Detection of the XE subvariant of SARS-CoV-2: A perspective

Abstract

Dear Editor, New variants of SARS-CoV-2 have been emerging since the beginning of the COVID-19 pandemic [1]. The virus evolves into new variants to attain better fitness than the original viral strain; thus, the variants are thought to infect the human host more efficiently and successfully. This evolutionary tendency is not unique to SARS-CoV-2; all viruses are known to mutate to gain survival advantages, including high receptor-binding affinity, infectivity, replication fitness, high transmissibility and virulence, resistance to neutralizing antibodies and immune evasion, and augmenting the disease severity and reinfection chance [2]. When writing this correspondence, The World Health Organization had listed two currently circulating variants of concern (VOCs; Delta and Omicron), three previously circulating VOCs (Alpha, Beta, and Gamma), eight previously circulating variants of interest (VOIs; Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, and Mu), and two variants under monitoring (VUMs; B.1.640 and XD). The number of new cases of SARS-CoV-2 has been decreasing globally as of April 2022; however, >200 countries have been experiencing the latest case surges due to the Omicron VOC [3]. On March 25, 2022, the U.K. Health Security Agency announced that a new recombinant BA.1–BA.2 variant of Omicron (designated XE) was detected through gene sequencing first on January 19, 2022. Subsequently, more cases were detected in East of England, London, and the South East. The same agency announced that 637 cases were positive with XE, and that all possible recombinant viral variants were closely monitored, but the transmissibility of the variant was unknown (https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1063424/Tech-Briefing-39-25March2022_FINAL.pdf). Mixed infections by different sublineages of a VOC or even different VOCs can occur if they are actively circulating together. Such coinfections may cause emergence of new recombinant subvariants likely with a better evolutionary survival fit. XE thus could cause infections with higher circulation advantage among the human hosts as these have been observed during the COVID-19 pandemic. The World Health Organization follows the news about this variant; other countries including Thailand have reported the detection of XE [4]. Meanwhile, a different recombinant variant termed Deltacron was first reported in Paris in February 2022. This variant has resulted from the recombination of the Delta and Omicron VOCs. Since February 2022, different variants of this hybrid have been reported in other parts of Europe and the U.S.A [5]. Future perspective Detection of XE and different forms of the “Deltacron” variants in distant countries suggests that the same or different variants will soon be appearing and reported by other countries, too; thus, a rise in numbers of COVID-19 cases is expected. However, experiencing another pandemic peak boosted by such variants, as was experienced with the Delta, Beta, Omicron, and Gamma [6,7] variants, is difficult to predict. The present global overview of the progress of the pandemic and global countermeasures indicates that >11 billion doses of an approved anti-COVID-19 vaccine were administered, and only <65% of the world population have received at least one dose of a vaccine (https://ourworldindata.org/covid-vaccinations?country=OWID_WRL). This big vaccination shortfall gravely challenges the future global management of the pandemic. Indeed, the low global vaccination rate encourages emergence of the SARS-CoV-2 subvariants because the virus can still circulate actively among some members of the communities, including unvaccinated adults or children, immunocompromised individuals, or those older than ≈75 years. Meanwhile, many countries have eased or lifted the COVID-19 countermeasures regarding mass-gatherings and have opened their borders to international travel. Although XE characteristically may be like Omicron, and a profound change in disease severity or transmissibility compared with those by the precursor strains is unexpected, emergence of another VOC could majorly threaten the public health globally, especially if a more virulent strain surges in countries with low vaccination rates. We believe equitable global vaccination campaigns must be reinforced to better prepare the world for emergence of an unexpectedly virulent variant. Please state any conflicts of interest None. Please state any sources of funding for your research This study received no specific grant from any funding agency in the public, commercial, or not-for-profit sector. Research registration Unique Identifying number (UIN) 1. Name of the registry: Not applicable. 2. Unique Identifying number or registration ID: Not applicable. 3. Hyperlink to your specific registration (must be publicly accessible and will be checked): Author statement Farid Rahimi: Conceptualization, Data Curation, Writing – Original Draft, Writing – review & editing. Amin Talebi Bezmin Abadi: Conceptualization, Data Curation, Writing – Original Draft, Writing – review & editing. All authors critically reviewed and approved the final version of the manuscript before submitting. Guarantor Both authors. Data statement Data not available/not applicable. Funding None. Provenance and peer review Not commissioned, internally peer-reviewed. Declaration of competing interest Authors have no competing interests to declare.