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

Abstract

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.

Identification and Molecular Characteristics of a Novel Single-Stranded RNA Virus Isolated from Culextritaeniorhynchus in China

“…The results also suggest that HMV2 strains from different geographical ranges may have originated from a common ancestor or may have genetically recombined in the same way. In addition, it had been suggested that some viruses infect hosts over wide geographic areas, possibly being introduced via being wind-blown, cyclonic action, or flying animals ( 13 ), and that HMV2 may have spread widely across different regions in this manner. Eventually, the exact mechanism of recombination evolution and the virus type of HMV2 could not be determined from these existing data, and in-depth studies need to be conducted to determine the origin and class of this virus.…”

“…At the same time, the development of metagenomic sequencing technology has promoted the detection and monitoring of mosquito viruses, thereby resulting in the discovery and research of a large number of new mosquito viruses, including Getah virus ( 12 ), Ross River virus ( 13 ), Banna orbivirus ( 14 ), and many others. This provided new insights into the complexity and diversity of the viruses that are carried by mosquitoes, and these had important implications for the dynamic surveillance of pathogens and the responses to emerging and reemerging infectious diseases ( 15 ).…”

Metavirome Analysis of Culex tritaeniorhynchus Reveals Novel Japanese Encephalitis Virus and Chikungunya Virus

“…Reagents together with methods used in RNA extraction and metaviral sequencing have been expounded in our previous study ( Feng et al, 2022 ). Moreover, the DNA barcodes employed in metaviral sequencing are displayed in Table 1 .…”

An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal

“…The West African phylogeny is deep-rooted in West Africa, with approximate inferred root in the 1960s, coinciding with the first recorded spillover from enzootic cycles 2 . Recently isolated detection in China has been described before 16 . In order to understand viral emergence and transmission dynamics of this novel clade in Senegal, we employed a Bayesian phylogenetic reconstruction approach.…”