Genetic Similarity and Differences of MERS-CoV and SARS-CoV-2 in Saudi Arabia: Implications for Detection

Abstract

Members of Coronavirdiae, including Middle East Respiratory Syndrome coronavirus (MERS-CoV) and Severe Acute Respiratory Syndromesevere coronavirus 2 (SARS-CoV-2), exert a negative impact on animal and human health in Saudia Arabia. Hence, this study is aimed to reveal the genetic affinities and intricate microbiome dynamics of both viruses within the Saudi Arabian context whilst concurrently crafting specific primers for their detection. Nasopharyngeal swab samples from 2016 to 2020 for MERS-CoV, and from 2020 to 2021 for SARS-CoV-2, were collected, following Saudi Arabia's stringent biosafety and biosecurity protocols. Utilising a methodology that integrated state-of-the-art sequencing techniques, human nasopharyngeal swab samples from 2016 to 2020 for MERS-CoV, and from 2020 to 2021 for SARS-CoV-2, were collected. Samples were analysed using Illumina sequencing for genetic homology and mutation analysis, and sequence-independent, single-primer-amplification nanopore sequencing for exhaustive background microbiome analysis, were seamlessly integrated. The genomic profiles of viruses recovered from Saudi Arabian patients were then exhaustively compared to the earliest genomes that are used in the study. This study successfully utilized Sequence-Independent, Single-Primer Amplification (SISPA) with Nanopore sequencing at Liverpool University to identify the background microbiome associated with MERS-CoV (2016–2020) and SARS-CoV-2 (2020–2021) in Saudi Arabia. These findings provide insights into the composition and structure of the microbiome associated with these viral infections, enhancing our understanding of the microbial environment present during these outbreaks. The analysis also underscored the disparities between the earliest genomes that are used in the study of MERS-CoV (NC_019843) and the collected MERS-CoV samples from 2016 to 2020, which included two samples each year labelled P1 and P2. Additionally, sequences from GenBank from MERS-CoV from 2016 to 2019, which are KX154693, KX154692, MH310912, MH310911, MK462256, MK462255, MN365233, and MN365232, were incorporated. These sequences exhibited a conserved E gene. Similarly, the earliest genomes that are used in the study of SARS-CoV-2 (NC_045512) and the collected SARS-CoV-2 samples from 2020 to 2021, which included two samples each year labelled P1 and P2, included the SARS-CoV-2 variants from GenBank: MW837147, MW837148, OV054768 (B.1.1.7), OX008586 (B.1.351), OX000832 (P.1), OX014251 (B.1.617.2), and OW996240 (B.1.1.529). The E gene remained conserved in these variants. Notably, the conserved genes S, N, and ORF1ab were analysed between the earliest genomes that are used in the study of SARS-CoV- 2 (NC_045512) and its variants from GenBank (MW837147, MW837148, OV054768 [B.1.1.7], OX008586 [B.1.351], OX000832 [P.1], OX014251 [B.1.617.2], OW996240 [B.1.1.529]), alongside samples of MERS-CoV collected two samples each year from 2016 to 2020. Genetic homology percentages were determined between these MERS-CoV samples, and the SARS-CoV-2 the earliest genomes that are used in the study and variants: NC_045512 (51%), SARS-CoV 2020 P1,P2 (51%), SARS-CoV 2020 P1,P2 (51%), OV054768 (B.1.1.7) (51%), OX008586 (B.1.351) (54%), OX000832 (P.1) (54%), OX014251 (B.1.617.2) (52%), and OW996240 (B.1.1.529) (53%). This study provides insights into the genetic homology and the microbiome context, advocating for the efficiency of specialized multiplex coronavirus primers and probes for precise detection. These findings substantially enhance the current understanding of these viruses and their variants, underscoring the imperative need for sustained research in the domain of viral genomics.