Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

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Attack rate in Manaus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) incidence peaked in Manaus, Brazil, in May 2020 with a devastating toll on the city's inhabitants, leaving its health services shattered and cemeteries overwhelmed. Buss et al. collected data from blood donors from Manaus and São Paulo, noted when transmission began to fall, and estimated the final attack rates in October 2020 (see the Perspective by Sridhar and Gurdasani). Heterogeneities in immune protection, population structure, poverty, modes of public transport, and uneven adoption of nonpharmaceutical interventions mean that despite a high attack rate, herd immunity may not have been achieved. This unfortunate city has become a sentinel for how natural population immunity could influence future transmission. Events in Manaus reveal what tragedy and harm to society can unfold if this virus is left to run its course.

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Abstract

The spread of COVID-19 in Manaus, Brazil, shows that a largely unmitigated epidemic can infect a high fraction of the population and cause high mortality.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly in Manaus, the capital of Amazonas state in northern Brazil. The attack rate there is an estimate of the final size of the largely unmitigated epidemic that occurred in Manaus. We use a convenience sample of blood donors to show that by June 2020, 1 month after the epidemic peak in Manaus, 44% of the population had detectable immunoglobulin G (IgG) antibodies. Correcting for cases without a detectable antibody response and for antibody waning, we estimate a 66% attack rate in June, rising to 76% in October. This is higher than in São Paulo, in southeastern Brazil, where the estimated attack rate in October was 29%. These results confirm that when poorly controlled, COVID-19 can infect a large proportion of the population, causing high mortality.

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Estimates of the severity of coronavirus disease 2019: a model-based analysis

Robert Verity, Lucy C Okell, Ilaria Dorigatti … (2020)

Summary Background In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. Methods We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. Findings Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9–19·2) and to hospital discharge to be 24·7 days (22·9–28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56–3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23–1·53), with substantially higher ratios in older age groups (0·32% [0·27–0·38] in those aged <60 years vs 6·4% [5·7–7·2] in those aged ≥60 years), up to 13·4% (11·2–15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4–3·5] in those aged <60 years [n=360] and 4·5% [1·8–11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39–1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0–7·6) in those aged 80 years or older. Interpretation These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death. Funding UK Medical Research Council.

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Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

Quan-Xin Long, Xiao-Jun Tang, Qiu-Lin Shi … (2020)

The clinical features and immune responses of asymptomatic individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been well described. We studied 37 asymptomatic individuals in the Wanzhou District who were diagnosed with RT-PCR-confirmed SARS-CoV-2 infections but without any relevant clinical symptoms in the preceding 14 d and during hospitalization. Asymptomatic individuals were admitted to the government-designated Wanzhou People's Hospital for centralized isolation in accordance with policy1. The median duration of viral shedding in the asymptomatic group was 19 d (interquartile range (IQR), 15-26 d). The asymptomatic group had a significantly longer duration of viral shedding than the symptomatic group (log-rank P = 0.028). The virus-specific IgG levels in the asymptomatic group (median S/CO, 3.4; IQR, 1.6-10.7) were significantly lower (P = 0.005) relative to the symptomatic group (median S/CO, 20.5; IQR, 5.8-38.2) in the acute phase. Of asymptomatic individuals, 93.3% (28/30) and 81.1% (30/37) had reduction in IgG and neutralizing antibody levels, respectively, during the early convalescent phase, as compared to 96.8% (30/31) and 62.2% (23/37) of symptomatic patients. Forty percent of asymptomatic individuals became seronegative and 12.9% of the symptomatic group became negative for IgG in the early convalescent phase. In addition, asymptomatic individuals exhibited lower levels of 18 pro- and anti-inflammatory cytokines. These data suggest that asymptomatic individuals had a weaker immune response to SARS-CoV-2 infection. The reduction in IgG and neutralizing antibody levels in the early convalescent phase might have implications for immunity strategy and serological surveys.

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Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020

Kenji Mizumoto, Katsushi Kagaya, Alexander Zarebski … (2020)

On 5 February 2020, in Yokohama, Japan, a cruise ship hosting 3,711 people underwent a 2-week quarantine after a former passenger was found with COVID-19 post-disembarking. As at 20 February, 634 persons on board tested positive for the causative virus. We conducted statistical modelling to derive the delay-adjusted asymptomatic proportion of infections, along with the infections’ timeline. The estimated asymptomatic proportion was 17.9% (95% credible interval (CrI): 15.5–20.2%). Most infections occurred before the quarantine start.

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Author and article information

Journal

Journal ID (nlm-ta): Science

Journal ID (iso-abbrev): Science

Journal ID (publisher-id): SCIENCE

Journal ID (hwp): science

Title: Science (New York, N.y.)

Publisher: American Association for the Advancement of Science

ISSN (Print): 0036-8075

ISSN (Electronic): 1095-9203

Publication date (Print): 15 January 2021

Publication date (Electronic): 08 December 2020

Volume: 371

Issue: 6526

Pages: 288-292

Affiliations

[1 ]Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.

[2 ]Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil.

[3 ]Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.

[4 ]Fundação Pró-Sangue–Hemocentro de São Paulo, São Paulo, Brazil.

[5 ]Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.

[6 ]Fundação Hemominas–Fundação Centro de Hematologia e Hemoterapia de Minas Gerais, Belo Horizonte, Brazil.

[7 ]Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil.

[8 ]Department of Virology and Experimental Therapy, Institute Aggeu Magalhaes, Oswaldo Cruz Foundation, Recife, Brazil.

[9 ]Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

[10 ]Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.

[11 ]Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil.

[12 ]Center of Mathematics, Computing and Cognition–Universidade Federal do ABC, São Paulo, Brazil.

[13 ]Oxford School of Global and Area Studies, Latin American Centre, University of Oxford, Oxford, UK.

[14 ]Vitalant Research Institute, San Francisco, CA, USA.

[15 ]University of California, San Francisco, CA, USA.

[16 ]MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.

[17 ]Instituto Gonçalo Moniz–Fundação Oswaldo Cruz (Fiocruz), Salvador, Brazil.

[18 ]Department of Zoology, University of Oxford, Oxford, UK.

[19 ]Institute for Applied Economic Research–Ipea, Brasília, Brazil.

Author notes

[*]

These authors contributed equally to this work.

[† ]Corresponding author. Email: sabinoec@ 123456usp.br (E.C.S.); nfaria@ 123456ic.ac.uk (N.R.F.)

Author information

Lewis F. Buss https://orcid.org/0000-0002-9009-9301

Carlos A. Prete Jr. https://orcid.org/0000-0002-3907-423X

Claudia M. M. Abrahim https://orcid.org/0000-0001-9597-9618

Alfredo Mendrone Jr. https://orcid.org/0000-0002-3090-4575

Tassila Salomon https://orcid.org/0000-0002-8123-3118

Cesar de Almeida-Neto https://orcid.org/0000-0002-8490-4634

Rafael F. O. França https://orcid.org/0000-0002-1846-6007

Maria C. Belotti https://orcid.org/0000-0001-5595-8775

Maria P. S. S. Carvalho https://orcid.org/0000-0002-3750-8110

Allyson G. Costa https://orcid.org/0000-0002-7312-6822

Myuki A. E. Crispim https://orcid.org/0000-0002-8553-8699

Suzete C. Ferreira https://orcid.org/0000-0002-4190-0238

Susie Gurzenda https://orcid.org/0000-0001-9210-3661

Charles Whittaker https://orcid.org/0000-0002-5003-2575

Pedro da Silva Peixoto https://orcid.org/0000-0003-2358-3221

Marcio K. Oikawa https://orcid.org/0000-0003-2416-1864

Anna S. Nishiya https://orcid.org/0000-0002-0623-1999

Vanderson Rocha https://orcid.org/0000-0003-0094-619X

Nanci A. Salles https://orcid.org/0000-0001-7580-4597

Andreza Aruska de Souza Santos https://orcid.org/0000-0003-3585-8683

Martirene A. da Silva https://orcid.org/0000-0002-4733-170X

Brian Custer https://orcid.org/0000-0001-6251-366X

Kris V. Parag https://orcid.org/0000-0002-7806-3605

Manoel Barral-Netto https://orcid.org/0000-0002-5823-7903

Moritz U. G. Kraemer https://orcid.org/0000-0001-8838-7147

Rafael H. M. Pereira https://orcid.org/0000-0003-2125-7465

Oliver G. Pybus https://orcid.org/0000-0002-8797-2667

Michael P. Busch https://orcid.org/0000-0002-1446-125X

Márcia C. Castro https://orcid.org/0000-0003-4606-2795

Christopher Dye https://orcid.org/0000-0002-2957-1793

Vítor H. Nascimento https://orcid.org/0000-0002-0543-4735

Nuno R. Faria https://orcid.org/0000-0001-8839-2798

Ester C. Sabino https://orcid.org/0000-0003-2623-5126

Article

Publisher ID: abe9728

DOI: 10.1126/science.abe9728

PMC ID: 7857406

PubMed ID: 33293339

SO-VID: 64a3712c-c505-48e2-bda6-cfff3c2ff14d

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 28 September 2020

Date accepted : 02 December 2020

Funding

Funded by: doi http://dx.doi.org/10.13039/501100000265, Medical Research Council;

Award ID: MR/S0195/1

Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo;

Award ID: 18/14389-0

Funded by: Itau Unibanco Todos pela Saude;

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Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

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Attack rate in Manaus

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Novel Coronavirus Disease COVID-19

Most cited references 28

Estimates of the severity of coronavirus disease 2019: a model-based analysis

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020

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