The unexpected dynamics of COVID-19 in Manaus, Brazil: Was herd immunity achieved?
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Abstract
In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scale epidemic that collapsed the local health system, and resulted in extreme death rates. Several key studies reported that ∼76% of residents of Manaus were infected (attack rate AR≃76%) by October 2020, suggesting protective herd immunity had been reached. Despite this, in November an unexpected second wave of COVID-19 struck again, and proved to be larger than the first creating a catastrophe for the unprepared population. It has been suggested that this could only be possible if the second wave was driven by reinfections. Here we use novel methods to model the epidemic from mortality data, evaluate the impact of interventions, in order to provide an alternative explanation as to why the second wave appeared. The method fits a “flexible” reproductive number R 0 ( t ) that changes over the epidemic, and found AR≃30-34% by October 2020, for the first wave, which is far less than required for herd immunity, yet in-line with recent seroprevalence estimates. The two-strain model provides an accurate fit to observed epidemic datasets, and finds AR≃70% by March 2021. Using genomic data, the model estimates transmissibility of the new P.1 virus lineage, as 1.9 times as transmissible as the non-P1. The model thus provides a reasonable explanation for the two-wave dynamics in Manaus, without the need to rely on reinfections which until now have only been found in small numbers in recent surveillance efforts.
Significance
This paper explores the concept of herd immunity and approaches for assessing attack rate during the explosive outbreak of COVID-19 in the city of Manaus, Brazil. The event has been repeatedly used to exemplify the epidemiological dynamics of the disease and the phenomenon of herd immunity, as claimed to be achieved by the end of the first wave in October 2020. A novel modelling approach reconstructs these events, specifically in the presence of interventions. The analysis finds herd immunity was far from being attained, and thus a second wave was readily possible, as tragically occurred in reality. Based on genomic data, the multi-strain model gives insights on the new highly transmissible variant of concern P.1 and role of reinfection.
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SciScore for 10.1101/2021.02.18.21251809: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar …
SciScore for 10.1101/2021.02.18.21251809: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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