The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection

Abstract

RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as –log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.

Genetic diversity of murine norovirus populations less susceptible to chlorine

“…Several mechanisms via which virus populations adapt to disinfection have been reported. The responses of virus populations, including rotavirus, echovirus 11, coxsackievirus B5, MS2 coliphage, and MNV to exposure to various disinfectants, such as chlorine dioxide, ultraviolet radiation, calcium hydroxide, and ozone, have been investigated ( Carratalà et al, 2017 ; Zhong et al, 2017a , b ; Torii et al, 2021 ; Kadoya et al, 2022 ; Oishi et al, 2022 ). A study found that MNV populations exhibited lower susceptibility to calcium hydroxide due to a specific mutation in the VP1 protein, which causes the substitution of lysine at position 345 with arginine ( Oishi et al, 2022 ).…”

“…The entire serial passage experiment of MNV was performed in duplicate (rounds 1 and 2) for each population to assess the reproducibility of the responses to chlorine ( Figure 1 ). Furthermore, as the susceptibility of the RNA virus population to disinfectants may differ, the virus population in each passage was analyzed separately for the first and second rounds ( Rachmadi et al, 2018 ; Kadoya et al, 2022 ; Oishi et al, 2022 ).…”

“…Site-specific nucleotide diversity was estimated using SNPGenie ( Nelson et al, 2015 ). π is the average number of pairwise differences per site in a population of sequences that was calculated using the following formula: where p is the site of polymorphism, Ni is the nucleotide difference proportion at the i th site, L is the sequence length, ki is the coverage of the sequence at the i th site, and Ai , Ci , Gi , and Ti are the sums of the four bases at the i th site ( Nei and Gojobori, 1986 ; Nelson et al, 2015 ; Kadoya et al, 2022 ). The nucleotide diversity in nonsynonymous and synonymous coding sites (π N and π S, respectively) was determined separately using the same formula as the nucleotide diversity.…”

“…Chlorination inactivates viruses by damaging their nucleic acids and proteins, which interfere with viral genome replication ( Qiao et al, 2022 ). The concentration of the disinfectant, exposure time, pH, temperature, and virus type are the essential factors determining the effectiveness of the disinfection ( Rachmadi et al, 2018 ; Lin et al, 2020 ; Kadoya et al, 2022 ; Oishi et al, 2022 ). Numerous studies have highlighted the variability in disinfection sensitivity among different virus types and even within specific serotypes and genotypes.…”

“…Consequently, RNA viruses can evolve rapidly and adapt to various environmental conditions. Certain genetic variations within the viral genome can cause resistance or reduce the sensitivity to disinfectants ( Kadoya et al, 2022 ; Oishi et al, 2022 ). However, the genetic characteristics that contribute to alterations in susceptibility to particular disinfectants are not understood.…”