Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018.

Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.

Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas.

Since introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, although much is unknown about its circulation in the midwestern states. Here, we analyze 24 novel partial and near complete CHIKV genomes from Cuiaba, an urban metropolis located in the Brazilian midwestern state of Mato Grosso (MT). Nanopore technology was used for sequencing CHIKV complete genomes. Phylogenetic and epidemiological approaches were used to explore the recent spatio-temporal evolution and spread of the CHIKV-ECSA genotype in Midwest Brazil as well as in the Americas. Epidemiological data revealed a reduction in the number of reported cases over 2018-2020, likely as a consequence of a gradual accumulation of herd-immunity. Phylogeographic reconstructions revealed that at least two independent introductions of the ECSA lineage occurred in MT from a dispersion event originating in the northeastern region and suggest that the midwestern Brazilian region appears to have acted as a source of virus transmission towards Paraguay, a bordering South American country. Our results show a complex dynamic of transmission between epidemic seasons and suggest a possible role of Brazil as a source for international dispersion of the CHIKV-ECSA genotype to other countries in the Americas.