Amplicon-based nanopore minion sequencing of patients with COVID-19 omicron variant from India

Abstract

SARS-CoV-2 infection has been playing havoc with emerging omicron variants of concern (VoC). Here, we report sequencing of the omicron variant in 13 patients from India using Oxford Nanopore Technology (ONT) Minion, wherein a rapid amplicon based sequence analysis was performed to assess and compare with existing 34 mutations in spike glycoprotein. We highlight and discuss the nature of these mutations that are unique and common to other populations. This is perhaps the first report on omicron variants from India using a long read sequencing chemistry.

Is Omicron really mild? – Comparative analysis of comorbidities and disease outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants

“…The archived positive specimens were subjected to amplicon-based nanopore sequencing using GridION MK1 sequencer (Oxford Nanopore Technologies Ltd., United Kingdom) as per standardized protocol [ 4 ]. The study was approved by the Institutional Ethics Committee (F.1/IEC/MAMC/92/04/2022/No441).…”

Is Omicron really mild? - Comparative analysis of comorbidities and disease outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants

“…The archived positive specimens were subjected to amplicon-based nanopore sequencing using GridION MK1 sequencer (Oxford Nanopore Technologies Ltd., United Kingdom) as per standardized protocol. [6] The study protocol was approved by the Institutional Ethics Committee, Maulana Azad Medical College, New Delhi, India (F.1/IEC/MAMC/92/04/2022/No441). Telephonic interviews were conducted, wherein a willingness to participate was verified from each participant.…”