Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan

Abstract

Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

“…We show that in Karachi there was a shift from S, L, V and G clades in March to predominantly the GH clade strains from May onwards [ 17 ]. Traveler- associated strains belonged to S and GH clades.…”

“…The pandemic was initially associated with travelers but local transmission was identified within two weeks of the first known COVID-19. G and S clade strains were shown to be present in the first wave of COVID-19 in Pakistan [ 17 ]. Genetic studies of SARS-CoV-2 from the second wave in Pakistan have identified B.1 and its sub-clades together with B.6 lineage strains to be present [ 18 ].…”

Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil

“…These mutations may increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes [6]. The global emergence of several variants of concern (VOCs), recently re-named by WHO, including the UK variant (Alpha or B.1.1.7), the South Africa variant (Beta or B.1.351), Brazil variant (Gamma or P.1 and P.2), and Delta or B.1.617.2 variant in India lead the genomic surveillance essential to monitoring mutations [7]. We hereby report the complete genome sequences and phylogenetic analysis of 24 SARS-CoV-2 genomes from Tocantins, North region of Brazil including our P.1-related sequences.…”

COVID‐19 situation in Pakistan: A broad overview

“…Health authorities need to ramp up genetic sequencing to map any new variants of the virus to tailor the response accordingly. 2 In addition to these measures, the health authorities also need to focus on risk communication and community engagement to deal with the misconceptions regarding COVID-19. Pakistan is lagging behind the neighbouring countries in the vaccination drive and merely relying on international aid for vaccination will not serve the purpose.…”