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Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences

Publication

Date: 30th April 2020 | Source: BioRxiv

Authors: Abdoulie Kanteh, Jarra Manneh, Sona Jabang, Mariama A Kujabo, Bakary Sanyang, Mary Aigbiremo Oboh, Abdoulie Bojang, Haruna S Jallow, Davis Nwakama, Ousman Secka, Anna Roca, Alfred Amambua-Ngwa, Martin Antonio, Ignatius Baldeh, Karen Forest, Ahmadou Lamin Samateh, Umberto D'Alessandro, Abdul Karim Sesay.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility.

This study generated Whole Genome data to determine the origin and pattern of transmission of SARS-CoV-2 from the first six cases tested in The Gambia.

Total RNA from SARS-CoV-2 was extracted from inactivated nasopharyngeal-oropharyngeal swabs of six cases and converted to cDNA following the ARTIC COVID-19 sequencing protocol. Libraries were constructed with the NEBNext ultra II DNA library prep kit for Illumina and Oxford Nanopore Ligation sequencing kit and sequenced on Illumina MiSeq and Nanopore GridION, respectively. Sequencing reads were mapped to the Wuhan reference genome and compared to eleven other SARS-CoV-2 strains of Asian, European and American origins.

A phylogenetic tree was constructed with the consensus genomes for local and non-African strains. Three of the Gambian strains had a European origin (UK and Spain), two strains were of Asian origin (Japan).

In The Gambia, Nanopore and Illumina sequencers were successfully used to identify the sources of SARS-CoV-2 infection in COVID-19 cases.

Read the full text Read about direct RNA sequencing of SARS-Cov-2 Read more on nanopore sequencing in COVID-19

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