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

• DOI: 10.3855/jidc.14900
• Publication Date: 2021-11-11T21:49:57Z
• Authors: Samina Naz Mukry; Shariq Ahmed; Ali Raza Bukhari; Aneeta Shahni; Gul Sufaida; Arshi Naz; Tahir Sultan Shamsi
• Keywords: Minion; Pandemic; Coronavirus; Molecular Epidemiology

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. virus has constantly mutating and local transmission cases from different countries vary due host dependent viral adaptation. Many distinct clusters variant SARS-CoV-2 defined globally. In this study, the epidemiology studied locally transmitted isolates Karachi were sequenced compared identify any possible variants.
 Methodology: real time PCR performed on nasopharyngeal specimen confirm with Orf 1ab E gene as targets. through oxford nanopore technology MinION platform. Isolates second wave COVID-19 outbreak compared.
 Results: overall positivity rate for 26.24% highest number positive June. Approximately, 37.45% subjects aged between 19-40 years. All belonged GH clade shared missense mutation D614G spike protein linked increased worldwide. Another A222V coexisted COVID-19.
 Conclusions: Based present findings it is suggested that varies those reported other parts Pakistan. Slight variability also observed viruses wave. Variability potential vaccine target may result failed trials, therefore information variants always useful effective design and/or selection.