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Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.

ABSTRACT: The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus' rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. Our phylogenetic reconstructions indicated the circulation of the East-Central-South-African (ECSA) lineage in Rio de Janeiro. Time-measured phylogenetic analysis combined with CHIKV notified case numbers revealed the ECSA lineage was introduced in Rio de Janeiro around June 2015 (95% Bayesian credible interval: May to July 2015) indicating the virus was circulating unnoticed for 5 months before the first reports of CHIKV autochthonous transmissions in Rio de Janeiro, in November 2015. These findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases.

SUBMITTER: Xavier J

PROVIDER: S-EPMC6559644 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.

Xavier Joilson J Giovanetti Marta M Fonseca Vagner V Thézé Julien J Gräf Tiago T Fabri Allison A Goes de Jesus Jaqueline J Lima de Mendonça Marcos Cesar MC Damasceno Dos Santos Rodrigues Cintia C Mares-Guia Maria Angélica MA Cardoso Dos Santos Carolina C Fraga de Oliveira Tosta Stephane S Candido Darlan D Ribeiro Nogueira Rita Maria RM Luiz de Abreu André A Kleber Oliveira Wanderson W Campelo de Albuquerque Carlos F CF Chieppe Alexandre A de Oliveira Tulio T Brasil Patrícia P Calvet Guilherme G Carvalho Sequeira Patrícia P Rodrigues Faria Nuno N Bispo de Filippis Ana Maria AM Alcantara Luiz Carlos Junior LCJ

PloS one 20190611 6

The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus' rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real ...[more]

PMID: 31185030

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Project description:Chikungunya virus (CHIKV) is an arthropod-borne virus (arbovirus) transmitted by Aedes mosquitoes. The human infection usually manifests as a febrile and incapacitating arthritogenic illness, self-limiting and non-lethal. However, since 2013, CHIKV spreading through the tropics and to the Americas was accompanied by an increasing number of cases of atypical disease presentation, namely severe neuropathies and neonatal infection due to intrapartum vertical transmission. The pathophysiological mechanisms underlying these conditions have not been fully elucidated. However, arbovirus intrahost genetic diversity is thought to be linked to viral pathogenesis. To determine whether particular viral variants could be somehow associated, we analyzed the intrahost genetic diversity of CHIKV in three infected patients with neurological manifestations and three mothers infected during the intrapartum period, as well as their babies following vertical transmission. No statistically supported differences were observed for the genetic variability (nucleotide substitutions/gene length) along the genome between the groups. However, the newborn and cerebrospinal fluid samples (corresponding to virus passed through the placenta and/or the blood-brain barrier (BBB)) presented a different composition of their intrahost mutant ensembles compared to maternal or patient serum samples, even when concurrent. This finding could be consistent with the unidirectional virus transmission through these barriers, and the effect of selective bottlenecks during the transmission event. In addition, a higher proportion of defective variants (insertions/deletions and stop codons) was detected in the CSF and maternal samples and those were mainly distributed within the viral non-structural genes. Since defective viral genomes in RNA viruses are known to contribute to the outcome of acute viral infections and influence disease severity, their role in these atypical cases should be further investigated. Finally, with the in silico approach adopted, we detected no relevant non-conservative mutational pattern that could provide any hint of the pathophysiological mechanisms underlying these atypical cases. The present analysis represents a unique contribution to our understanding of the transmission events in these cases and generates hypotheses regarding underlying mechanisms, that can be explored further.

Dataset Information

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.

Publications

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.

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