Dataset Information

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

ABSTRACT: During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.

SUBMITTER: Lamarca AP

PROVIDER: S-EPMC9676039 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

Lamarca Alessandra Pavan AP de Almeida Luiz G P LGP Francisco Ronaldo da Silva RDS Cavalcante Liliane L Brustolini Otávio O Gerber Alexandra L AL Guimarães Ana Paula de C APC de Oliveira Thiago Henrique TH Dos Santos Nascimento Érica Ramos ÉR Policarpo Cintia C de Souza Isabelle Vasconcellos IV de Carvalho Erika Martins EM Ribeiro Mario Sergio MS Carvalho Silvia S Dias da Silva Flávio F de Oliveira Garcia Marcio Henrique MH de Souza Leandro Magalhães LM Da Silva Cristiane Gomes CG Ribeiro Caio Luiz Pereira CLP Cavalcanti Andréa Cony AC de Mello Claudia Maria Braga CMB Tanuri Amilcar A Vasconcelos Ana Tereza R de ATR

Microbial genomics 20220901 9

During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has i ...[more]

PMID: 36106981

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Project description:BackgroundHTLV-1/2 infection can cause severe and disabling diseases in children and adults. The aim of the study was to estimate the prevalence of HTLV-1/2 infection in pregnant women living in the metropolitan area of Rio de Janeiro.Methodology/principal findings1,204 pregnant women were tested upon hospital admission for delivery in two public hospitals in the cities of Rio de Janeiro and Mesquita, between November, 2012 and April, 2013. The samples were screened by chemiluminescent microparticle immunoassay (CMIA) and reactive ones were confirmed by Western blot (WB). Epi-info software was used for building the database and performing the statistical analysis. Eight patients had confirmed HTLV-1/2 infection (7 HTLV-1, one HTLV-2), equivalent to a prevalence rate of 0.66%. Two further reactive screening tests had negative Western blot results and therefore were considered negative in the statistical analysis. All HTLV-1/2-positive patients were born in Rio de Janeiro, most were non-Caucasian (87.5%), in a stable relationship (62.5%), had at least ten years of formal education (62.5%) and a monthly family income of up to US$600.00 (87.5%). There was only one case of coinfection with syphilis and none with HIV. The mean age of the infected women was 28.4 (SD = 6.3) years and of the seronegative ones was 24.8 (SD = 6.5) (p = 0.10). The median number of pregnancies were 3.0 and 1.0 (p = 0.06) and the median number of sexual partners were 3.5 and 3.0 (p = 0.33) in the seropositive and negative groups, respectively. There were no statistically significant differences between the groups.Conclusions/significanceA significant prevalence of HTLV-1/2 was found in our population. The socio-epidemiological profile of carrier mothers was similar to the controls. Such findings expose the need for a public health policy of routine HTLV-1/2 screening in antenatal care, since counselling and preventive measures are the only strategies currently available to interrupt the chain of transmission and the future development of HTLV-1/2-related diseases.

Dataset Information

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

Publications

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

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