Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan

  • Samina Naz Mukry Department of Molecular Biology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Shariq Ahmed Department of Molecular Biology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Ali Raza Bukhari Department of Molecular Biology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Aneeta Shahni Department of Transplant Immunology and Applied Microbiology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Gul Sufaida Department of Molecular Biology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Arshi Naz Department of Molecular Biology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
  • Tahir Sultan Shamsi Department of Post Graduate Studies and Research, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
Keywords: SARS-CoV-2, variants, COVID-19, locally transmitted virus

Abstract

Introduction: The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants.

Methodology: The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared.

Results: The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19.

Conclusions: Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.

Published
2021-10-31
How to Cite
1.
Mukry SN, Ahmed S, Raza Bukhari A, Shahni A, Sufaida G, Naz A, Shamsi TS (2021) Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan. J Infect Dev Ctries 15:1376-1383. doi: 10.3855/jidc.14900
Section
Coronavirus Pandemic