The unexpected dynamics of COVID-19 in Manaus, Brazil: Was herd immunity achieved?

Abstract

The arrival of SARS-COV-2 in late March 2020 in the state of Amazonas, Brazil, captured worldwide attention and concern. The rapid growth of the epidemic, a health system that had collapsed, and mass gravesites for coping with growing numbers of dead, were broadcast by the media around the world. Moreover, a majority of the local Amazonian indigenous communities were physically distant from appropriate medical services, to the point where warnings of genocide were issued. In a recent Science paper (December 2020), Buss et al. reported that some 76% of the residents of the city of Manaus, the capital of Amazonas, had been infected by October 2020. This estimate of the COVID-19 attack rate was based on a seroprevalence analysis of blood donor data, which despite its shortcomings was thought to be a sufficiently reliable proxy of the larger population. An attack rate of this magnitude (76%) implied that herd immunity had already been reached and the community was relatively protected from further infection. Yet in December 2020, a harsh second wave of COVID-19 struck Manaus, and currently appears to be even larger than the first wave. Here we use mathematical modelling of mortality data in Manaus, and in various states of Brazil, to understand why a second wave appeared against all expectations. Our analysis is based on estimating a "flexible" reproductive number R_0 (t) from the mortality data, as it changes in time over the epidemic.

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

“…Another hypothesis is that the SARS-CoV-2 attack rate in Manaus was overestimated. Our study supports that a drastic reduction in median Re (from 2.1-2.6 to around April-May 2020, consistent with independent epidemiological modeling studies 10,11 , coinciding with the timing of implementation of nonpharmaceutical interventions (NPI) that effectively increased social distancing. Although those NPIs were not sufficiently stringent to consistently reduce Re to <1.0, they maintained a stationary state of low endemic viral community transmission from May to September 2020 (refs.…”

“…Although those NPIs were not sufficiently stringent to consistently reduce Re to <1.0, they maintained a stationary state of low endemic viral community transmission from May to September 2020 (refs. 10,11 ). These findings support that the NPIs implemented in Amazonas brought the first epidemic wave under relative control before herd immunity became established, and were sufficiently effective to provide population 'herd protection' until December 2020 (ref.…”

“…These findings support that the NPIs implemented in Amazonas brought the first epidemic wave under relative control before herd immunity became established, and were sufficiently effective to provide population 'herd protection' until December 2020 (ref. 11 ). Mitigation measures were relaxed from September 2020 onwards, and the Re of clade 28-AM-I returned to >1.0.…”

COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1

“…A drastic reduction in the median Re (from 2.1-2.6 to 0.9-1.0) for Amazonian lineages B.1.195 and B.1.1.28 around April-May 2020, was reconstructed in our analysis. This is entirely consistent with the epidemic trajectories estimated from epidemiological modeling 7,8 and further coincides with the timing of implementation of NPIs that effectively increased social distancing in Amazonas. This evidence indicates that the rst epidemic wave in Amazonas was brought under relative control by the implementation of NPIs, before herd-immunity.…”

“…This evidence indicates that the rst epidemic wave in Amazonas was brought under relative control by the implementation of NPIs, before herd-immunity. Our results also con rm that NPIs were not stringent enough to consistently reduce the Re of SARS-CoV-2 Amazonian lineages to below 1.0 and that a stationary state of endemic community transmission was maintained from May to September 2020 7,8 . September 2020 onwards, mitigation measures were relaxed, and the Re of clade 28-AM-I returned to above 1.0.…”