Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade

Front. Cell. Infect. Microbiol.

et al. 2022

We collected 5,500 mosquitoes belonging to six species in three locations in China. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The affluent viral sequences that were detected and annotated belong to 22 viral taxonomic families. Then, PCR was performed to confirm the results, followed by phylogenetic analysis. Herein, part of mosquito virome was identified, including chikungunya virus (CHIKV), Getah virus (GETV), and Ross river virus (RRV). After metagenomic analysis, seven CHIKV sequences were verified by PCR amplification, among which CHIKV-China/YN2018-1 had the highest homology with the CHIKV isolated in Senegal, 1983, with a nucleotide (nt) identity of at least 81%, belonging to genotype West Africa viral genes. Five GETV sequences were identified, which had a high homology with the GETV sequences isolated from Equus caballus in Japan, 1978, with a (nt) identity of at least 97%. The newly isolated virus CHIKV-China/YN2018-1 became more infectious after passage of the BHK-21 cell line to the Vero cell line. The newly identified RRV gene had the highest homology with the 2006 RRV isolate from Australia, with a (nt) identity of at least 94%. In addition, numerous known and unknown viruses have also been detected in mosquitoes from Yunnan province, China, and propagation tests will be carried out.

Section: Discussionmentioning

confidence: 76%

Metagenomic Analysis of Togaviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes from Chikungunya and Ross River Viruses

Feng

Front. Cell. Infect. Microbiol.

et al. 2022

“…The E2-L248F from clade I has been reported in Asian lineage sequences from Colombia (2014-2015) and Philippines (2012) 45,46 . Isolates from Thailand, Indonesia, Lao PDR, Cameroon and India also presented the 6K-I54V mutation observed in clade I 44,47–50 . Despite the detection of these mutations in different countries (indicating homoplasy) by other previous studies, there is no information about the functional impact of such substitutions on CHIKV fitness, thus warranting further experimental studies to elucidate the potential effects of SNVs on lineage-specific evolutionary adaptation.…”

Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 92%

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil

Xavier

Alcântara

Fonseca

et al. 2023

Preprint

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.

“…Further sequence alignment results showed that E1 gene mutations in CHIKV-China/P2020-1 were identified in both 5th and 10th generations: mutation from A (alanine) to V (valine) at 226 aa, which had the same type and site. Research indicated that the E1-A226V mutation at position 226 in the E1 protein can considerably enhance the adaptability of CHIKV to Aedes albopictus ( Agbodzi et al., 2021 ). Our subsequent study demonstrated that the viral titers of the 5th and 10th generations in Vero cells were markedly higher than those in BHK-21 cells, revealing that interspecies transmission can make CHIKV more contagious, thus increasing the threat to human health.…”

Section: Discussionmentioning

confidence: 99%

Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome

Zheng

Front. Cell. Infect. Microbiol.

et al. 2022

Swab samples were collected from 34 pangolins in Guangxi Province, China. Metavirome sequencing and bioinformatics approaches were undertaken to determine the abundant viral sequences in the viromes. The results showed that the viral sequences belong to 24 virus taxonomic families. To verify the results, PCR combined with phylogenetic analysis was conducted. Some viral sequences including Japanese encephalitis virus (JEV), Getah virus (GETV), and chikungunya virus (CHIKV) were detected. On the basis of the metavirome analysis, seven segments belonging to JEV were further identified through PCR amplification. Sequence comparison showed that, among seven sequences, JEV-China/P2020E-1 displayed the highest nucleotide (80.6%), with the JEV isolated in South Korea, 1988, and all of which belonging to genotype III. Seven CHIKV sequences were detected, with the highest homology (80.6%) to the Aedes africanus in Côte d’Ivoire, 1993. Moreover, passage from BHK-21 to Vero cells makes the newly isolated CHIKV-China/P2020-1 more contagious. In addition, the newly verified GETV sequences shared 86.4% identity with the 1955 GETV isolated from Malaysia. Some sudden and recurrent viruses have also been observed from the virome of pangolin in Guangxi Province, China; hence, dissemination tests will be implemented in the future.