Possible assistance of host microbiome in SARS-CoV-2 fitness

Patrick SLAMA
2020 Qeios  
T he COVID-19 outburst that has immobilized a large part of the world originated in late 2019. It was associated with a bat-carried SARS-like virus, SARS-CoV-2. Many features of the disease nevertheless leave physicians and hospitals puzzled with respect to known viral infections. One issue is the discontinuous detection of viral RNA among patients, as well as its differential detection in faeces with respect to respiratory tract samples. Discontinuous detection will raise problems when cities
more » ... oblems when cities and countries return to full activity, and already has in South Korea, where it was proposed that about one patient out of seven could become re-infected. A possible explanation for this proposed 're-infection' would be interactions of the virus with its host's microbiome. A possible rationale for the discontinuous detection of the virus [1] and its extended presence in faeces samples can be found exploring existing sequencing data [2] . In some RNA-seq analyses, bacteria from geni Prevotella and Veillonella are indeed present [3] , often in much more abundant amounts than SARS-CoV-2 RNA. Chakraborty recently suggested this could provide some explanations regarding the 're-infection' phenomena and discontinuous RNA detections [4] . Here we propose that an interaction between bacteria and the virus is indeed involved in the observed virulence, but not through the phage mechanism alluded to by Chakraborty, which seems unlikely owing to the known genetics of SARS-CoV-2. T he hypothesis that those, or other gut commensal bacteria, could increase the infectivity of the SARS-CoV-2 virus, is indeed supported by existing knowledge on a possible facilitation of viral infection by bacteria. In mouse, it was shown that animals with antibiotics-depleted gut flora were less susceptible to poliovirus disease, with poliovirus binding bacteria through their lipopolysaccharide molecules [5] . Co-infection of coronavirus PEDV with Chlamyidiaceae was also observed in cell cultures, with larger inclusions in co-infected cells [6] . In humans, coinfection by Epstein-Barr virus in Mycoplasma pneumoniae patients was recently shown Qeios, CC-BY 4.0 · Article,
doi:10.32388/05aapp fatcat:uxp4dsnjebglphxyedieagzy4q