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

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.

Fig. 1. Abbott SARS-CoV-2 N IgG chemiluminescence assay performance and antibody dynamics in different clinical samples.

(A) Signal-to-cutoff (S/C) values using the Abbott chemiluminescence assay (CMIA) in the following clinical samples (from left to right): 821 routine blood donation samples from Manaus in February 2020, >1 month before the first notified case in the city; 49 samples collected at 20 to 33 days after symptom onset from SARS-CoV-2 PCR-positive patients in São Paulo requiring hospital care; 193 patients in São Paulo with PCR-confirmed symptomatic COVID-19 not requiring hospital care, with plasma donation samples taken in the early convalescent period; 107 samples from the same nonhospitalized plasma donor cohort from the late convalescent period; 133 samples that tested positive on either the Abbott CMIA or the Roche Elecsys assay out of 1000 routine blood donations collected in July 2020 and tested in parallel from the Fundação Pró-Sangue blood center (São Paulo). Upper dashed line denotes the manufacturer’s threshold for positive result of 1.4 S/C; lower dashed line denotes an alternative threshold of 0.4 S/C. In the box plots of Abbott IgG CMIA S/C, the central line is the median; upper and lower hinges are the 25th and 75th centiles, respectively; whiskers show the range, extending to a maximum of 1.5 times the interquartile range from the hinge. (B) S/C values of the Abbott CMIA for 104 convalescent plasma donors who were sampled at two different times. (C) Histogram of the slopes among 88 individuals shown in (B) who tested positive (>1.4 S/C) at the first time point. POS, post–onset of symptoms.

Fig. 2. Monthly antibody prevalence and signal-to-cutoff (S/C) reading in Manaus and São Paulo.

(A and C) SARS-CoV-2 antibody prevalence estimates in Manaus (A) and São Paulo (C) with a range of corrections, from left to right: reweighting positive tests, at positivity threshold of 1.4 S/C, to the age and sex distribution of each city; further correcting for sensitivity and specificity at this assay threshold; reweighting positive tests for age and sex at a reduced threshold of 0.4 S/C; correcting for sensitivity and specificity at this threshold; and finally correcting for seroreversion. Error bars are 95% confidence intervals. Gray bars are standardized daily mortality using confirmed COVID-19 deaths from the SIVEP-Gripe (Sistema de Informação de Vigilância Epidemiológica da Gripe; https://covid.saude.gov.br/) notification system and standardized by the direct method using the total projected Brazilian population for 2020 as reference. Black lines are rescaled cumulative deaths, such that the maximum is set to the maximum seroprevalence estimate for each city. Mortality data are plotted according to the date of death. (B and D) Distribution of S/C values over the nine monthly samples are shown for Manaus (B) and São Paulo (D). Each point represents the S/C reading for a single donation sample. Upper dashed line denotes the manufacturer’s threshold (1.4 S/C units); lower dashed line denotes an alternative threshold (0.4 S/C units); black box plots show the median (central lines), interquartile range (hinges), and range extending to 1.5 times the interquartile range from each hinge (whiskers) of S/C values above 0.4 (i.e., excluding very low and likely true-negative values).