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Variants of Interest (WHO) 07/6 2021
Variants of Interest (WHO)
Listed below are the Variants of Interest (VOI) currently recognised by the World Health Organization.[11] Other organisations such as the CDC in the United States may use a slightly different list.[12] For example, prior to their June 29, 2021 update, the CDC listed Epsilon as a VOC rather than a VOI.[140]
Epsilon (lineages B.1.429, B.1.427, CAL.20C)[edit]
Main article: SARS-CoV-2 Epsilon variant
The Epsilon variant or lineage B.1.429, also known as CAL.20C[141] or CA VUI1,[142] 21C[20] or 20C/S:452R,[89] is defined by five distinct mutations (I4205V and D1183Y in the ORF1ab-gene, and S13I, W152C, L452R in the spike protein's S-gene), of which the L452R (previously also detected in other unrelated lineages) was of particular concern.[61][143] B.1.429 is possibly more transmissible, but further study is necessary to confirm this.[143] CDC has listed B.1.429 and the related B.1.427 as "variants of concern," and cites a preprint for saying that they exhibit a ~20% increase in viral transmissibility, have a "Significant impact on neutralization by some, but not all," therapeutics that have been given Emergency Use Authorization (EUA) by FDA for treatment or prevention of COVID-19, and moderately reduce neutralisation by plasma collected by people who have previously infected by the virus or who have received a vaccine against the virus.[44][144] According to WHO, it has been labelled as Epsilon variant.
Epsilon (CAL.20C) was first observed in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic.[145] It was not detected again until September when it reappeared among samples in California, but numbers remained very low until November.[146][147] In November 2020, the Epsilon variant accounted for 36 per cent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the Epsilon variant accounted for 50 per cent of samples.[143] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department,[148] the variant was also detected in multiple counties in Northern California. From November to December 2020, the frequency of the variant in sequenced cases from Northern California rose from 3% to 25%.[149] In a preprint, CAL.20C is described as belonging to clade 20C and contributing approximately 36% of samples, while an emerging variant from the 20G clade accounts for some 24% of the samples in a study focused on Southern California. Note however that in the US as a whole, the 20G clade predominates, as of January 2021.[61] Following the increasing numbers of Epsilon in California, the variant has been detected at varying frequencies in most US states. Small numbers have been detected in other countries in North America, and in Europe, Asia and Australia.[146][147] After an initial increase, its frequency rapidly dropped from February 2021 as it was being outcompeted by the more transmissible Alpha. In April, Epsilon remained relatively frequent in parts of northern California, but it had virtually disappeared from the south of the state and had never been able to establish a foothold elsewhere; only 3.2% of all cases in the United States were Epsilon, whereas more than two-thirds were Alpha.[40]
Zeta (lineage P.2
Main article: SARS-CoV-2 Zeta variant
Zeta variant or lineage P.2, a sub-lineage of B.1.1.28 like P.1 (the Gamma variant), was first detected in circulation in the state of Rio de Janeiro; it harbours the E484K mutation, but not the N501Y and K417T mutations.[115] It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.[112][150]
Under the simplified naming scheme proposed by the World Health Organization, P.2 has been labelled Zeta variant, and is considered a variant of interest (VOI), but not yet a variant of concern.[11]
Eta (lineage B.1.525)[edit]
Main article: SARS-CoV-2 Eta variant
The Eta variant or lineage B.1.525, also called VUI-21FEB-03[13] (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188,[13] 21D[20] or 20A/S:484K,[89] does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion (a deletion of the amino acids histidine and valine in positions 69 and 70) as found in Alpha, N439K variant (B.1.141 and B.1.258) and Y453F variant (Cluster 5).[151] Eta differs from all other variants by having both the E484K-mutation and a new F888L mutation (a substitution of phenylalanine (F) with leucine (L) in the S2 domain of the spike protein). As of 5 March, it had been detected in 23 countries.[152][153][52] It has also been reported in Mayotte, the overseas department/region of France.[152] The first cases were detected in December 2020 in the UK and Nigeria, and as of 15 February, it had occurred in the highest frequency among samples in the latter country.[52] As of 24 February 56 cases were found in the UK.[13] Denmark, which sequences all its COVID-19 cases, found 113 cases of this variant from 14 January to 21 February, of which seven were directly related to foreign travels to Nigeria.[153]
UK experts are studying it to understand how much of a risk it could be. It is currently regarded as a "variant under investigation", but pending further study, it may become a "variant of concern". Prof Ravi Gupta, from the University of Cambridge spoke to the BBC and said lineage B.1.525 appeared to have "significant mutations" already seen in some of the other newer variants, which is partly reassuring as their likely effect is to some extent more predictable.[154]
Under the simplified naming scheme proposed by the World Health Organization, lineage B.1.525 has been labelled variant Eta.[11]
Theta (lineage P.3)[edit]
Main article: SARS-CoV-2 Theta variant
On 18 February 2021, the Department of Health of the Philippines confirmed the detection of two mutations of COVID-19 in Central Visayas after samples from patients were sent to undergo genome sequencing. The mutations were later named as E484K and N501Y, which were detected in 37 out of 50 samples, with both mutations co-occurrent in 29 out of these. There were no official names for the variants and the full sequence was yet to be identified.[155] It is also labelled as Theta variant by WHO.
On 13 March, the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P.3.[156] On the same day, it also confirmed the first COVID-19 case caused by the Gamma variant in the country. Although the Gamma and Theta variants stem from lineage B.1.1.28, the department said that the impact of the Theta variant on vaccine efficacy and transmissibility is yet to be ascertained. The Philippines had 98 cases of the Theta variant on 13 March.[157] On 12 March it was announced that Theta had also been detected in Japan.[158][159] On 17 March, the United Kingdom confirmed its first two cases,[160] where PHE termed it VUI-21MAR-02.[13] On 30 April 2021, Malaysia detected 8 cases of the Theta variant in Sarawak.[161]
Iota (lineage B.1.526)[edit]
Main article: SARS-CoV-2 Iota variant
In November 2020, a mutant variant was discovered in New York City, which was named lineage B.1.526.[162] As of 11 April 2021, the variant has been detected in at least 48 U.S. states and 18 countries. In a pattern mirroring Epsilon, Iota was initially able to reach relatively high levels in some states, but in the spring of 2021 it was outcompeted by the more transmissible Alpha.[40] It is labelled as Iota variant by the WHO.
Kappa (lineage B.1.617.1
Main article: SARS-CoV-2 Kappa variant
Kappa variant[11] is one of the three sublineages of lineage B.1.617. It is also known as lineage B.1.617.1, 21B[20] or 21A/S:154K,[89] and was first detected in India in December 2020.[163] By the end of March 2021, the Kappa variant accounted for more than half of the sequences being submitted from India.[164] On 1 April 2021, it was designated a variant under investigation (VUI-21APR-01) by Public Health England.[43]
Lambda (lineage C.37
Main article: SARS-CoV-2 Lambda variant
The Lambda variant, also known as lineage C.37, was first detected in Peru in August 2020 and was designated by the WHO as a variant of interest on 14 June 2021.[11] It spread to at least 30 countries[165] around the world and maybe more resistant to vaccine compared to other strains.[166][167] It is also suggested that lambda variant is more infectious than alpha or gamma variant.[166] The lambda variant has also been detected in Australia.[165]
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