Variants of SARS-CoV-2

First sequenced in August 2020 in Nigeria,[17] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[18] Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with UK's VOC-202012/01. It shares no other mutations with VOC-202012/01 and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.[17]

First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month,[19] Variant of Concern 202012/01 (VOC-202012/01),[20] was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[21] and also as lineage B.1.1.7 or 20I/501Y.V1 (formerly 20B/501Y.V1).[3][22][23] Since then, its prevalence odds have doubled every 6.5 days, the presumed generational interval.[24][25] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation. There is some evidence that this variant has 30–70% increased transmissibility,[26] and early analyses suggest an increase in lethality.[26]

In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[27] was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[28]

The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".[29] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[30]

On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H/501Y.V2 (formerly 20C/501Y.V2), or lineage B.1.351,[23] was first detected in South Africa and reported by the country's health department.[31] Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases.[32][33] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[31][32]

Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[31][34] K417N, and E484K.[35][36] The N501Y mutation has also been detected in the United Kingdom.[31][37]

Lineage P.1 was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new lineage was first identified in four people who arrived in Tokyo having travelled from the Amazonas state on 2 January 2021.[38] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the P.1 new lineage in the Amazon rain forest.[39] This variant of SARS-CoV-2 has been named P.1 lineage (although it is a descendant of B.1.1.28, the name B.1.1.28.1 is not permitted and thus the resultant name is P.1) and has 17 unique amino acid changes, 10 of which in its spike protein, including N501Y and E484K.[39] The new lineage was absent in samples from March to November from Manaus, Amazonas state, but it was identified in 42% of the samples from December 2020 collected in the same city, suggesting a recent increase in frequency.[39] A separate preprint by Voloch et al. identified another sub-lineage of the B.1.1.28 lineage circulating in the state of Rio de Janeiro, Brazil, now named P.2 lineage,[40] that harbours the E484K mutation. The P.2 lineage is not directly related with the P.1 lineage identified in Manaus.[39][41] Although both lineages harbour the E484K mutation, the mutation was acquired independently through convergent evolution.[39]

CAL.20C[42] was first observed by researchers at Cedars-Sinai Medical Center in July 2020 in one of 1,230 virus samples collected in Los Angeles County. The variant, designated lineage B.1.429, contains mutation L452R and was not detected again in Southern California until October 2020. In November 2020, the CAL.20C variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the CAL.20C variant accounted for 50 percent of samples.[43] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department,[44] 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%.[45] 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.[5]

D614G is a mutation that affects the spike protein of SARS-CoV-2. The frequency of this mutation in the viral population has increased during the pandemic. G (glycine) has replaced D (aspartic acid) in many countries, especially in Europe though more slowly in China and the rest of East Asia, supporting the hypothesis that G increases the transmission rate, which is consistent with higher viral titers and infectivity in vitro.[1] In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic.[46][47][48][49] PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.[50]

The global prevalence of D614G correlates with the prevalence of loss of smell (anosmia) as a symptom of COVID-19, possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.[51]

Variants containing the D614G mutation are considered to be part of the G clade by GISAID[1] and the B.1 clade by the PANGOLIN tool.[52]

E484K has been reported to be an "escape mutation" from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity".[53] The P.1. lineage described in Japan and Manaus,[54] the P.2 lineage (also known as B.1.1.248 lineage, Brazil)[55] and 501.V2 (South Africa) exhibit this mutation.[53] A limited number of B.1.1.7 genomes with E484K mutation have also been detected.[56] The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[57] Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralizing virus bearing the E484K mutation.[58][59] On 2 February 2021, medical scientists in the United Kingdom reported the detection of E484K in 11 samples (out of 214,000 samples), a mutation that may compromise current vaccine effectiveness.[60][61]

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[50] This change is believed by Public Health England to increase binding affinity because of its position inside the spike glycoprotein's receptor-binding domain, which binds ACE2 in human cells; data also support the hypothesis of increased binding affinity from this change.[20] Variants with N501Y include P.1 (Brazil/Japan),[53][62] Variant of Concern 202012/01 (UK), 501.V2 (South Africa), and COH.20G/501Y (Columbus, Ohio). This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.[63][64]