Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

OVID-19 is a severe acute respiratory infection (SARI) that emerged in early December 2019 in Wuhan, China 1. The outbreak was declared a public health emergency of international concern by the World Health Organization on 30 January 2020. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an enveloped, single-stranded positive-sense RNA virus that belongs to the Betacoronavirus genus and Coronaviridae family 2. SARS-CoV-2 is closely related genetically to bat-derived SARS-like coronaviruses 3. Human-to-human transmission occurs primarily via respiratory droplets and direct contact, similar to human influenza viruses, SARS-CoV and Middle East respiratory syndrome coronavirus 4. The most commonly reported clinical symptoms are fever, dry cough, fatigue, dyspnoea, anosmia, ageusia, or some combination of these 1,4,5. As of 16 June 2020, more than 7.9 million cases have been confirmed worldwide, resulting in 434,796 deaths 6. Brazil declared COVID-19 a national public health emergency on 3 February 2020 7. After the development of a national emergency plan and the early establishment of molecular diagnostic facilities across Brazil's network of public health laboratories, the country reported its first confirmed COVID-19 case on 25 February 2020, in a traveller returning to São Paulo from northern Italy 8. São Paulo is the largest city in South America and no other Brazilian city receives a greater proportion of international flights 9. Currently, Brazil has one of the fastest-growing COVID-19 epidemics in the world, now accounting for 1,864,681 cases and 72,100 deaths, comprising over 55% of the total number of reported cases in Latin America and the Caribbean (as of 14 July 2020) 6. About 21% of Latin American and Caribbean populations are estimated to be at risk of severe COVID-19 illness 10. The region has been experiencing large outbreaks, with growing epidemics in Brazil,

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.One-Sentence SummaryWe report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

The family Hepeviridae includes enterically transmitted small quasi-enveloped or non-enveloped positive-sense single-stranded RNA viruses infecting mammals and birds (subfamily Orthohepevirinae) or fish (Parahepevirinae). Hepatitis E virus (genus Paslahepevirus) is responsible for self-limiting acute hepatitis in humans; the infection may become chronic in immunocompromised individuals and extrahepatic manifestations have been described. Avian hepatitis E virus (genus Avihepevirus) causes hepatitis–splenomegaly syndrome in chickens. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Hepeviridae, which is available at www.ictv.global/report/hepeviridae.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.