INFERRED RESOLUTION THROUGH HERD IMMMUNITY OF FIRST COVID-19 WAVE IN MANAUS, BRAZILIAN AMAZON
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Abstract
As in many other settings, peak excess mortality preceded the officially reported ‘first wave’ peak of the COVID-19 epidemic in Manaus, Brazil, reflecting delayed case recognition and limited initial access to diagnostic testing. To avoid early information bias, we used detailed age and gender stratified death certificate and hospitalisation data to evaluate the epidemic’s trajectory and infer the cause of its decline using a stochastic model. Our results are consistent with heterogenous transmission reducing over time due to the development of herd immunity. Relative to a baseline model that assumed homogenous mixing across Manaus, a model that permitted a small, self-isolated population fraction raised the estimated herd-immunity threshold from 28% to 30% and reduced the final attack rate from 86% to 65%. In the latter scenario, a substantial proportion of vulnerable, older individuals remained susceptible to infection. Given uncertainties regarding the distancing behaviours of population subgroups with different social and economic characteristics, and the duration of sterilising or transmission-modifying immunity in exposed individuals, we conclude that the potential for epidemic outbreaks remains, but that future waves of infection are likely to be much less pronounced than that already experienced.
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SciScore for 10.1101/2020.09.25.20201939: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.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: We detected the following sentences addressing limitations in the study:An important caveat is that estimated attack rates accumulate all infections and are agnostic to the presence or degree of symptoms. Severity of the clinical course of COVID-19 is associated with magnitude and persistence of the host immune response [27]. In consequence, our estimates of ‘exposure’ cannot be directly related to predicted …
SciScore for 10.1101/2020.09.25.20201939: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.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: We detected the following sentences addressing limitations in the study:An important caveat is that estimated attack rates accumulate all infections and are agnostic to the presence or degree of symptoms. Severity of the clinical course of COVID-19 is associated with magnitude and persistence of the host immune response [27]. In consequence, our estimates of ‘exposure’ cannot be directly related to predicted antibody seroprevalence at the end of the first wave [28]. It is reasonably anticipated that population immunity will wane over time, requiring robust memory responses [29] to prevent reinfection or modify the clinical course [30]. Our findings support emerging evidence that population heterogeneity of SARS-CoV-2 transmission, attributable to a range of biological and sociological factors, reduces the herd immunity threshold [24, 31, 32]. Reduction of superspreading events through constraints on mixing group sizes is concordant with genomic studies showing successive extinction of imported strains under the influence of social and mobility restrictions [33]. While future infection clusters and outbreaks remain possible in Manaus due to unexposed subgroups, population-level immunity will likely constrain widespread transmission unless immunity wanes. As in other settings, underlying vulnerability of older age groups may be further exacerbated over time by reduced health seeking behaviours of individuals with pre-existing and new medical conditions [34]. Social measures should be informed by understanding of key enablers of superspreading and a...
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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SciScore for 10.1101/2020.09.25.20201939: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.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.
About SciScore
SciScore …
SciScore for 10.1101/2020.09.25.20201939: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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