Variants of SARS-CoV-2
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are viruses that, while similar to the original, have genetic changes that are of enough significance to lead virologists to label them separately. SARS-CoV-2 is the virus that causes coronavirus disease 2019 (COVID-19). Some have been stated, to be of particular importance due to their potential for increased transmissibility,[1] increased virulence, or reduced effectiveness of vaccines against them.[2][3] These variants contribute to the continuation of the COVID-19 pandemic.
"New coronavirus variant" redirects here. For recent species of coronavirus, see Novel coronavirus and Coronavirus.As of April 2024, only Omicron is designated as a circulating variant of concern by the World Health Organization.[4]
As it is currently not known when the index case or "patient zero" occurred, the choice of reference sequence for a given study is relatively arbitrary, with different notable research studies' choices varying as follows:
The variant first sampled and identified in Wuhan, China is considered by researchers to differ from the progenitor genome by three mutations.[81][87] Subsequently, many distinct lineages of SARS-CoV-2 have evolved.[75]
Viruses generally acquire mutations over time, giving rise to new variants. When a new variant appears to be growing in a population, it can be labelled as an "emerging variant". In the case of SARS-CoV-2, new lineages often differ from one another by just a few nucleotides.[14]
Some of the potential consequences of emerging variants are the following:[42][88]
Variants that appear to meet one or more of these criteria may be labelled "variants under investigation" or "variants of interest" pending verification and validation of these properties. The primary characteristic of a variant of interest is that it shows evidence that demonstrates it is the cause of an increased proportion of cases or unique outbreak clusters; however, it must also have limited prevalence or expansion at national levels, or the classification would be elevated to a "variant of concern".[19][78] If there is clear evidence that the effectiveness of prevention or intervention measures for a particular variant is substantially reduced, that variant is termed a "variant of high consequence".[18]
Variants of interest (WHO)
Listed below are the Variants of Interest (VOI) which are recognised by the World Health Organization.[17] Other organisations such as the CDC in the United States may at times use a slightly different list.[18]
As of 15 March 2023,[117] The WHO defines a VOI as a variant "with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, virulence, antibody evasion, susceptibility to therapeutics and detectability" and that it is circulating more than other variants in over one WHO region to such an extent that a global public health risk can be suggested.[118] Furthermore, the update stated that "VOIs will be referred to using established scientific nomenclature systems such as those used by Nextstrain and Pango".[118]
As of 20 December 2023, the WHO lists XBB.1.5, XBB.1.16, EG.5, BA.2.86 and JN.1 as circulating variants of interest.[119]
Variants under monitoring (WHO)
Listed below are Variants under Monitoring (VUM) which are recognised by the WHO. VUM's are defined as variants with genetic changes suspected to affect virus characteristics and some indication of posing a future risk, but with unclear evidence of phenotypic or epidemiological impact, requiring enhanced monitoring and repeat assessment after new evidence.[17]
As of 21 November 2023, the WHO lists DV.7, XBB, XBB.1.9.1, XBB.1.9.2, XBB.2.3 as circulating variants under monitoring.[4]
Other notable variants
Lineage B.1.1.207 was first sequenced in August 2020 in Nigeria;[219] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[42] Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with the Alpha variant. It shares no other mutations with the Alpha variant and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.[219] As of May 2021, lineage B.1.1.207 has been detected in 10 countries.[220]
Lineage B.1.1.317, while not considered a variant of concern, is noteworthy in that Queensland Health forced 2 people undertaking hotel quarantine in Brisbane, Australia to undergo an additional 5 days' quarantine on top of the mandatory 14 days after it was confirmed they were infected with this variant.[221]
Lineage B.1.616, being identified in Brittany, Western France in early January 2021 and designated by WHO as "Variant under investigation" in March 2021, was reported to be difficult to detect from nasopharyngeal swab sampling method of coronavirus detection, and detection of the virus needs to rely on samples from lower respiratory tract.
Lineage B.1.618 was first isolated in October 2020. It has the E484K mutation in common with several other variants, and showed significant spread in April 2021 in West Bengal, India.[222][223] As of 23 April 2021, the PANGOLIN database showed 135 sequences detected in India, with single-figure numbers in each of eight other countries worldwide.[224]
In July 2021, scientists reported in a preprint which was published in a journal in February 2022, the detection of anomalous unnamed unknown-host SARS-CoV-2 lineages via wastewater surveillance in New York City. They hypothesized that "these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir".[225][226]
Lineage B.1.640.2 (also known as the IHU variant[227]) was detected in October 2021 by researchers at the Institut Hospitalo-Universitaire (IHU) in Marseille.[228] They found the variant in a traveler who returned to France from Cameroon and reportedly infected 12 people.[229][230] The B.1.640 lineage, which includes B.1.640.2, was designated a variant under monitoring (VUM) by the World Health Organization (WHO) on 22 November 2021.[231] However, the WHO has reported that lineage B.1.640.2 has spread much slower than the Omicron variant, and so is of relatively little concern.[230][232] According to a preprint study, lineage B.1.640.2 has two already known spike protein mutations – E484K and N501Y – among a total of 46 nucleotide substitutions and 37 deletions.[229][233][234]
In March 2022, researchers reported SARS-CoV-2 variant recombinant viruses that contain elements of Delta and Omicron – Deltacron (also called "Deltamicron").[235][236][237][238][239] Recombination occurs when a virus combines parts from a related virus with its genetic sequence as it assembles copies of itself. It is unclear whether Deltacron – which is not to be confused with "Deltacron" reported in January albeit the first detection was also in January[239][240] – will be able to compete with Omicron and whether that would be detrimental to health.[241]
In July 2023, Professor Lawrence Young, a virologist at Warwick University announced a super mutated Delta variant from a swab of an Indonesian case with 113 unique mutations, with 37 affecting the spike protein.[242]
Recombinant variants
The British government has reported a number of recombinant variants of SARS-CoV-2.[291] These recombinant lineages have been given the Pango lineage identifiers XD, XE, and XF.[292]
XE is a recombinant lineage of Pango lineages BA.1 and BA.2.[293] As of March 2022 XE was believed to have a growth rate 9.8% greater than BA.2.[291]