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1.
Emerg Microbes Infect ; 9(1): 1824-1834, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-684732

ABSTRACT

The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country. To better understand the recent epidemic in the second most populous state in southeast Brazil - Minas Gerais (MG) - we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into MG. Epidemiological estimates of the reproductive number (R) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in R from the first reported case to the end of April 2020. The estimated date of SARS-CoV-2 introduction into Brazil was consistent with epidemiological data from the first case of a returned traveller from Lombardy, Italy. These findings highlight the nature of the COVID-19 epidemic in MG and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens..


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Genome, Viral , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Adult , Aged , Brazil/epidemiology , Female , Geography , Humans , Male , Middle Aged , Pandemics , Whole Genome Sequencing , Young Adult
2.
Pathog Glob Health ; 114(2): 64-67, 2020 03.
Article in English | MEDLINE | ID: covidwho-795

ABSTRACT

The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019-2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the Rhinolophus bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25th, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to Betacoronavirus. Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of Betacoronavirus among animals and Rhinolophus of the bat family.


Subject(s)
Betacoronavirus/genetics , Chiroptera/virology , Coronavirus Infections/genetics , Coronavirus/genetics , Evolution, Molecular , Genome, Viral , Phylogeny , Pneumonia, Viral/genetics , Animals , Bayes Theorem , China/epidemiology , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , DNA, Viral/genetics , Disease Outbreaks , Disease Reservoirs/virology , Global Health , Humans , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Sequence Analysis, Protein , Zoonoses/epidemiology , Zoonoses/genetics
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