A retrospective whole genome sequencing of SARS-CoV-2 isolate from respiratory sample of an individual from Ota – Ogun State, Nigeria

• Published in: Gene reports Vol. 37; p. 102032
• Main Authors: Joseph, Olajumoke Olufunmilayo, Dahunsi, Samuel Olatunde, Okoh, Anthony
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01-12-2024
• Subjects: Mutations; SARS-CoV-2; Spike; Vaccine; Whole Genome Sequencing; Spike; Mutations; SARS-CoV-2; Vaccine; Whole Genome Sequencing
• ISSN: 2452-0144; 2452-0144
• DOI: 10.1016/j.genrep.2024.102032

Severe acute respiratory syndrome coronavirus – 2 (SARS-CoV-2) which was responsible for the COVID-19 pandemic has now been considered an endemic virus, that will continually produce sporadic outbreaks in different communities around the globe. Although, there are several surveillance studies on SARS-CoV-2 globally, including Nigeria, there is still an important need to understand the uniqueness of the strains of the virus that was circulating immediately after the pandemic, to add to the global database of information that will aid vaccine production and future preparedness against another SARS - related CoV pandemic.
Towards the end of the pandemic, between February – August 2022, SARS-CoV-2 was detected in a surveillance project in Ota – Ogun State Nigeria. We carried out a retrospective whole genome sequencing (WGS) analysis of SARS-CoV-2 in the previously reported positive sample, at Inqaba biotech in South Africa. RNA extraction was carried out using the Quick – RNA viral kit (Zymo) and library preparation was done by NEBNext ARTIC SARS-CoV-2 FS Library Prep kit (Illumina) according to the manufacturer's instruction. The WGS was carried out on the NextSeq500 platform by Illumina. The fastq file containing the unassembled raw sequence reads were submitted to NCBI SARS-CoV-2 resources, and a BioProject accession number PRJNA1076330 was issued. The DRAGEN Targeted Microbial, GISAID-CoVsurver mutation, BLAST and MAFFT applications were used for analysis.
The spike (s) gene of the study sequence possessed seven mutations (G142D, A163V, V213G, D614G, H655Y, N679K, P681H) and shared 99.4 % identity with those of the Wuhan reference sequence WIV04. The non-structural proteins (NSP) – 7,8,9,10 and 16 shared 100 % identity with bat/Yunnan/RaTG13 (a SARS- related CoV found in bats) sequence on GISAID. Although, the study sequence was obtained from an asymptomatic individual, the S mutations observed are known to be related to virulence, antigenic shift, enhanced transmissibility and host change. Thus, upon successful exploitation of this asymptomatic variant, it may possibly be transformed to a potential candidate for SARS-CoV-2 vaccine in future.
•Retrospective whole genome sequencing (WGS) analysis of SARS-CoV-2.•The WGS was carried out on the NextSeq500 platform by Illumina.•The spike (s) gene of the study sequence possessed seven mutations.•Avirulent type with S mutations linked to virulence and enhanced transmissibility.•Possibility of being a potential vaccine candidate upon exploitation.