Update on SARS-CoV-2 variants: ECDC assessment of the XBB.1.5 sub-lineage

2023-01-06 17:16:06 By : Ms. Miss Liu

European Centre for Disease Prevention and Control

An agency of the European Union Marijuana Test Strip

Update on SARS-CoV-2 variants: ECDC assessment of the XBB.1.5 sub-lineage

XBB.1.5 is a sub-lineage of the SARS-CoV-2 lineage XBB, and is currently estimated to have a large growth advantage over previously circulating lineages in North America (139%) and Europe (137%), although these estimates are associated with significant uncertainty. There is a possibility that this variant could have an increasing effect on the number of COVID-19 cases in the EU/EEA, but not within the coming month as the variant is currently only present in the EU/EEA at very low levels.

XBB.1.5 is a sub-lineage of XBB, with an additional spike RBD mutation S486P. This lineage was first detected in the US with sample collection dates as of 22 October 2022, and since then the lineage has been increasing. As of 3 January 2023, 3 456 sequences had been deposited in GISAID EpiCoV belonging to XBB.1.5, with the mutational profile in Spike region - Q183E, F486P and F490S. Most of these submissions are from the US (3 080 sequences), and the United Kingdom (106 sequences). The variant has also been detected in several other countries including EU/EEA countries – Denmark, France, Austria, Netherlands, Germany, Italy, Spain, Sweden, Iceland, Belgium, Czechia, Portugal, and Ireland.

The lineage is currently estimated to have a large growth advantage over previously circulating lineages in North America (139%) and Europe (137%), although these estimates are associated with significant uncertainty. The US Centers for Disease Prevention and Control (US CDC) report a doubling time of nine days in the proportion of XBB.1.5 and the US-CDC nowcast system estimates the current proportion of the variant to be around 40% in the US, with the variant likely to become dominant in the country within a week. The US CDC also presented growth data comparing XBB.1.5 to previously successful variants, indicating that XBB 1.5 exhibits the second highest growth advantage to date, second only to BA.1 (the original Omicron lineage). This does not necessarily mean that the variant will become dominant in the EU/EEA, since major differences in variant circulation have been observed between North America and Europe several times during the pandemic.

The most likely explanation of the growth advantage is the already high level of immune escape demonstrated by XBB, combined with the effect of the spike change S486P, which could provide either a transmissibility advantage, additional immune escape, or both. This mutation has previously been rare during the pandemic, probably due to it requiring two amino acid substitutions in the same codon to change from phenylalanine to proline. In fact, other variants with this change have emerged before without becoming successful. Further laboratory and epidemiological investigations are required to elucidate the mechanism of the growth advantage conferred by this change for the XBB variant specifically. There is currently not enough information available to assess any change in infection severity associated with the variant.

There is a possibility that this variant could have an increasing effect on the number of COVID-19 cases in the EU/EEA, but not within the coming month as the variant is currently only present in the EU/EEA at very low levels.

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Update on SARS-CoV-2 variants: ECDC assessment of the XBB.1.5 sub-lineage

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