Host-dependent editing of SARS-CoV-2 in COVID-19 patients

Abstract

A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.

Commentary on “Poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2”

“…We agree that this can be further optimized and, indeed, subsequent studies proposed more refined approaches to reduce the number of false positive calls (e.g., (Picardi and Mansi 2022 )). It is indeed reassuring that different pipelines converged to the same conclusions (Di Giorgio et al 2020 ; Farkas et al 2020 ; Popa et al 2020 ; Wang et al 2021 ; Graudenzi et al 2021 ; Gregori et al 2021 ; Lythgoe et al 2021 ; Pathak et al 2021 ; Song et al 2021 ; Tonkin-Hill et al 2021 ; Voloch et al 2021 ). While we agree that the mutational spectrum is not significantly affected by the filters reanalyzed by Zong et al ( 2022 ), these filters were nonetheless necessary to avoid introducing bias in the estimation of the allelic fraction of the observed changes.…”

“…We agree that this can be further optimized and, indeed, subsequent studies proposed more refined approaches to reduce the number of false positive calls (e.g., (Picardi and Mansi 2022 )). It is indeed reassuring that different pipelines converged to the same conclusions (Di Giorgio et al 2020 ; Farkas et al 2020 ; Popa et al 2020 ; Wang et al 2021 ; Graudenzi et al 2021 ; Gregori et al 2021 ; Lythgoe et al 2021 ; Pathak et al 2021 ; Song et al 2021 ; Tonkin-Hill et al 2021 ; Voloch et al 2021 ).…”

“…We and others have hypothesized that the genetic information of the SARS-CoV-2 could be affected by the cellular RNA editing machinery based on the ADAR and APOBEC proteins. The hypothesis originates from two observations: (a) several viral genomes show mutational patterns that could be ascribed to the activity of host deaminases (Cattaneo et al 1988 ; Vartanian et al 1991 ; Harris et al 2003 ; Mahieux et al 2005 ; Noguchi et al 2005 ; Taylor et al 2005 ; Zahn et al 2007 ; Phuphuakrat et al 2008 ; Vartanian 2008 ; Carpenter et al 2009 ; Doria et al 2009 , 2011 ; George et al 2009 ; Clerzius et al 2011 ; Pfaller et al 2011 ; Suspene et al 2011 ; Samuel 2012 ; Cuevas et al 2015 ; Tomaselli et al 2015 ; Peretti et al 2018 ; Rosani et al 2019 )—this has been confirmed experimentally in several cases—and (b) there is an excess of transition changes occurring both at the intra-host (Di Giorgio et al 2020 ; Farkas et al 2020 ; Popa et al 2020 ; Wang et al 2021 ; Graudenzi et al 2021 ; Gregori et al 2021 ; Lythgoe et al 2021 ; Song et al 2021 ; Tonkin-Hill et al 2021 ; Voloch et al 2021 ; Picardi and Mansi 2022 ) and inter-host scale (Simmonds 2020 ; van Dorp et al 2020 ; Jacob-Hirsch et al 2020 ; Klimczak et al 2020 ; Kosuge et al 2020 ; Mourier et al 2020 ; Popa et al 2020 ; Azgari et al 2021 ; Deng et al 2021 ; Rice et al 2021 ; Sadykov et al 2021 ; Simmonds and Azim Ansari 2021 ; Tasakis et al 2021 ; Matyášek et al 2021 ; Pang et al 2021 ; Ramazzotti et al 2021 ). Such excess is not explainable with the known mutational pattern introduced by the RNA-dependent RNA polymerase or by the SARS-CoV-2 proofreading machinery (Smith et al 2013 ; Kabinger et al…”

“…With this aim, our expectations were quite clear: if RNA editing by ADARs and/or APOBECs plays a role in intra-host diversification of the virus; A > G / T > C and C > T / G > A substitutions should outnumber all other types. This is quite evident from the mutational patterns observed, both in our and in other follow-up analyses (Farkas et al 2020 ; Simmonds 2020 ; van Dorp et al 2020 ; Klimczak et al 2020 ; Kosuge et al 2020 ; Azgari et al 2021 ; Pathak et al 2021 ; Ramazzotti et al 2021 ; Rice et al 2021 ; Sadykov et al 2021 ; Simmonds and Azim Ansari 2021 ; Song et al 2021 ; Tasakis et al 2021 ; Tonkin-Hill et al 2021 ; Friedman et al 2021 ; Voloch et al 2021 ; Wang et al 2021 ; Graudenzi et al 2021 ; Gregori et al 2021 ; Lythgoe et al 2021 ; Matyášek et al 2021 ; Pang et al 2021 ; Picardi and Mansi 2022 ). Furthermore, even though the intra-host single-nucleotide polymorphism (SNV) pattern might be questionable due to sequencing errors, we observed a similar enrichment also in inter-host SNVs from SARS-CoV-2 genomic sequences, which has been confirmed by further studies, including those using more refined approaches (i.e., mutational signatures (Popa et al 2020 ; Graudenzi et al 2021 ).…”

Next-Generation Sequencing for Confronting Virus Pandemics

“…As an example, Hepatitis delta virus uses an ADAR-1 editing mechanism to create the large and short isoforms of the hepatitis delta antigen, both of which are necessary to complete its replication cycle [ 119 ]. In the case of SARS-CoV-2, analysis by NGS of its spike gene [ 120 ] showed that ADAR1 editing was the predominant mechanism generating SARS-CoV-2 genetic variability, although a pattern of nucleotide substitutions suggestive of the ADAR-1 activity was detected only in a small fraction of replicating genomes. However, it seems that the mutations produced by this enzyme were not fixed in the infected human population, suggesting that, by now, nsp12-induced mutations occurring in patients with high viremia and persistent infection would be the main source of new SARS-CoV-2 variants, while those produced by ADAR1 may play an antiviral role [ 120 ].…”