"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betty","family":"Melgarejo","sequence":"additional","affiliation":[{"name":"Departmental Health Service of Cochabamba"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irenice","family":"Coronado-Arr\u00e1zola","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nair A.","family":"Monta\u00f1o","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo I.","family":"Almonacid","sequence":"additional","affiliation":[{"name":"Pontificia Universidad Cat\u00f3lica de Chile"},{"name":"Institute for Biological and Medical Engineering, Pontificia Universidad Cat\u00f3lica de Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael A.","family":"Medina","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04teye511","id-type":"ROR","asserted-by":"publisher"}],"name":"Pontificia Universidad Cat\u00f3lica de Chile"},{"name":"Emory Center of Excellence of Influenza Research and Response (Emory-CEIRR)"},{"name":"Center for Research on Influenza Pathogenesis and Transmission (CRIPT) Center of Excellence of Influenza Research and Response (CEIRR)"},{"name":"Emory University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lineth","family":"Garcia","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Biom\u00e9dicas (IIBISMED)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5409-225X","authenticated-orcid":false,"given":"Catalina","family":"Pardo-Roa","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04teye511","id-type":"ROR","asserted-by":"publisher"}],"name":"Pontificia Universidad Cat\u00f3lica de Chile"},{"name":"Emory Center of Excellence of Influenza Research and Response (Emory-CEIRR)"},{"name":"Pontificia Universidad Cat\u00f3lica de Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2025,8,15]]},"reference":[{"key":"S095026882510037X_r5","unstructured":"[5] Viceministerio de Promoci\u00f3n Vigilancia Epidemiol\u00f3gica y Medicina Tradicional Genomic Surveillance of COVID-19 in Bolivia March 2020 to March 2021. La Paz; 2021"},{"key":"S095026882510037X_r1","unstructured":"[1] World Health Organization. WHO Normative Review: COVID-19 Surveillance April 11, 2023 [Internet]. Available from: https:\/\/www.who.int\/en\/emergencies\/diseases\/novel-coronavirus-2019\/covid-19-policy-briefs"},{"key":"S095026882510037X_r8","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2021.104894"},{"key":"S095026882510037X_r4","unstructured":"[4] GISAID - NextStrain [Internet]. [cited 2022 March 6]. Available from: https:\/\/www.gisaid.org\/"},{"key":"S095026882510037X_r6","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2022.114462"},{"key":"S095026882510037X_r2","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines9101195"},{"key":"S095026882510037X_r10","unstructured":"[10] Technologies OxN (2021) Amplicon Barcoding with Native Barcoding Expansion 96 (EXP-NBD196, SQK-LSK109) Protocol, Version: NBA_9102_v109_revF_09Jul2020. Oxford Nanopore Technologies. Available from: https:\/\/community.nanoporetech.com\/protocols\/amplicon-barcoding-with-native-barcoding-expansion-96-exp-nbd196-and-sqk\/v\/nba_9102_v109_revf_09jul2020#faq-tab&"},{"key":"S095026882510037X_r9","article-title":"Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore","author":"Tyson","year":"2020","journal-title":"bioRxiv [Preprint]"},{"key":"S095026882510037X_r3","doi-asserted-by":"publisher","DOI":"10.3390\/v13030439"},{"key":"S095026882510037X_r7","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2021.104996"}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S095026882510037X","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T16:11:34Z","timestamp":1759853494000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S095026882510037X\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":10,"alternative-id":["S095026882510037X"],"URL":"https:\/\/doi.org\/10.1017\/s095026882510037x","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"value":"0950-2688","type":"print"},{"value":"1469-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]},"assertion":[{"value":"\u00a9 The Author(s), 2025. Published by Cambridge University Press","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http:\/\/creativecommons.org\/licenses\/by\/4.0), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}],"article-number":"e94"}}