Tracking SARS-CoV2 variants and strains: an overview of Nigeria Centre for Disease Control's first 596 sequences, November,2021

ABSTRACT

Introduction/ Background: There are 249,851,155 cases of COVID-19 globally as of 6th November 2021. SARS-CoV-2, accounts for 5,053,813 deaths worldwide. In Nigeria 212,511 cases and 2,902 deaths were recorded at the same time point. his report describes the first 596 SARS-CoV-2 genomes sequenced at the National Reference Laboratory (NRL) of NCDC. Methods: Samples sequenced include positive samples from baseline surveillance and in-bound travellers from several states in-country. Isolates were obtained from nasopharyngeal and oropharyngeal swabs and Library preparation was done using ARTIC NEB SARSCoV- 2 or the NEBNext FS Library preparation kits and sequencing on Oxford Nanopore MinION or Illumina MiSeq. Sequence analysis was done using ARTIC bioinformatics pipeline for MinION and Illumina Basespace DRAGEN COVID Lineage app for MiSeq sequence data respectively Results: Of the 596 sequences, 51.8% were Delta variants, 17.4% Eta variants, and 1.0% Alpha variants. The sequences represented mostly the second and third waves of the COVID-19 pandemic in Nigeria, mostly driven by the Eta and Delta variants respectively. The first wave was driven by D614G, L452R and Y1155F spike mutations, while the second wave was characterized by the Eta variant and the Third wave was driven by Delta variants. Impact Genomic surveillance has been recognised as a major element for pandemic response and has become a necessity for public health. To monitor local transmission and importation of SARS-CoV-2 variants in Nigeria, whole genome sequencing of SARS-CoV-2 was carried out as part of the response to the ongoing COVID-19 pandemic. Conclusion: There were multiple introductions of SARS-CoV-2 variants into Nigeria despite all the measures in place at various points of entry. The importance of timely detection of circulating variants of SARS-CoV-2 for effective preparedness and response activities cannot be overemphasised. Sequencing helped inform rational public health advisory and response.