Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil.

Marcelo Henrique Santos Paiva,Michelle Da Silva Barros,Larissa Krokovsky,Gonzalo Bello,Luciane Caroline Albuquerque Bezerra,Paola Cristina Resende,Matheus Filgueira Bezerra,Alexandre Freitas Da Silva,Duschinka Ribeiro Duarte Guedes,Renata Pessôa Germano Mendes,Derciliano Lopes Da Cruz,Bruna Santos Lima Figueiredo De Sá,Constância Flávia Junqueira Ayres,Maria Almerice Lopes Da Silva,Luydson Richardson Silva Vasconcelos,Caroline Targino Alves Da Silva,Severino Jefferson Ribeiro Da Silva,Laís Ceschini Machado,Tiago Gräf,Kamila Gaudêncio Da Silva Sales,Wheverton Ricardo Correia Do Nascimento,Cássia Docena,Filipe Zimmer Dezordi,Sinval Pinto Brandão-Filho,Gabriel Luz Wallau,Claudio Eduardo Cavalcanti,Antônio Mauro Rezende ,Armando De Menezes-Neto ,Elisama Helvécio ,Rodrigo Moraes Loyo

doi:10.3390/v12121414

Abstract

Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling.

Highlights

Acute respiratory infection is caused by several viral pathogens such as influenza, rhinoviruses, and coronaviruses (CoV), that can infect the upper and lower respiratory tract of humans leading to compromised oxygenation and eventually multiple organ failure and death [1]
We found five clades supported by ultrafast bootstrap and/or TBE containing Pernambuco genomes mixed with sequences from other countries and six clades having more than 2 sequences from Pernambuco state alone (Table S6)
The genomic analysis of 101 SARS-CoV-2 genomes from the beginning of the epidemic at Pernambuco state, Brazil, revealed at least five independent international importation events of SARS-CoV-2 strains, that effectively seeded community transmission, occurred from late February to mid-April which is in line with studies focusing on other Brazilian states

Summary

Introduction

Acute respiratory infection is caused by several viral pathogens such as influenza, rhinoviruses, and coronaviruses (CoV), that can infect the upper and lower respiratory tract of humans leading to compromised oxygenation and eventually multiple organ failure and death [1]. SARS-CoV in 2002 and MERS-CoV, in 2012, spilled over to the human population affecting thousands of people, but these viruses were not well adapted to human-to-human transmission and the outbreaks came into control before massive human spread [2]. A few weeks later the genome of the etiological agent was sequenced and revealed a new coronavirus named SARS-CoV-2 [3]. Different from the SARS-CoV-1 and MERS-CoV, SARS-CoV-2 is well adapted to sustained human-to-human transmission. It is highly infectious, spreading through symptomatic and asymptomatic individuals [4]

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Results

Conclusion