Evidence for a role of phenotypic mutations in virus adaptation

Abstract

Phage adapts to a host modified to hinder the essential recruitment of a host protein No genetic mutations are fixed at the engineered virus-host interaction interface Adaptation is likely linked to phenotypic mutations caused by transcription errors Sub-genomic RNAs may enable this kind of adaptation mechanism in coronaviruses

A protocol to study bacteriophage adaptation to new hosts

“…In addition, a final step including DNA extraction allows for new generation sequencing of viral genome. Figure adapted from Luzon-Hidalgo et al., 2021 . …”

“…A control experiment where wild type T7 inoculates the original host is also shown (black). Figure taken from Luzon-Hidalgo et al., 2021 . Note: Results presented in Figure 5 B for two laboratory evolution experiments demonstrate host promiscuity of evolved T7 but they do not provide experimental evidence regarding the efficiency of virus replication.…”

“…To address this question, in Luzón-Hidalgo et al. 2021 , we have carried out a number of rounds of adaptation of T7 to the engineered host with an ancestral thioredoxin that shares only 57% of its sequence with E. coli thioredoxin, its natural proviral factor, and which hinders virus replication around 6–7 orders of magnitude.…”

“…Our protocol includes steps of phage amplification, plaque and liquid lysis assays, and DNA extraction for next-generation sequencing of the viral genome over several rounds of laboratory evolution thus allowing the investigation of the sequence determinants of viral adaptation. For complete information on the generation and use of this protocol, please refer to Luzon-Hidalgo et al. (2021) .…”

“…For complete information on the generation and use of this protocol, please refer to Luzon-Hidalgo et al. (2021) .…”