Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.
Joilson XavierLuiz AlcantaraVagner FonsecaMauricio LimaEmerson CastroHegger FritschCarla OliveiraNatalia GuimarãesTalita AdelinoMariane EvaristoEvandra S RodriguesElaine Vieira SantosDebora de La-RoqueLaise de MoraesStephane TostaAdelino NetoAlexander RosewellAna Flavia MendonçaAnderson LeiteAndreza VasconcelosArabela L Silva de MelloBergson VasconcelosCamila A MontalbanoCamila ZanlucaCarla FreitasCarlos F C de AlbuquerqueClaudia Nunes Duarte Dos SantosCleiton S SantosCliomar Alves Dos SantosCrhistinne C Maymone GonçalvesDalane TeixeiraDaniel F L NetoDiego CabralElaine C de OliveiraEthel L Noia MacielFelicidade Mota PereiraFelipe IaniFernanda P de CarvalhoGabriela AndradeGabriela BezerraGislene G de Castro LichsGlauco Carvalho PereiraHaline BarrosoHelena Cristina Ferreira FranzHivylla FerreiraIago GomesIrina N RiedigerIsabela RodriguesIsadora C de SiqueiraJacilane SilvaJairo Mendez RicoJaqueline LimaJayra AbrantesJean Phellipe M do NascimentoJudith N WasserheitJulia PastorJurandy J F de MagalhãesKleber Giovanni LuzLidio G Lima NetoLivia C V FrutuosoLuana Barbosa da SilvaLudmila SenaLuis Arthur F de SousaLuiz Augusto PereiraLuiz DemarchiMagaly C B CâmaraMarcela G AsteteMaria AlmironMaricelia LimaMarina C S Umaki ZardinMayra M PresibellaMelissa B FalcãoMichael GaleNaishe FreireNelson MarquesNoely F O de MouraPedro E Almeida Da SilvaPeter RabinowitzRivaldo V da CunhaKaren S TrintaRodrigo F do Carmo SaidRodrigo KatoRodrigo StabeliRonaldo de JesusRoselene Hans SantosSimone K HaddadSvetoslav N SlavovTamires AndradeThemis RochaThiago CarneiroVanessa NardyVinicius da SilvaWalterlene G CarvalhoWesley C Van VoorhisWildo N AraujoAna M B de FilippisMarta GiovanettiPublished in: medRxiv : the preprint server for health sciences (2023)
The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to the generation of 422 CHIKV genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These new genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersion dynamics of the CHIKV East-Central-South-African (ECSA) lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C>T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving CHIKV ECSA lineage genetic diversity in Brazil.