Rapid Identification of SARS-CoV-2 Lineages from Two Major Clusters in Pahang, Malaysia Using MinION Sequencer

• Main Authors: Zainulabid, Ummu Afeera, Wan Ramli, Wan Nurliyana, Aslam, Ayesha, Hussain, Mushtaq, Haroon, Raihanah, Ahmad, Hajar Fauzan
• Format: Conference or Workshop Item
• Language: English; English; English
• Published: 2022
• Subjects: RC111 Infectious and Parasitic Diseases
• Online Access: http://irep.iium.edu.my/98421/1/Rapid%20Identification%20of%20SARS-CoV-2%20Lineages%20from%20Two%20Major%20Clusters%20in%20Pahang%2C%20Malaysia%20Using%20MinION%20Sequencer.pdf; http://irep.iium.edu.my/98421/2/Conference-Schedule%20ICBME2022.pdf; http://irep.iium.edu.my/98421/3/ICBME%202022%20Program%20Book.pdf; http://irep.iium.edu.my/98421/

Background: Rapid identification of variants is needed to take prompt action for public health measures. It was proven that a combination of public health knowledge and Oxford Nanopore Technologies (ONT) could assist in understanding genomic epidemiology. Objective: This study explores the utility of employing the Oxford Nanopore Sequencing in understanding the genomic epidemiology in 2 large clusters in Pahang, Malaysia. Methods: The total RNAs from clinical specimens of combined oropharyngeal and nasopharyngeal swabs representing two major clusters in Pahang, Malaysia, were extracted and proceeded for long-read sequencing. Results: We report 2 variants of concern from this investigation – Beta and Delta variants. We observed that the Taman Tanah Putih Baru and Pasar Kemunting clusters were caused by B.1.351 (ß) and B.1.617 (∆) variants, respectively. Conclusion: Long-read sequencing devices from Oxford Nanopore Technologies (ONT) provide a viable alternative with several benefits. ONT devices are small, inexpensive, and need little laboratory infrastructure or technical expertise to prepare samples. They can also be utilised to perform quick sequencing analysis with flexibility and aid in understanding genomic epidemiology.