Does adaptation to vertebrate codon usage relate to flavivirus emergence potential?

Abstract

Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher CAI towards the host has been associated with higher viral titers, we explored temporal trends of several historic and extensively sequenced zoonotic flaviviruses and relationships within the genus itself. To showcase evolutionary and epidemiological relationships associated with silent, adaptive synonymous changes of viruses, we used codon usage tables from human housekeeping and antiviral immune genes, as well as tables from arthropod vectors and vertebrate species involved in the flavivirus maintenance cycle. We argue that temporal trends of CAI changes could lead to a better understanding of zoonotic emergences, evolutionary dynamics, and host adaptation. CAI appears to help illustrate historically relevant trends of well-characterized viruses, in different viral species and genetic diversity within a single species. CAI can be a useful tool together with in vivo and in vitro kinetics, phylodynamics, and additional functional genomics studies to better understand species trafficking and viral emergence in a new host.

The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host

“…Expected values are calculated by counting the total number of synonymous codons for a given amino acid in the sequence divided by the number of existing codons that code for it. The codon usage frequencies of Rhinolophus affinis were retrieved from High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUT) database (Athey et al 2017 ), while codon usage table representing human house-keeping genes is described elsewhere (Paola et al 2018 ).…”

Origin of Canine Distemper Virus: Consolidating Evidence to Understand Potential Zoonoses

“…In RNA viruses, codon usage is under selection because the viruses are completely dependent on host tRNAs and the bias results from viruses matching the codon usage of their hosts (Jenkins and Holmes, 2003). Evolution can sometimes favor viruses that match their host codon usage to promote the replication speed and adaptation to the host as has been reported in other RNA viruses (Goni et al, 2012; Lauring et al, 2012; Di Paola et al, 2018; Freire et al, 2018).…”

Genetic Adaptations, Biases, and Evolutionary Analysis of Canine Distemper Virus Asia-4 Lineage in a Fatal Outbreak of Wild-Caught Civets in Thailand

“…Mutation pressure, the external environment, selective transcription, and natural selection are listed as factors that determine codon usage bias. As with other RNA viruses [58][59][60][61], CDV depends on the host susceptibility with respect to survival and transmission. Thus, the CDV codon usage pattern may interact with the virus' ability to infect, adapt, and escape from the host immune responses.…”