Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain

Abstract

A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at inter-host level. Four throat swab samples from COVID-19 infected patients were pooled, with RNA-Seq read retrieved from SRA NCBI to detect 21 SNPs and a replacement across the SARS-CoV-2 genomic population. Twenty-two RNA modification sites on viral transcripts were identified that may cause inter-host genetic diversity of this virus. In addition, the canonical genomic RNAs of N ORF showed higher expression in transcriptomic data and reverse transcriptase quantitative PCR compared to other SARS-CoV-2 ORFs, indicating the importance of this ORF in virus replication or other major functions in virus cycle. Phylogenetic and ancestral sequence analyses based on the entire genome revealed that SARS-CoV-2 is possibly derived from a recombination event between SARS-CoV and Bat SARS-like CoV. Ancestor analysis of the isolates from different locations including Iran suggest shared Chinese ancestry. These results propose the importance of potential inter-host level genetic variations to the evolution of SARS-COV-2, and the formation of viral quasi-species. The RNA modifications discovered in this study may cause amino acid sequence changes in polyprotein, spike protein, product of ORF8 and nucleocapsid (N) protein, suggesting further insights to understanding the functional impacts of mutations in the life cycle and pathogenicity of SARS-CoV-2.

New Insights Into the Physiopathology of COVID-19: SARS-CoV-2-Associated Gastrointestinal Illness

“…It is currently well-established that intrahost SARS-CoV-2 variability is frequent across the viral genome in COVID-19 patients ( 79 – 81 ). It was also reported that intrahost SARS-CoV-2 variability is higher in cancer patients compared to non-cancer counterparts ( 82 ).…”

A non-coding A-to-T Kozak site change related to the transmissibility of Alpha, Delta and Omicron VOCs

“…The mutations (g.a28271-, and g.gat28280cta) alter the Kozak sites of N and ORF9b, and may influence the translational efficiency of the two genes. Protein N has the highest translation rate(24,25) and its expression is associated with the replication of the genomic RNA(26). The product of ORF9b has an interferon (IFN) antagonistic activity and can suppress the IFN production(27).…”

Key Factors That Enable the Pandemic Potential of RNA Viruses and Inter-Species Transmission: A Systematic Review

“…Particularly, single nucleotide polymorphisms (SNP) profiles reveal that ORFs that codify for RdRp and S proteins, ORF8, and NP of SARS-CoV-2 have suffered mutations at the host level, evidencing a key point for changes related to transmissibility and virulence. Using high-throughput sequencing (HTS) and transcriptomics data from studies in humans infected with SARS-CoV-2, Ghorbani et al [ 29 ], defined a high-resolution map of the SNP hot spots of the SARS-CoV-2 in a viral population at the inter-host level showing that at least 22 sites have significant differences in mapped readings suggesting potential RNA modifications. The positions of the SNPs in the coding regions of the SARS-CoV-2 ORFs were located in RdRp ORF (14 SNP), S ORF (4 SNP), ORF8 (2 SNP), and N ORF (1 SNP).…”

“…More studies are needed to compare enough virus sequences from different geographic locations to better understand the intra-host behavior and selection pressure. The amount of modifications at NSP8 suggests that this could affect its replication rate and if crossing of the host barrier is allowed, its replication would be faster and more efficient [ 7 , 19 , 29 , 30 ]. It is reported that some of the most representative homoplasies in the genome of this virus are found at site 11.083 which comprises a region of ORF1a that encodes the non-structural protein Nsp6, and at site 21.575 that corresponds to the spike protein.…”

“…Thus, the monitoring of accessory genes should also be a priority during vaccine development. In the case of SARS-CoV-2, the ORF10 encoding a presumed ubiquitin ligase is the most expressed accessory gene in the virus [ 29 ]. In this sense, the participation of these accessory genes as key players in immune evasion is an important aspect to understand the specific response against the pathogen.…”