Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo,
Department of Infectious Diseases and Parasitises and Institute of Tropical Medicine of the Faculty of Medicine of the University of São Paulo, São Paulo,

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European and Asian countries

Second wave, consistent with many remaining susceptible

Manaus, Brazil

Blood donors, 76% had been infected by October 2020

Also, estimated attack rates in Amazon Basin, 70%

Estimated SARS-CoV-2 attack rate in Manaus, above theoretical herd immunity threshold of 67%

(based on a reproduction number of 3)

But January 2021

Manaus hospital admissions, 3,431

(552 in Dec 1–19, 2020)

May to November, relaxation of control measures, low admissions for 7 months

There are at least four non-mutually exclusive possible explanations for the resurgence of COVID-19 in Manaus.

Why a resurgence of cases?

First factor, first wave overestimated

Attack rate could have been overestimated during the first wave

June, seroprevalence, 52·5%

Second factor, waning immunity

Waning of IgG antibody titres observed in blood donors

Most of the SARS-CoV-2 infections in Manaus occurred 7–8 months before resurgence in January, 2021

(No observed behaviour change in Manaus, reduced population mobility)

If resurgence in Manaus is due to waning, similar resurgence everywhere



Third factor, antigenic escape

New SARS-CoV-2 lineages

Circulating in Brazil, B.1.1.7 and P.1

P.1 detected in Manaus on Jan 12, 2021

P.1 lineage, accrued ten unique spike protein mutations,

Including E484K

P.2 lineage also detected Manaus

P.2 independently accrued the spike E484K mutation

In-vitro evidence that E484K mutation reduces neutralisation by polyclonal antibodies in convalescent sera

Antigenic escape

Fourth factor, increased transmissibility

SARS-CoV-2 lineages circulating in the second wave might have higher inherent transmissibility

Eg. Relative prevalence of P.1 lineage, up to 42% by December, 2020

P.1 lineage

Shares several independently acquired mutations

B.1.1.7 (N501)

B.1.325 (K417N/T, E484K, N501Y)

Conclusions

Variants need to be quickly investigated

Genetic, immunological, clinical, and epidemiological characteristics

Serological and genomic surveillance in Manaus is a priority

Determining vaccine is also crucial
Rapid sharing of lineage-specific frequencies underlying reinfection

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