1
|
García-Carreras B, Hitchings MDT, Johansson MA, Biggerstaff M, Slayton RB, Healy JM, Lessler J, Quandelacy T, Salje H, Huang AT, Cummings DAT. Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S. Nat Commun 2023; 14:2235. [PMID: 37076502 PMCID: PMC10115837 DOI: 10.1038/s41467-023-37944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Reconstructing the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial laboratories have conducted nationwide serosurveys for the U.S. CDC. They employed three assays, with different sensitivities and specificities, potentially introducing biases in seroprevalence estimates. Using models, we show that accounting for assays explains some of the observed state-to-state variation in seroprevalence, and when integrating case and death surveillance data, we show that when using the Abbott assay, estimates of proportions infected can differ substantially from seroprevalence estimates. We also found that states with higher proportions infected (before or after vaccination) had lower vaccination coverages, a pattern corroborated using a separate dataset. Finally, to understand vaccination rates relative to the increase in cases, we estimated the proportions of the population that received a vaccine prior to infection.
Collapse
Affiliation(s)
- Bernardo García-Carreras
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Matt D T Hitchings
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Michael A Johansson
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew Biggerstaff
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rachel B Slayton
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica M Healy
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Justin Lessler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Carolina Population Center, Chapel Hill, NC, USA
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Angkana T Huang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| |
Collapse
|
2
|
Prete CA, Buss LF, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Barral-Netto M, Tavares NM, Franca RFO, Boaventura VS, Miyajima F, Mendrone-Junior A, de Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Araujo FLV, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, da Silva SMN, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Silva-Junior AL, Busch MP, Castro MC, Dye C, Ratmann O, Faria NR, Nascimento VH, Sabino EC. SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study. eLife 2022; 11:e78233. [PMID: 36135358 PMCID: PMC9545556 DOI: 10.7554/elife.78233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Understanding these patterns is crucial to understand future outbreaks of SARS-CoV-2 or other respiratory pathogens in the country. Methods We tested 97,950 blood donation samples for IgG antibodies from March 2020 to March 2021 in 8 of Brazil's most populous cities. Residential postal codes were used to obtain representative samples. Weekly age- and sex-specific seroprevalence were estimated by correcting the crude seroprevalence by test sensitivity, specificity, and antibody waning. Results The inferred attack rate of SARS-CoV-2 in December 2020, before the Gamma variant of concern (VOC) was dominant, ranged from 19.3% (95% credible interval [CrI] 17.5-21.2%) in Curitiba to 75.0% (95% CrI 70.8-80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system's collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43-3.53). Conclusions These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread. Funding This work was supported by Itaú Unibanco 'Todos pela Saude' program; FAPESP (grants 18/14389-0, 2019/21585-0); Wellcome Trust and Royal Society Sir Henry Dale Fellowship 204311/Z/16/Z; the Gates Foundation (INV- 034540 and INV-034652); REDS-IV-P (grant HHSN268201100007I); the UK Medical Research Council (MR/S0195/1, MR/V038109/1); CAPES; CNPq (304714/2018-6); Fundação Faculdade de Medicina; Programa Inova Fiocruz-CE/Funcap - Edital 01/2020 Number: FIO-0167-00065.01.00/20 SPU N°06531047/2020; JBS - Fazer o bem faz bem.
Collapse
Affiliation(s)
- Carlos A Prete
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | | | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
| | - Tassila Salomon
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | - Isabel CG Moura
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Fabio Miyajima
- Fundação Oswaldo CruzManguinhosBrazil
- Universidade Federal do CearáFortalezaBrazil
| | | | | | - Nanci A Salles
- Fundação Pró Sangue Hemocentro de São Paulo (FPS)São PauloBrazil
| | | | | | - Luana M de Souza
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Luciane K Schier
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Patricia M Inoue
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Lilyane A Xabregas
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Myuki AE Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Nelson Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | | | - Luciana MB Carlos
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | - Veridiana Pessoa
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | | | | | | | - Anna F Cavalcante
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria IB Valença
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria V da Silva
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Esther Lopes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Luiz A Filho
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Sheila OG Mateos
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Gabrielle T Nunes
- Fundação Oswaldo CruzManguinhosBrazil
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Alexander L Silva-Junior
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
- Universidade Federal do AmazonasManausBrazil
- Centro Universitário do NorteManausBrazil
| | - Michael P Busch
- Vitalant Research InstituteSan FranscicoUnited States
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Christopher Dye
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
| | - Vítor H Nascimento
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
| |
Collapse
|