Applications of Metagenomics in Vector Surveillance for Effective Prediction and Control of Mosquito-Borne Viral Disease Outbreaks

Monitoring biological vectors of disease is an indispensable public health and national security endeavor for tropical countries. Older protocols for surveillance involve tedious and resource-demanding programs, but low sequencing costs and advances in metagenomics have brought this within the reach of any country wishing to protect its citizens from emerging or introduced viral pathogens. Vector population density and distribution are usually insufficient for specific risk assessment because actual disease transmission rate is a complex function of the density of infected vectors /fecundity indices and environmental factors. A much bigger problem is that, while epidemiological surveillance systems designed to detect introduction of novel viruses exist, there are no systems that can predict epidemic risk based on pure entomological information. Coping with imported cases of Aedes-borne arboviruses like dengue virus (DENV), chikungunya virus (CHIKV), yellow fever virus (YFV), and Zika virus (ZIKV) presents a daunting challenge since current Nigerian mosquito control generally have limited experience with an Ae. aegypti-borne virus epidemics. The outbreak of ZIKV around the world from imported index cases illustrates the urgency of the need to create a flexible mosquito-arbovirus surveillance system that could be applied to any type of mosquito. Although general environmental baseline biology studies would yield information on prevalence of arthropod vectors in the community, individual mosquito lines surveillance programs will not allow for a rapid response to emerging cases from genetic drifts or imported vector communities. Moreover, a given mosquito genus like the Aedes spp. can transmit several arboviruses (yellow fever virus, ZIKV, and dengue virus), so vector population and distribution statistics are of limited use in tracking specific viral diseases if the viral density is not measured simultaneously. Different mosquito species like Ae aegypti, Ae africanus, and Ae albopictus can spread the ZIKV, emphasizing need for differential / community vector approach. The complex ecology of host range, climate interactions, and multiple transmission routes of these vectors and viruses underscore the vital need to develop a mosquito surveillance protocol that simultaneously identifies the mosquito and the arboviral symbiont using same environmental vector pool. Moreover, the unpredictable trend of zoonotic viral illnesses based on spontaneous mutations can only be mitigated by simple routine biotech surveillance. This chapter discusses viral disease surveillance and argues that it is critically important for countries in the tropics, especially Africa, to establish cutting-edge molecular surveillance systems that proactively capture the introduction or emergence of new virus diseases to its population. The benefits of such an endeavor far outweigh the costs. It has the potential to protect public health, agriculture and food security, and the environment. In an era of systematic release of genetically modified mosquitoes which could become host to unknown virobionts and or promote mutations in extant viruses, establishing such surveillance protocols should be among the highest public health and national security priority of any government.