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SARS-CoV-2 Delta variant

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Not to be confused with the deltacoronavirus which mainly affects birds.
For lineage B.1.617.1, see SARS-CoV-2 Kappa variant.

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SARS-CoV-2 Delta variant, also known as lineage B.1.617.2, is a variant of lineage B.1.617 of SARS-CoV-2, the virus that causes COVID-19.[1] It was first detected in India in late 2020.[2][3] The World Health Organization (WHO) named it the Delta variant on 31 May 2021.[4]

It has mutations in the gene encoding the SARS-CoV-2 spike protein[5] causing the substitutions T478K, P681R and L452R,[6] which are known to affect transmissibility of the virus as well as whether it can be neutralised by antibodies for previously circulating variants of the COVID-19 virus.[7] Public Health England (PHE) in May 2021 observed secondary attack rates to be 51–67% higher than the alpha variant.[8]

On 7 May 2021, PHE changed their classification of lineage B.1.617.2 from a variant under investigation (VUI) to a variant of concern (VOC) based on an assessment of transmissibility being at least equivalent to B.1.1.7 (Alpha variant), first identified in the UK (as the Kent variant).[9] Subsequently on 11 May 2021, the WHO also classified this lineage VOC, and said that it showed evidence of higher transmissibility and reduced neutralisation. The variant is thought to be partly responsible for India's second wave of the pandemic beginning in February 2021.[10][11][12]

On 18 June 2021, Public Health England issued Technical Briefing 16 on SARS-CoV-2 variants, documenting 73 deaths among 60,655 UK cases of SARS-CoV-2 Delta variant with a fatality rate of only 0.1%. This compared with a fatality rate of 1.9% (some 19 times higher, 4,259 deaths out of 224,021 cases) associated with the original Alpha variant.[13]

Classification

The Delta variant has mutations in the gene encoding the SARS-CoV-2 spike protein[5] causing the substitutions E484Q and L452R.[7] It is identified as the 21A clade under the Nextstrain phylogenetic classification system.[14]

At the end of May 2021, the WHO assigned the label Delta to lineage B.1.617.2 after introducing a new policy of using Greek letters for variants of concern and variants of interest.[4]

Other sublineages of B.1.617

There are three sublineages of B.1.617 categorised so far.

B.1.617.1 (VUI-21APR-01) was designated a Variant Under Investigation in April 2021 by Public Health England. Later in April 2021, two other variants B.1.617.2 (VUI-21APR-02) and B.1.617.3 (VUI-21APR-03) were designated as Variants Under Investigation. While B.1.617.3 shares the L452R and E484Q mutations found in B.1.617.1, B.1.617.2 lacks the E484Q mutation. B.1.617.2 has the T478K mutation, not found in B.1.617.1 and B.1.617.3.[15][16] Simultaneously, the ECDC released a brief maintaining all three sublineages of B.1.617 as VoI, estimating that a "greater understanding of the risks related to these B.1.617 lineages is needed before any modification of current measures can be considered".[17]

Mutations

  • Amino acid mutations of SARS-CoV-2 Delta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.
    Amino acid mutations of SARS-CoV-2 Delta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.
Defining mutations in the
SARS-CoV-2 Delta variant
Gene Nucleotide Amino acid
ORF1b P314L
P1000L
Spike G142D
T19R
R158G
L452R
T478K
D614G
P681R
D950N
E156del
F157del
M I82T
N D63G
R203M
D377Y
orf3a S26L
orf7a V82A
T120I
Sources: CDC[18] Covariants.org[19]

The Delta/ B.1.617.2 genome has 13 mutations (15 or 17 according to some sources,[which?] depending on whether more common mutations are included) which produce alterations in the amino-acid sequences of the proteins it encodes.[3] Four of them, all of which are in the virus's spike protein code, are of particular concern:

  • D614G. The substitution at position 614, an aspartic acid-to-glycine substitution, is shared with other highly transmissible variants like Alpha, Beta and Gamma.[20]
  • T478K.[20][21] The exchange at position 478 is a threonine-to-lysine substitution.[22]
  • L452R. The substitution at position 452, a leucine-to-arginine substitution, confers stronger affinity of the spike protein for the ACE2 receptor and decreased recognition capability of the immune system.[7][23] These mutations, when taken individually, are not unique to the variant; rather, their simultaneous occurrence is.[7][24]
  • P681R. The substitution at position 681, a proline-to-arginine substitution, which, according to William A. Haseltine, may boost cell-level infectivity of the variant "by facilitating cleavage of the S precursor protein to the active S1/S2 configuration".[25]

The E484Q mutation is not present in the B.1.617.2 genome.[25][26]

"Delta plus" variant

See also: Variants of SARS-CoV-2 § Delta (lineage B.1.617.2)

Delta with K417N corresponds to lineages AY.1 and AY.2[27] and has been nicknamed "Delta plus" or "Nepal variant". It has the K417N mutation[28] which is also present in the Beta variant.[29] The exchange at position 417 is a lysine-to-asparagine substitution.[30]

Symptoms

See also: Symptoms of COVID-19

The most common symptoms may have changed from the most common symptoms previously associated with standard COVID-19. Infected people may mistake the symptoms for a bad cold and not realize they need to isolate. Common symptoms reported have been headaches, sore throat, a runny nose or a fever.[31][better source needed][32] In the United Kingdom, where the Delta variant makes up 91 percent of new cases, one study found that the most reported symptoms were headache, sore throat, and runny nose.[33]

Treatment

See also: Treatment and management of COVID-19

The treatment for those infected by the SARS-CoV-2 Delta variant is as per others infected by COVID-19.

Vaccine efficacy

ICMR found that convalescent sera of the COVID-19 cases and recipients of Bharat Biotech's BBV152 (Covaxin) were able to neutralise VUI B.1.617 although with a lower efficacy.[34]

Anurag Agrawal, the director of the Institute of Genomics and Integrative Biology (IGIB), said the study on the effectiveness of the available vaccines on lineage B.1.617 suggests that post-vaccination, the infections are milder.[35]

Anthony Fauci, the Chief Medical Advisor to the President of US, has also expressed his confidence regarding the preliminary results. In an interview on 28 April, he said:

This is something where we're still gaining data daily. But the most recent data was looking at convalescent Sera of COVID-19 cases and people who received the vaccine used in India, the Covaxin. It was found to neutralise the 617 variants.[36]

Another study by the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad found Covishield (Oxford–AstraZeneca) vaccinated sera offers protection against lineage B.1.617.[37]

The WHO has said current vaccines will continue to be effective against the variant. In an update in May, they said there may be some evidence of "reduced neutralization".[38] A study conducted by the Public Health England, has found that both Pfizer-BioNTech and AstraZeneca-Oxford vaccines provide a 33% protection against symptomatic disease caused by the variant after the first dose. Two weeks after the second dose the Pfizer-BioNTech vaccine was found to be 88% effective at stopping symptomatic disease from the Delta variant while the AstraZeneca-Oxford vaccine was 60% effective against the variant.[39][40]

A group of researchers from the Francis Crick Institute, published in The Lancet shows that humans fully vaccinated with the Pfizer-BioNTech vaccine are likely to have more than five times lower levels of neutralizing antibodies against the Delta variant.[41][42]

In June 2021, Public Health England announced it had conducted a study which found that after two shots, the Pfizer-BioNTech vaccine and the AstraZeneca vaccine are respectively 96% and 92% effective at preventing hospitalisation from the Delta variant.[43][44]

Epidemiology

Emerging research suggests the variant may be more transmissible than previously evolved ones.[45] Whether the effectiveness of currently-deployed vaccines is affected remains under investigation.[46][47][48]

Surveillance data from the Indian government's Integrated Disease Surveillance Programme (IDSP) shows that around 32% of patients, both hospitalised and outside hospitals, were aged below 30 in the second wave compared to 31% during the first wave, among people aged 30–40 the infection rate stayed at 21%. Hospitalisation in the 20-39 bracket increased to 25.5% from 23.7% while the 0-19 range increased to 5.8% from 4.2%. The data also showed a higher proportion of asymptomatic patients were admitted during the second wave, with more complaints of breathlessness.[49]

The latest available data from early June indicates the prevalence ratio of the Delta variant with respect to the Alpha variant in the U.S., the Netherlands and Germany was in the 0.11 to 0.20 range. Surveillance data from the U.S., Germany and the Netherlands indicates the Delta variant is growing by about a factor of 4 every two weeks with respect to the Alpha variant, so it is expected to become the dominant variant around the turn of the month in these countries.[50][51][52][53][54][55][56]

In India, the United Kingdom, Portugal, Germany the delta variant is already the dominant strain.[57][58]

Statistics

By 22 June 2021, more than 4,500 sequences of the variant had been detected in about 78 countries.[2][59][60] Reported numbers of sequences in countries with detections are:

Cases by country
Country/Area Confirmed Delta variant cases:
(PANGOLIN)[61] as of 29 June 		Confirmed cases
(GISAID)[2] as of 30 May 		Confirmed cases,
all 3 sublineages of B.1.617
(PANGOLIN)[62] as of 1 June 		Cases (other sources) First detection
 India 6,724 3,364 3,571 5 October 2020
 United Kingdom 71,829 8,956 9,273 22 February 2021
 United States 4,260 1,539 1,542 23 February 2021
 Singapore 823 156 156 26 February 2021
 Australia 196 145 144 16 March 2021
 Canada 171 163 - 3,147[63] 15 March 2021
 Germany 1,392 420 420 1 March 2021
 Fiji - - - 42[64] 28 April 2021
 Israel 96 38 35 41[65][66][67] 16 April 2021
 Denmark 275 105 105 8 March 2021
 Japan 200 174 165 28 March 2021
 Bahrain - 19 19 5 April 2021
 Poland 82 34 34 16[68] 26 April 2021
 Ireland 188 155 155 26 February 2021
  Switzerland 212 61 64 29 March 2021
 Belgium 384 98 120 25 March 2021
 France 296 88 85 21 February 2021
 New Zealand - 15 15 9 March 2021
 China - 7 7 24 April 2021
   Nepal - 7 - 9[69] 28 April 2021
 Angola - 8 8 14 January 2021
 Hong Kong - 10 8 22 April 2021
 Portugal 736 38 52 5 April 2021
 Sweden 167 17 17 26 March 2021
 Luxembourg 51 7 6 15 April 2021
 The Netherlands 245 51 50 6 April 2021
 Italy 417 80 81 2 April 2021
 South Korea - 6 7 26 March 2021
 Spain 556 65 65 22 April 2021
 Turkey - 1 - 5[70] 28 April 2021
 Finland 126 1 - 60[71][72][73] 18 March 2021
 Jordan - 5 4 21 April 2021
 Russia 398 4 4 16[74] 21 April 2021
 Bangladesh 43 20 20 9[75][76] 28 April 2021
 Czech Republic - 7 2 24 April 2021
 Greece - 2 2 23 March 2021
 Guadeloupe - 2 2 10 March 2021
 Indonesia 215 32 32 3 April 2021
 Argentina - 1 - 2[77] 24 April 2021
 Morocco - 1 - 2[78] 3 May 2021
 Thailand 94 1 - 2[79] 24 April 2021
 Sint Maarten - 4 - 19 March 2021
 Algeria - - - 6[80] April 2021
 Aruba - 3 3 16 April 2021
 Austria - 5 - 17 April 2021
 Botswana - 1 - 2[81] 28 April 2021
 Cambodia - 1 - 5 April 2021
 Curacao - 1 - 23 April 2021
 Cyprus - - - 4[82] 19 May 2021
 DR Congo - 6 - 5[83] 3 May 2021
 Haiti - - - (number unreported)[84]
 Iran - 6 6 3[85] 11 May 2021
 Kenya - - - 5[83][86] May 2021
 Kyrgyzstan - - - (number unreported)[84]
 Malaysia - 4 - 10 April 2021
 Mexico 211 26 27 5 April 2021
 Nigeria - - - 1[83] May 2021
 Norway 117 20 20 1[87] 15 April 2021
 Panama - - - 1[88] April 2021
 Romania - 19 19 26 April 2021
 Reunion - 1 - 4 May 2021
 Slovenia - 2 - 20 April 2021
 South Africa 185 14 15 4[89] 30 April 2021
 Sri Lanka - 1 - 1[90] 30 April 2021
 Uganda - 5 4 1[91] 26 March 2021
 Philippines - - - 17[92][93][94] 11 May 2021[95]
 Uzbekistan - - - (number unreported)[84]
 Vietnam 54 - - 12[96][97] 18 April 2021
 Brazil - 2 2 10 [98] [99] 20 May 2021[100] [101] [102]
 Qatar - 8 - 19 April 2021
 Guam - 1 - 26 April 2021
 Ghana - 5 - 20 April 2021
 Pakistan - 1 - 16 May 2021
 Lithuania - - - 1[103] 17 June 2021
World (74 countries) Total: 77,544
(solely B.1.617.2)		 Total: 16,049 Total: 16,366
incl. B.1.617.1, B.1.617.2, and B.1.617.3		 3,341 Total as of 26 June 2021.

History

In countries other than India, the first cases of the variant were detected in late February 2021, including the United Kingdom on 22 February, the United States on 23 February and Singapore on 26 February.[62][3][2]

British scientists at Public Health England redesignated the B.1.617.2 variant on 7 May 2021 as "variant of concern" (VOC-21APR-02),[104] after they flagged evidence in May 2021 that it spreads more quickly than the original version of the virus. Another reason was that they identified 48 clusters of B.1.617.2, some of which revealed a degree of community transmission.[105][106] With cases from the Delta variant having risen quickly, British scientists considered the Delta variant having overtaken the Alpha variant as the dominant variant of SARS-CoV-2 in the UK in early June 2021.[107] Researchers at Public Health England later found that over 90% of new cases in the UK in the early part of June 2021 were the Delta variant; they also cited evidence that the Delta variant was associated with an approximately 60% increased risk of household transmission compared to the Alpha variant.[108]

Canada's first confirmed case of the variant was identified in Quebec on 21 April 2021, and later the same day 39 cases of the variant were identified in British Columbia.[109] Alberta reported a single case of the variant on 22 April 2021.[110] Nova Scotia reported two Delta variant cases in June 2021.[111]

Fiji also confirmed its first case of the variant on 19 April 2021 in Lautoka, and has since then climbed up to 42 cases and counting.[112] The variant has been identified as a super-spreader and has led to the lockdowns of five cities (Lautoka, Nadi, Suva, Lami and Nausori), an area which accounts for almost two-thirds of the country's population.

On 29 April 2021, health officials from Finland's the Ministry of Social Affairs and Health (STM) and the Finnish Institute for Health and Welfare (THL) reported that the variant had been detected in three samples dating back to March 2021.[71]

The Philippines confirmed its first two cases of the variant on 11 May 2021, despite the imposed travel ban of the country from the nations in the Indian subcontinent (except for Bhutan and Maldives). Both patients have no travel history from India for the past 14 days, but instead from Oman and UAE.[113]

North Macedonia confirmed its first case of the variant on 7 June 2021 after a person who was recovering from the virus in Iraq was transported to North Macedonia. In a laboratory test, the variant was detected in the person. On 22 June 2021, the country reported its second case of the Delta variant in a colleague of the first case who had also been in Iraq and who subsequently developed symptoms.[114]

The detection of B.1.617 was hampered in some countries by a lack of specialised kits for the variant and laboratories that can perform the genetic test.[115][116] For example, as of 18 May, Pakistan had not reported any cases, but authorities noted that 15% of COVID-19 samples in the country were of an "unknown variant"; they could not say if it was B.1.617 because they were unable to test for it. Other countries had reported travellers arriving from Pakistan that were infected with B.1.617.[115]

In June 2021, scientist Vinod Scaria of India's Institute of Genomics and Integrative Biology highlighted the existence of the B.1.617.2.1 variant, also known as AY.1 or Delta plus, which has an additional K417N mutation compared to the Delta variant.[28] B.1.617.2.1 was detected in Europe in March 2021, and has since been detected in Asia and America.[28]

Society and culture

International reactions

After the rise in cases from the second wave, at least 20 countries imposed travel bans and restrictions on passengers from India in April and May. UK prime minister Boris Johnson cancelled his visit to India twice, while Japanese Prime Minister Yoshihide Suga postponed his April trip.[117][118][119]

In May 2021, residents of two tower blocks in Velbert, Germany were quarantined after a woman in the building tested positive for the variant.[120]

In May, Delhi Chief Minister Arvind Kejriwal said that a new coronavirus variant from Singapore was extremely dangerous for children and could result in a third wave in India. Singapore's Ministry of Health said there was no Singapore variant nor any evidence of a coronavirus variant extremely dangerous to children,[121][122] and that the increase in COVID-19 cases came from the Delta variant.[122]

On 14 June, the British prime minister Boris Johnson announced that the proposed end of all restrictions on "Freedom Day" (21 June) in the United Kingdom was delayed for up to four weeks and vaccination roll-out was accelerated following concerns over the Delta variant, which accounted for the vast majority (90%) of new infections. UK scientists have said that the Delta variant is between 40% and 80% more transmissible than the previously-dominant Alpha variant, which was first identified in the UK (as the Kent variant).[123]

See also

References

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