Emergence of new SARS-CoV-2 variant under investigation in Saudi Arabia

Abstract Genomic surveillance helps public health tracking the path of a pandemic, understand its transmission route, and how quickly the virus is spreading and adapting through mutation and recombination. In late 2020, the Infectious Diseases Research Department (IDRD) at King Abdullah International Medical Research Center (KAIMRC) initiated a surveillance program focused on monitoring the dissemination of SARS-CoV-2 variants by sequencing the receptor-binding domain (RBD) of 20 to 32% of all community-acquired SARS-CoV-2 positive cases identified from November 2020 to February 2021 at King Abdulaziz Medical City (KAMC) in Riyadh. Sequence analysis detected among sequenced isolates a SARS-CoV-2 variant harboring an N501T substitution in the receptor-binding domain (RBD). COVID-19 cases linked to this new variant under investigation, first detected in isolates from November, grew exponentially in 2021 to account alone for more than 62 % (142/228) of all SARS-CoV-2 positive cases studied in February, thus suggesting that this variant might have increased transmissibility. Genome sequencing showed that this variant has evolved from the pangolin lineage B.1.1 and diverged from the original strain of Wuhan in China by ten amino acid changes located in ORF1a (P3359L and Q3729K), ORF1b (P314L), spike (S) protein (F157S, N501T, D614G), ORF6 (F2S) and nucleocapsid (N) protein (I84V, R203K and G204R). Isolates belonging to the new variant were further split into two sub-groups based on additional changes in the spike. Of these, one sub-group carried the Y144*, G257S, T859N and A899S variations combined, while one carried the H49Y variation alone. Patients infected with this new variant did not show any increase in the severity of infections. The rapid rise of the new variant among community-acquired SARS-CoV-2 cases suggests a national spread, although this needs to be further assessed carefully.