The “novel coronavirus”, SARS-CoV-2, never went away and continues to multiply, mutate, and spread across the world. The XEC variant was thus first identified in Berlin in early August 2024, in routine surveillance samples that had been collected two months previously. In September, XEC was then identified in samples that had been obtained even earlier-in May, in Italy. XEC has been reported from 27 countries in Europe and North America at the time of writing.
XEC is described as a recombinant variant, being the product of the exchange of genetic material between the KS.1.1 and KP. 3.3 variants, which in turn evolved from the JN.1 subvariant of the Omicron strain. JN.1 was the dominant variant during the winter of 2023.
The nomenclature of coronavirus variants can be confusing. It is hence worth making a detour to explore this facet of modern virology. SARS-CoV-2 variants are classified according to lineage (or clade) and component mutations. Three phylogenetic nomenclature systems, which trace the evolutionary history of the coronavirus, are in place for naming lineages and variants. These naming systems have been developed by GISAID (Global Initiative on Sharing All Influenza Data), Nextstrain, and Pango (Phylogenetic Assignment of Named Global Outbreak), which are open-source databases that identify and track variants using genome sequencing. Lineages, which share a common ancestor, are named by Latin alphabet letters and numbers, followed by dots which denote “descendant of.’
The Virus Evolution Working Group of the WHO, which was established in June 2020, introduced a naming scheme using the letters of the Greek alphabet, of which there are 24, for designated “variants of concern” and “variants of interest”. This scheme, introduced on 31 May 2021, replaced the practice of naming these variants for the country where they were first identified, which was considered by the WHO to be “stigmatizing and discriminatory”. All letters from Alpha to Mu had been used by November 2021, when the next two letters, Nu and Xi were bypassed in favour of Omicron (B.1.1.529), a variant that first emerged in South Africa. Nu sounds like “new’, while Xi is a common name in China. As Greek letters ran out, mythological entities and star constellations have since shared their names with newer variants.
Not all mutations benefit viruses, and some can even be detrimental. Some mutations may, however, confer a selective survival advantage, allowing the mutated virus to evade the host’s immune system or to resist currently available antiviral drugs. XEC is believed to be more contagious, and its spread is possibly facilitated by the T22N mutation (inherited from KS.1.1) and the Q493E mutation (inherited from KP.3.3), both in the spike protein. XEC is primarily transmitted in respiratory droplets. The symptoms produced by this variant are reportedly mild and resemble the “cold” and “flu-like” symptoms of other Covid variants. Spread may be further hastened by falling protective neutralising antibody levels in the population. As it stands, hospital admissions from Covid-19 and positive test results for SARS-CoV-2 in symptomatic people at sentinel “spotter” laboratories are rising in England. There are concerns that XEC, which has already arrived, may lead to a spike in cases and become the dominant strain in England this winter.
The autumn booster vaccination campaign in the UK began to invite bookings for Covid-19 vaccinations from 23 September 2024 onwards. An updated vaccine, targeting the JN.1 variant and hence likely to be effective against XEC, will be administered to selected target populations between 3 October and 20 December 2024. Those eligible for vaccination include all adults aged 65 and over, residents in care homes for the elderly, those aged 6 months to 64 years with underlying health conditions or treatments that increase their risk of serious illness, and frontline health and social care workers and staff in care homes for older adults. The NHS will contact eligible patients directly, but they can also book themselves in via the NHS app, pharmacies, drop-in clinics, or by phoning 119. As experience with Covid, and confidence in containing the spread of virus, have evolved, self-isolation for symptomatic people, although advisable, is no longer mandatory. Lockdown-type restrictions seem most unlikely, although mask wearing, hand sanitising, and other measures may be advised in particular circumstances.
The advent of XEC has inspired some interesting news stories and some inconsistent expert commentaries. As usual, advice is best sought from the nation’s public health authorities, to the exclusion of the many alternatives.
Ashis Banerjee