δ subvariants of SARS-COV-2 in Israel, Qatar and Bahrain: Optimal vaccination as an effective strategy to block viral evolution and control the pandemic

Abstract

ABSTRACTδ variant has rapidly become the predominant pandemic driver and yielded four subvariants (δ1, δ2, δ3 and δ4). Among them, δ1 has been mainly responsible for the latest COVID-19 waves in India, Southeast Asia, Europe and the USA. A relevant question is how δ subvariants may have driven the pandemic in the rest of the world. In both Israel and Qatar, mRNA-based vaccination has been rolled out competitively, but the outcomes are quite different in terms of controlling the recent waves resulting from δ variant. This raises the question whether δ subvariants have acted differently in Israel and Qatar. In both countries, δ variant was first identified in April 2021 and δ1 subvariant constituted ∼50% δ genomes from April to May 2021. But the situation started to diverge in June 2021: In Israel, δ1 variant was encoded by 92.0% δ genomes, whereas this fraction was only 43.9% in Qatar. Moreover, a δ1 sublineage encoding spike T791I was identified in Israel but not Qatar. This sublineage accounted for 31.8% δ genomes sequenced in June 2021 and declined to 13.3% in October 2021. In August 2021, δ1 also became dominant in Qatar and a major sublineage encoding spike D1259H emerged. This sublineage has evolved further and acquired additional spike substitutions, including K97E, S255F, I693S, I712S, I1104L, E1258D and/or V1177I, in Qatar and other countries, such as Czech Republic, France and Mexico. Monthly distribution of the above sublineages suggests that the one from Qatar is much more of concern than that from Israel. Different from what was in Israel and Qatar, δ2 subvariant has also been important in Bahrain, whereas a δ2 sublineage encoding spike V1264L and A1736V of NSP3 was dominant in June 2021, but was gradually taken over by δ1 subvariant. These results suggest that δ1 and δ2 subvariants continue their evolution in different countries. The recent successful pandemic control in Israel, Qatar and Bahrain supports that δ1 and δ2 subvariants are still sensitive to timed vaccination, thereby urging the use of optimal immunity as a strategy to block SARS-COV-2 evolution and control the pandemic.