Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings - SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiology - Virological

https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586

Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings

Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings

Nuno R. Faria^1,2,3, Ingra Morales Claro^3,4, Darlan Candido^2,3, Lucas A. Moyses Franco^3,4, Pamela S. Andrade^3,4, Thais M. Coletti^3,4, Camila A. M. Silva^3,4, Flavia C. Sales^3,4, Erika R. Manuli^3,4, Renato S. Aguiar⁵, Nelson Gaburo⁶, Cecília da C. Camilo⁷, Nelson A. Fraiji⁸, Myuki A. Esashika Crispim⁸, Maria do Perpétuo S. S. Carvalho⁸, Andrew Rambaut⁹, Nick Loman¹⁰, Oliver G. Pybus², Ester C. Sabino^3,4, on behalf of CADDE Genomic Network¹¹

1. MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom.
2. Department of Zoology, University of Oxford, Oxford, United Kingdom.
3. Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
4. Department of Infectious Disease, School of Medicine, University of São Paulo, São Paulo, Brazil.
5. Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
6. DB Diagnósticos do Brasil, São Paulo, Brazil.
7. CDL Laboratório Santos e Vidal Ltda., Manaus, Brazil.
8. HEMOAM, Fundação de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.
9. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
10. Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
11. https://www.caddecentre.org/ 44

Summary
We have detected a new variant circulating in December in Manaus, Amazonas state, north Brazil, where very high attack rates have been estimated previously. The new lineage, named P.1 (descendent of B.1.1.28), contains a unique constellation of lineage defining mutations, including several mutations of known biological importance such as E484K, K417T, and N501Y. Importantly, the P.1 lineage was identified in 42% (13 out of 31) RT-PCR positive samples collected between 15 to 23 December, but it was absent in 26 publicly available genome surveillance samples collected in Manaus between March to November 2020. These findings indicate local transmission and possibly recent increase in the frequency of a new lineage from the Amazon region. The higher diversity and the earlier sampling dates of P.1. in Manaus corroborates the travel info of recently detected cases in Japan, suggesting the direction of travel was Manaus to Japan. The recent emergence of variants with multiple shared mutations in spike raises concern about convergent evolution to a new phenotype, potentially associated with an increase in transmissibility or propensity for re-infection of individuals.