{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:38:35Z","timestamp":1760150315219,"version":"build-2065373602"},"reference-count":27,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T00:00:00Z","timestamp":1698969600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2020\/10127-1","2021\/11944-6","U01 AI151698"],"award-info":[{"award-number":["2020\/10127-1","2021\/11944-6","U01 AI151698"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Butantan Foundation","award":["2020\/10127-1","2021\/11944-6","U01 AI151698"],"award-info":[{"award-number":["2020\/10127-1","2021\/11944-6","U01 AI151698"]}]},{"name":"National Institutes of Health USA","award":["2020\/10127-1","2021\/11944-6","U01 AI151698"],"award-info":[{"award-number":["2020\/10127-1","2021\/11944-6","U01 AI151698"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of S\u00e3o Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the symptomatic individuals were excluded, and only asymptomatic cases were analyzed. During the Delta wave, a total of 4315 samples were collected, whereas 2372 samples were collected during the first Omicron wave. The incidence of the asymptomatic SARS-CoV-2 infection was 0.6% during the Delta wave and 0.8% during the Omicron wave. No statistical differences were found in the threshold amplification cycle. However, there was a statistical difference observed in the sublineage distribution between asymptomatic and symptomatic individuals. Our study determined the incidence of asymptomatic infection by monitoring individuals who remained symptom-free, thereby providing a reliable evaluation of asymptomatic SARS-CoV-2 carriage. Our findings reveal a relatively low proportion of asymptomatic cases, which could be attributed to our rigorous monitoring protocol for the presence of clinical symptoms. Investigating asymptomatic infection rates is crucial to develop and implement effective disease control strategies.<\/jats:p>","DOI":"10.3390\/v15112210","type":"journal-article","created":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T10:51:28Z","timestamp":1699008688000},"page":"2210","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Epidemiological and Genomic Analysis of Asymptomatic SARS-CoV-2 Infections during the Delta and Omicron Epidemic Waves in S\u00e3o Paulo City, Brazil"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0805-6140","authenticated-orcid":false,"given":"Svetoslav N.","family":"Slavov","sequence":"first","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"},{"name":"Ribeir\u00e3o Preto Medical School, Ribeir\u00e3o Preto 14051-140, SP, Brazil"},{"name":"Blood Center of Ribeir\u00e3o Preto, Ribeir\u00e3o Preto 14051-140, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex R. J.","family":"Lima","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriela","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Loyze P. O.","family":"de Lima","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia R. dos S.","family":"Barros","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4987-7757","authenticated-orcid":false,"given":"Elaine C.","family":"Marqueze","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio J.","family":"Martins","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maiara","family":"Martininghi","sequence":"additional","affiliation":[{"name":"Health Surveillance Coordination, Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Vigil\u00e2ncia em Sa\u00fade (COVISA), Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa","family":"Palmieri","sequence":"additional","affiliation":[{"name":"Health Surveillance Coordination, Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Vigil\u00e2ncia em Sa\u00fade (COVISA), Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luiz A. V.","family":"Caldeira","sequence":"additional","affiliation":[{"name":"Health Surveillance Coordination, Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Vigil\u00e2ncia em Sa\u00fade (COVISA), Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabiana E. V. da","family":"Silva","sequence":"additional","affiliation":[{"name":"Primary Care Coordination Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Aten\u00e7\u00e3o B\u00e1sica, Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giselle","family":"Cacherik","sequence":"additional","affiliation":[{"name":"Primary Care Coordination Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Aten\u00e7\u00e3o B\u00e1sica, Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aline L.","family":"Nicolodelli","sequence":"additional","affiliation":[{"name":"Primary Care Coordination Municipal Health Department of S\u00e3o Paulo, Coordenadoria de Aten\u00e7\u00e3o B\u00e1sica, Secretaria Municipal de S\u00e3o Paulo (SMS SP), S\u00e3o Paulo 01223-010, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Kashima","sequence":"additional","affiliation":[{"name":"Ribeir\u00e3o Preto Medical School, Ribeir\u00e3o Preto 14051-140, SP, Brazil"},{"name":"Blood Center of Ribeir\u00e3o Preto, Ribeir\u00e3o Preto 14051-140, SP, Brazil"},{"name":"University of S\u00e3o Paulo, Ribeir\u00e3o Preto 14051-140, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5849-7326","authenticated-orcid":false,"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil"},{"name":"Institute Rene Rachou Foundation Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil"},{"name":"Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico Rome, 00128 Roma, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6769-9931","authenticated-orcid":false,"given":"Luiz Carlos Junior","family":"Alcantara","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil"},{"name":"Institute Rene Rachou Foundation Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra C.","family":"Sampaio","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0501-8280","authenticated-orcid":false,"given":"Maria C.","family":"Elias","sequence":"additional","affiliation":[{"name":"Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, S\u00e3o Paulo 05507-000, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s41182-022-00490-9","article-title":"Asymptomatic versus Symptomatic SARS-CoV-2 Infection: A Cross-Sectional Seroprevalence Study","volume":"50","author":"Hashish","year":"2022","journal-title":"Trop Med. Health"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e2109229118","DOI":"10.1073\/pnas.2109229118","article-title":"Asymptomatic SARS-CoV-2 Infection: A Systematic Review and Meta-Analysis","volume":"118","author":"Sah","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/s13167-021-00267-w","article-title":"Modeling SARS-CoV-2 Spike\/ACE2 Protein\u2013Protein Interactions for Predicting the Binding Affinity of New Spike Variants for ACE2, and Novel ACE2 Structurally Related Human Protein Targets, for COVID-19 Handling in the 3PM Context","volume":"13","author":"Tragni","year":"2022","journal-title":"EPMA J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"970","DOI":"10.3201\/eid2703.210038","article-title":"Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020","volume":"27","author":"Claro","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Fernandes, G.A., Junior, A.P.N., Azevedo E Silva, G., Feriani, D., Fran\u00e7a E Silva, I.L.A., Caruso, P., and Curado, M.P. (2021). Excess Mortality by Specific Causes of Deaths in the City of S\u00e4o Paulo, Brazil, during the COVID-19 Pandemic. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0252238"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Slavov, S.N., de La-Roque, D.G.L., da Costa, P.N.M., Rodrigues, E.S., Santos, E.V., Borges, J.S., Evaristo, M., de Matos Ma\u00e7onetto, J., Marques, A.A., and Milhomens, J. (2022). Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil. Viruses, 14.","DOI":"10.3390\/v14102148"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Elias, M.C., Slavov, S.N., Lima, A.R.J., Martins, A.J., Barros, C.R.d.S., Moretti, D.B., Araujo, E.L., Marqueze, E.C., Ribeiro, G.M.F., and Bernardino, J.S.T. (2023). A Traveling SARS-CoV-2 Laboratory as Part of a Pandemic Response among Vulnerable Brazilian Populations. BMC Public Health, 23.","DOI":"10.1186\/s12889-022-14867-2"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1038\/s41564-022-01191-z","article-title":"Genomic Epidemiology of the SARS-CoV-2 Epidemic in Brazil","volume":"7","author":"Giovanetti","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3394","DOI":"10.1002\/jmv.27674","article-title":"SARS-CoV-2 Genomic Monitoring in the State of S\u00e3o Paulo Unveils Two Emerging AY.43 Sublineages","volume":"94","author":"Lima","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"NextStrain: Real-Time Tracking of Pathogen Evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: An R Package for Visualization and Annotation of Phylogenetic Trees With Their Covariates and Other Associated Data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5790","DOI":"10.1002\/jmv.28066","article-title":"Proportion of Asymptomatic Infection and Nonsevere Disease Caused by SARS-CoV-2 Omicron Variant: A Systematic Review and Analysis","volume":"94","author":"Yu","year":"2022","journal-title":"J. Med. Virol"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/cid\/ciac237","article-title":"High Asymptomatic Carriage With the Omicron Variant in South Africa","volume":"4","author":"Garrett","year":"2022","journal-title":"Clin. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1080\/22221751.2022.2030200","article-title":"Homologous or Heterologous Booster of Inactivated Vaccine Reduces SARS-CoV-2 Omicron Variant Escape from Neutralizing Antibodies","volume":"11","author":"Wang","year":"2022","journal-title":"Emerg. Microbes Infect."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e28138","DOI":"10.1002\/jmv.28138","article-title":"The Outbreak of SARS-CoV-2 Omicron Lineages, Immune Escape, and Vaccine Effectivity","volume":"95","author":"Zhou","year":"2023","journal-title":"J. Med. Virol."},{"key":"ref_17","first-page":"162","article-title":"SARS-CoV-2 Variant Biology: Immune Escape, Transmission and Fitness","volume":"21","author":"Carabelli","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Silva, J.D.P., de Lima, A.B., Alvim, L.B., Malta, F.S.V., Mendon\u00e7a, C.P.T.B., de Carvalho, A.H.B., Rios, J.S.H., Fonseca, P.L.C., Queiroz, D.C., and Santos, L.C.G.d.A.e. (2023). Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil. Viruses, 15.","DOI":"10.3390\/v15041017"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"E2247704","DOI":"10.1001\/jamanetworkopen.2022.47704","article-title":"Prevalence of Asymptomatic SARS-CoV-2 Infection in Japan","volume":"5","author":"Suzuki","year":"2022","journal-title":"JAMA Netw. Open"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"362","DOI":"10.7326\/M20-3012","article-title":"Prevalence of Asymptomatic SARS-CoV-2 Infection. A Narrative Review","volume":"173","author":"Oran","year":"2020","journal-title":"Ann. Intern. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"645","DOI":"10.3390\/idr13030061","article-title":"Viral Load Difference between Symptomatic and Asymptomatic COVID-19 Patients: Systematic Review and Meta-Analysis","volume":"13","author":"Zuin","year":"2021","journal-title":"Infect. Dis. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1136\/thoraxjnl-2020-215042","article-title":"Upper Respiratory Viral Load in Asymptomatic Individuals and Mildly Symptomatic Patients with SARS-CoV-2 Infection","volume":"76","author":"Ra","year":"2021","journal-title":"Thorax"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"106272","DOI":"10.1016\/j.ijantimicag.2020.106272","article-title":"Different Mutations in SARS-CoV-2 Associate with Severe and Mild Outcome","volume":"57","author":"Nagy","year":"2021","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e670","DOI":"10.1002\/iid3.670","article-title":"Immunologic Features of Asymptomatic Postvaccination Infections with the Delta Variant of SARS-CoV-2 in Adults","volume":"10","author":"Duan","year":"2022","journal-title":"Immun. Inflamm. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Mendiola-Pastrana, I.R., L\u00f3pez-Ortiz, E., R\u00edo de la Loza-Zamora, J.G., Gonz\u00e1lez, J., G\u00f3mez-Garc\u00eda, A., and L\u00f3pez-Ortiz, G. (2022). SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review. Life, 12.","DOI":"10.3390\/life12020170"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/s41586-023-06331-x","article-title":"A Common Allele of HLA Is Associated with Asymptomatic SARS-CoV-2 Infection","volume":"620","author":"Augusto","year":"2023","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1590\/1678-4685-gmb-2018-0076","article-title":"A Systematic Scoping Review of the Genetic Ancestry of the Brazilian Population","volume":"42","author":"Resende","year":"2019","journal-title":"Genet. Mol. Biol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/11\/2210\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:16:40Z","timestamp":1760131000000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/11\/2210"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,3]]},"references-count":27,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2023,11]]}},"alternative-id":["v15112210"],"URL":"https:\/\/doi.org\/10.3390\/v15112210","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2023,11,3]]}}}