Co-circulation of Chikungunya virus, Zika virus, and serotype 1 of Dengue virus in Western Bahia, Brazil

Abstract

Chikungunya, mayaro, dengue, zika, and yellow fever are mosquito-borne viral diseases caused, respectively, by Chikungunya virus, Mayaro virus (CHIKV and MAYV, respectively: Togaviridae: Alphavirus), Dengue virus, Zika virus, and Yellow fever virus (DENV, ZIKV, and YFV, respectively: Flaviviridae: Flavivirus). These viruses have an important epidemiological impact worldwide, especially in Brazil. Western Bahia is one of the less studied regions in that country regarding the circulation of these pathogens. In this study, we aimed to apply molecular biology assays to better know the mosquito-borne viruses circulating in Barreiras and Luís Eduardo Magalhães, two main cities of Western Bahia. From March to June 2021, we enrolled 98 patients with the clinical diagnosis of dengue. Personal information (gender and age) were retrieved at the moment of enrollment. Serum samples were obtained from volunteers and used in molecular detection of CHIKV, MAYV, DENV, ZIKV, and YFV by reverse transcription followed by real-time polymerase chain reaction as well as in genome sequencing aiming phylogenetic analysis. As the main result, we found that from the 98 patients 45 were infected by CHIKV, 32 were infected by serotype 1 of DENV (DENV-1) and six were infected by ZIKV, while 15 were negative for all arboviruses tested. In addition, phylogenetic analysis revealed that all CHIKV-positive samples were of the East/Central/South African (ECSA) genotype, while all DENV-1-positive samples were of the V genotype. These results clearly show that epidemiological surveillance cannot be based only on clinical evaluations. Laboratory diagnosis is important in arbovirus infection that are prevalent in a particular area. These findings also demonstrate the co-circulation of many arboviruses in Western Bahia in 2021.

Keywords: RT-PCR; Western Bahia; arbovirus; co-circulation; phylogeny.

Figure 1

Representation of the Brazilian territory as a map. Borders of Brazilian states are shown. Bahia (BA) state is highlighted in red. The neighbor states of Sergipe (SE), Alagoas (AL), Pernambuco (PE), Piauí (PI), Maranhão (MA), Tocantins (TO), Goiás (GO), Minas Gerais (MG), and Espírito Santo (ES) are indicated. Barreiras and Luís Eduardo Magalhães cities are indicated in the Western Bahia.

Figure 2

Phylogenetic analysis of CHIKV, based on partial sequences of the E1-3’UTR (untranslated) region. The phylogenetic tree was constructed using the maximum likelihood method with a bootstrap of 1,000 replicates. The dataset consisted of 32 CHIKV nucleotide sequences with: West African genotype (n = 06), Asian genotype (n = 06), ECSA genotype (n = 11) and the sequences generated in this study (n = 9). All sequences retrieved from NCBI are identified in the format: accession number/country/year of isolation. Sequences generated in this study are identified according to its internal number and country of isolation (blue dots). The bootstrap values are very similar to the isolates from southeastern Brazil, being grouped with the isolates from Rio de Janeiro. It is thus inferred that these isolates belong to the ECSA lineage, the isolates from Bahia (2020–2021) form a monophyletic group with high support value, indicating that they had the same evolutionary origin.

Figure 3

Phylogenetic analysis of DENV-1, based on a fragment of the E protein coding sequence. The phylogenetic tree was built using the maximum likelihood method with bootstrap of 1000 replicates. The five DENV-1 isolates generated in the study were aligned to 29 global reference sequences. All sequences retrieved from NCBI are identified in the format: accession number/ country/ year of isolation. Brazilian sequences: BR (Brazil), followed by the acronym of the Brazilian state. Regarding sequences generated in this study: four isolates (red dots, above) are closely related to other strains isolated in the Federal District (DF) and São Paulo (SP), in 2019. In addition, one isolate (red ball, below) is related to strains isolated in the state of Alagoas (AL), in 2019 and Amapá (AP), in 2015 (AP).