1. Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil
- Author
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Carlos Frederico Campelo de Albuquerque e Melo, Álvaro Salgado de Abreu, Italo Andrade Barbosa Lima, Helineide Ramos do Amaral, Zuinara Pereira Gusmão Maia, Melissa Barreto Falcão, Vagner Fonseca, Maricelia Lima Maia, Tatiana Maria Teodoro Rezende, André Luiz de Abreu, Paloma Viana Silva, Laís Ceschini Machado, Rivaldo Venâncio da Cunha, Mylena Ribeiro Pereira, Maria Aparecida Oliveira Lima, Stephane Tosta, Rafael F. O. França, Aline Sousa de Oliveira, Erenilde Marques de Cerqueira, Gabriel Luz Wallau, Marta Giovanetti, Daiana Carlos dos Santos, Nuno R. Faria, Felicidade Mota Pereira, Luiz Carlos Junior Alcantara, Siane Campos de Souza, Jaqueline Goes de Jesus, Mariana Carolina de Morais Sobral, and Joilson Xavier
- Subjects
Male ,RNA viruses ,0301 basic medicine ,Viral Diseases ,Epidemiology ,Pathology and Laboratory Medicine ,medicine.disease_cause ,Geographical locations ,Disease Outbreaks ,Database and Informatics Methods ,Monophyly ,0302 clinical medicine ,Residence Characteristics ,Genotype ,Medicine and Health Sciences ,Chikungunya ,Clade ,Phylogeny ,Data Management ,Genetics ,Chikungunya Virus ,Multidisciplinary ,Phylogenetic tree ,Phylogenetic Analysis ,Genomics ,Phylogenetics ,Infectious Diseases ,Medical Microbiology ,Arboviral Infections ,Viral Pathogens ,Viruses ,Medicine ,Female ,Pathogens ,Sequence Analysis ,Brazil ,Research Article ,Neglected Tropical Diseases ,Adult ,Computer and Information Sciences ,Lineage (genetic) ,Infectious Disease Control ,Bioinformatics ,Alphaviruses ,Science ,030231 tropical medicine ,Disease Surveillance ,Biology ,Research and Analysis Methods ,Microbiology ,Togaviruses ,Young Adult ,03 medical and health sciences ,medicine ,Humans ,Evolutionary Systematics ,Microbial Pathogens ,Taxonomy ,Evolutionary Biology ,Biology and life sciences ,Organisms ,Chikungunya Infection ,Computational Biology ,Outbreak ,South America ,Tropical Diseases ,Genome Analysis ,030104 developmental biology ,Social Class ,Infectious Disease Surveillance ,Chikungunya Fever ,People and places ,Sequence Alignment - Abstract
The chikungunya East/Central/South/Africa virus lineage (CHIKV-ECSA) was first detected in Brazil in the municipality of Feira de Santana (FS) by mid 2014. Following that, a large number of CHIKV cases have been notified in FS, which is the second-most populous city in Bahia state, northeastern Brazil, and plays an important role on the spread to other Brazilian states due to climate conditions and the abundance of competent vectors. To better understand CHIKV dynamics in Bahia state, we generated 5 complete genome sequences from a local outbreak raised in Serraria Brasil, a neighbourhood in FS, by next-generation sequencing using Illumina approach. Phylogenetic reconstructions revealed that the new FS genomes belongs to the ECSA genotype and falls within a single strongly supported monophyletic clade that includes other older CHIKV sequences from the same location, suggesting the persistence of the virus during distinct epidemic seasons. We also performed minor variants analysis and found a small number of SNPs per sample (b_29L and e_45SR = 16 SNPs, c_29SR = 29 and d_45PL and f_45FL = 21 SNPs). Out of the 93 SNPs found, 71 are synonymous, 21 are non-synonymous and one generated a stop codon. Although those mutations are not related to the increase of virus replication and/or infectivity, some SNPs were found in non-structural proteins which may have an effect on viral evasion from the mammal immunological system. These findings reinforce the needing of further studies on those variants and of continued genomic surveillance strategies to track viral adaptations and to monitor CHIKV epidemics for improved public health control.
- Published
- 2020