Abstract:

Genomics technology, especially metagenomic sequencing, has played an important role in identifying and tracing unknown viruses. While classical methods in virus taxonomy rely on phenotypic traits, the metagenomics pipeline assembles new virus genomes from short nucleotide fragments without the need for any a priori reference sequences. This new technology increases the efficiency in identifying viruses and hosts associated with those viruses. This is particularly useful in identifying viruses that can cause epidemics. One current challenge in accomplishing this, is the ability to trace the original and intermediate viral hosts. To do this, a comprehensive virus sequence library characterized by definite host information is needed. Unfortunately, such information is still limited. As wild and stock animals are main sources for pathogenic viruses, an extensive survey of the global virome is vitally important to help identify and prevent zoonotic epidemics. This review summarizes the application of genomics technologies in the identification of viruses and the hosts associated with those viruses, using the outbreak of SARS-CoV-2 as an example. We also address intrinsic drawbacks of current methodologies as well as the incompleteness of available virus libraries. We propose the necessity and feasibility in constructing a comprehensive virus database with host association that emphasizes the diversity of viruses and their interactions with other organisms.

Key words: SARS-CoV-2, high-throughput sequencing, virus diversity, host association, virus evolution