1.1 Genomic sequencing

Variants of SARS-CoV2 are detected by genomic sequencing – analysis of the full gene sequence of a virus isolate. Recall that the genome of SARS-CoV2 is 28,000 bases long and it encodes 4 structural proteins and a number of non-structural proteins (Figure 1).

Figure 1 Diagram of the genome of SARS-CoV2 and encoded proteins. (Repeated from Week 1 Figure 8)

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Two genes encode 16 non-structural proteins nsp1-nsp16. The genes for the four structural proteins (Spike, Envelope, Membrane glycoprotein, Nucleocapsid) and the auxiliary proteins (3a, 6,7,8,10) are indicated. There are untranslated regions (UTR) at the 5’ and 3’ ends of the genome. The non-structural and auxiliary proteins are required for virus replication, assembly and release.

Figure 1 Diagram of the genome of SARS-CoV2 and encoded proteins. (Repeated from Week 1 Figure 8)

Genomic sequencing takes considerably longer than detecting SARS-CoV2 infection by a lateral flow test or PCR. Once a positive sample has been identified, the virus genome is first extracted from the sample, isolated and then sequenced in segments. The sequences of overlapping segments are then assembled by computer, to produce the complete genome sequence of a variant. This process typically takes at least 2 days, but it is essential for tracking the appearance of new variants. At the time of writing (Jan. 2023) the Sanger Institute, which tracks variants in the UK, had sequenced 2.3 million SARS-CoV2 viral genomes.