Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
Nuno Rodrigues FariaThomas A MellanCharles WhittakerIngra Morales ClaroDarlan da Silva CandidoSwapnil MishraMyuki A E CrispimFlávia Cristina Silva SalesIwona HawrylukJohn T McCroneRuben J G HulswitLucas Augusto Moysés FrancoMariana Severo RamundoJaqueline Góes de JesusPamela Dos Santos AndradeThaís de Moura ColettiGiulia M FerreiraCamila Alves Maia da SilvaErika Regina ManuliRafael Henrique Moraes PereiraPedro S PeixotoMoritz U G KraemerNelson Gaburo-JúniorCecilia da C CamiloHenrique H HoeltgebaumWilliam Marciel de SouzaEsmenia C RochaLeandro Menezes de SouzaMariana C de PinhoLeonardo José Tadeu de AraújoFrederico Scott Varella MaltaAline Brito de LimaJoice do Prado SilvaDanielle A G ZauliAlessandro C de S FerreiraRicardo P SchnekenbergDaniel J LaydonPatrick G T WalkerHannah M SchlüterAna L P Dos SantosMaria S VidalValentina S Del CaroRosinaldo M F FilhoHelem M Dos SantosRenato Santana de AguiarJosé Luis Proença ModenaBruce Walker NelsonJames A HayMélodie MonodXenia MiscouridouHelen CouplandRaphael SonabendMichaela A C VollmerAxel GandyCarlos A PreteVítor Heloiz NascimentoMarc A SuchardThomas A BowdenSergei L K PondChieh-Hsi WuOliver RatmannNeil M FergusonChristopher DyeNicholas James LomanPhilippe LemeyAndrew RambautNelson A FraijiMaria do P S S CarvalhoOliver George PybusSeth R FlaxmanSamir BhattEster Cerdeira SabinoPublished in: Science (New York, N.Y.) (2021)
Cases of severe acute respiratory syndrome coronavirus 2 (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 (angiotensin-converting enzyme 2) 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- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 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.