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

ABSTRACT

Delta variant has rapidly become the predominant pandemic driver and yielded four subvariants (delta1, delta2, delta3 and delta4). Among them, delta1 has been mainly responsible for the latest COVID-19 waves in India, Southeast Asia, Europe and the USA. A relevant question is how delta 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 delta variant. This raises the question whether delta subvariants have acted differently in Israel and Qatar. In both countries, delta variant was first identified in April 2021 and delta1 subvariant constituted ~50% delta genomes from April to May 2021. But the situation started to diverge in June 2021 In Israel, delta1 variant was encoded by 92.0% delta genomes, whereas this fraction was only 43.9% in Qatar. Moreover, a delta1 sublineage encoding spike T791I was identified in Israel but not Qatar. This sublineage accounted for 31.8% delta genomes sequenced in June 2021 and declined to 13.3% in October 2021. In August 2021, delta1 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, delta2 subvariant has also been important in Bahrain, whereas a delta2 sublineage encoding spike V1264L and A1736V of NSP3 was dominant in June 2021, but was gradually taken over by delta1 subvariant. These results suggest that delta1 and delta2 subvariants continue their evolution in different countries. The recent successful pandemic control in Israel, Qatar and Bahrain supports that delta1 and delta2 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.