Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region, China

Abstract

Background Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently. Methods Mosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes. Results A total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes. Conclusion Viral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.

Virome in adult Aedes albopictus captured during different seasons in Guangzhou City, China

“…Viruses in Aedes , Culex , Anopheles , and Armigeres mosquitoes have been revealed using these methods. Some known viruses have been detected, such as DENV, ZIKV, and West Nile virus [ 39 – 43 ]. Novel viruses such as the Cuacua virus in Mansonia mosquitoes and the novel orbivirus in Culex fatigans mosquitoes have also been detected [ 37 , 44 ].…”

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland

“…Metagenomics studies published in recent years have identified diverse viromes in mosquitoes from around the world [ 31 , 34 , 37 , 43 , 45 , 66 , 90 , 107 , 108 , 109 , 110 , 111 , 112 ].These viromes appear to differ between species and can include anywhere from tens to hundreds of different virus species in a given sample, which often comprises several individuals of a species [ 31 , 34 , 37 , 43 , 45 , 66 , 90 , 107 , 108 , 109 , 110 , 111 , 112 ]. The nearest comparable study to Finland is a single-year, two-location study of 953 specimens of six mosquito species in Sweden [ 90 ].…”

Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?

“…In the case of viral communities in insects, even recently there was a "biased" conception of viruses as agents that cause disease; however, today, with the advances in metagenomics studies, the proper structural and functional diversity of insect viromes has begun to be elucidated [104][105][106]. Thus, metagenomics methods, especially during the last decade, have provided new insights into the complexity of insect-borne viruses [41,[107][108][109], relevant for active pathogen surveillance and response to emerging and reemerging infectious diseases [37,103,110,111].…”