Integration of Syndromic Surveillance and Rapid Genomic Response Enables Early Detection of Emerging SARS-CoV-2 Variants in Rio de Janeiro, Brazil

Integration of Syndromic Surveillance and Rapid Genomic Response Enables Early Detection of Emerging SARS-CoV-2 Variants in Rio de Janeiro, Brazil | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 12 February 2026 V1 Latest version Share on Integration of Syndromic Surveillance and Rapid Genomic Response Enables Early Detection of Emerging SARS-CoV-2 Variants in Rio de Janeiro, Brazil Authors : Victor Guimarães-Ribeiro , Lais Ferreira Bento , Jéssica Graça de Macedo Carvalho , Bruna Mendonça Silva , Larissa Macedo Pinto , Leonardo Corrêa da Silva Junior , Alice Sampaio Barreto da Rocha , … Show All … , Luciana Reis Appolinario , Elisa Cavalcante Pereira , Priscila Gonçalves Moura , Rodrigo Reis Moura , Thauane Silva , Ana Isabel Dias , Fernando do Couto Motta , Patrícia Alvarez da Silva Baptista , Monica Ferreira Moreira , Karoline Moreira Duffrayer , Erika Fonseca Camargo Marsico , Léa de Freitas Amaral 0000-0002-0914-7637 , Jade Veloso Freitas , Maria Clara Henrique Moreira Geraldo , Caio Luiz Pereira Ribeiro , Gislani Mateus Oliveira Aguilar , Manoel Barral-Netto , Siqueira Marilda , and Paola Cristina Resende 0000-0002-2884-3662 [email protected] Show Fewer Authors Info & Affiliations https://doi.org/10.22541/au.177087250.08063467/v1 140 views 61 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The history of recent epidemics or pandemics makes clear that delays in generating and releasing genomic data can directly limit our ability to detect, understand, and respond to emerging threats. Influenza-like illness (ILI) sentinel surveillance remains central to respiratory virus monitoring. Between September 2024 and July 2025, during episodic increases in ILI cases, in Rio de Janeiro, Brazil, an enhanced genomic surveillance strategy was implemented through collaboration between the Municipal Health Secretariat and the Laboratory of Respiratory Viruses and Measles (LVRE/IOC/Fiocruz). The strategy was triggered by epidemiological alerts from primary healthcare units performing routine SARS-CoV-2 antigen-detection rapid tests (Ag-RDTs). Increases in positivity prompted second-line RT-PCR and genomic sequencing. More than 200 nasopharyngeal samples were collected across 2-3 epidemiological weeks during each surge. SARS-CoV-2 RT-PCR–confirmed positives and samples with Ct<30 were sequenced using Illumina technology for lineage determination. Two enhanced surveillance operations were conducted within the study period. The first enabled the initial detection of the Variant Under Monitoring (VUM) XEC in Brazil. The second identified the emergence and local circulation of VUM XFG shortly after its WHO designation, as well as the first detection of VUM NB.1.8.1. In both events, local genomic signals preceded regional increases of these variants. Targeted genomic surveillance activated by syndromic and antigen-based alerts enabled the timely detection of emerging SARS-CoV-2 variants. This adaptive strategy highlights the importance of integrating genomic and epidemiological surveillance to ensure early identification and response in the post-pandemic period. Supplementary Material File (manuscript_ribeiro_20260209.docx) Download 749.91 KB Information & Authors Information Version history V1 Version 1 12 February 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords coronavirus influenza virus respiratory syncytial virus virus classification Authors Affiliations Victor Guimarães-Ribeiro Fundacao Oswaldo Cruz View all articles by this author Lais Ferreira Bento Fundacao Oswaldo Cruz View all articles by this author Jéssica Graça de Macedo Carvalho Fundacao Oswaldo Cruz View all articles by this author Bruna Mendonça Silva Fundacao Oswaldo Cruz View all articles by this author Larissa Macedo Pinto Fundacao Oswaldo Cruz View all articles by this author Leonardo Corrêa da Silva Junior Fundacao Oswaldo Cruz View all articles by this author Alice Sampaio Barreto da Rocha Fundacao Oswaldo Cruz View all articles by this author Luciana Reis Appolinario Fundacao Oswaldo Cruz View all articles by this author Elisa Cavalcante Pereira Fundacao Oswaldo Cruz View all articles by this author Priscila Gonçalves Moura Fundacao Oswaldo Cruz View all articles by this author Rodrigo Reis Moura Fundacao Oswaldo Cruz View all articles by this author Thauane Silva Fundacao Oswaldo Cruz View all articles by this author Ana Isabel Dias Fundacao Oswaldo Cruz View all articles by this author Fernando do Couto Motta Fundacao Oswaldo Cruz View all articles by this author Patrícia Alvarez da Silva Baptista Bio-Manguinhos View all articles by this author Monica Ferreira Moreira Universidade Federal do Rio de Janeiro Instituto de Quimica View all articles by this author Karoline Moreira Duffrayer Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Erika Fonseca Camargo Marsico Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Léa de Freitas Amaral 0000-0002-0914-7637 Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Jade Veloso Freitas Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Maria Clara Henrique Moreira Geraldo Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Caio Luiz Pereira Ribeiro Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Gislani Mateus Oliveira Aguilar Secretaria Municipal de Saude do Rio de Janeiro View all articles by this author Manoel Barral-Netto Instituto Goncalo Moniz View all articles by this author Siqueira Marilda Fundacao Oswaldo Cruz View all articles by this author Paola Cristina Resende 0000-0002-2884-3662 [email protected] Fundacao Oswaldo Cruz View all articles by this author Metrics & Citations Metrics Article Usage 140 views 61 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Victor Guimarães-Ribeiro, Lais Ferreira Bento, Jéssica Graça de Macedo Carvalho, et al. Integration of Syndromic Surveillance and Rapid Genomic Response Enables Early Detection of Emerging SARS-CoV-2 Variants in Rio de Janeiro, Brazil. Authorea . 12 February 2026. DOI: https://doi.org/10.22541/au.177087250.08063467/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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