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.

Countries with confirmed cases of Delta variant as of 9 July 2021 (GISAID)
Legend:
  5,000+ confirmed sequences
  1,000–4,999 confirmed sequences
  100–999 confirmed sequences
  10–99 confirmed sequences
  2–9 confirmed sequences
  1 confirmed sequence
  None or no data
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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][failed verification] Public Health England (PHE) in May 2021 observed secondary attack rates to be 51–67% higher than the alpha variant.[8] COVID-19 vaccines are effective in preventing severe disease or hospitalisation from infection with the variant, although some evidence suggests vaccinated people are more likely to develop symptoms from Delta than other variants of SARS-CoV-2.[9]

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);[10] the UK's SAGE subsequently estimated a "realistic" possibility of being 50% more transmissible.[11] 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.[12][13][14] It later contributed to a third wave in Fiji, the United Kingdom[15][16] and South Africa,[17] and the WHO warned in July 2021 it could have a similar effect elsewhere in Europe and Africa.[18][17] By late July it had also driven an increase in daily infections in parts of Asia,[19] the United States[20] and Australia.[21]

On 15 June 2021, the Center for Disease Control and Prevention declared Delta a variant of concern.[22]

Classification

The Delta variant has mutations in the gene encoding the SARS-CoV-2 spike protein[5] causing the substitutions D614G, T478K, P681R and L452R.[23][7] It is identified as the 21A clade under the Nextstrain phylogenetic classification system.[24]

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 lineage B.1.617 categorised so far.

B.1.617.1 was designated a Variant Under Investigation in April 2021 by Public Health England. Later in April 2021, two other variants B.1.617.2 and B.1.617.3 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.[25][26] 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".[27]

Mutations

  • Amino acid mutations of SARS-CoV-2 Delta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.[28]
    Amino acid mutations of SARS-CoV-2 Delta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.[28]
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[29] Covariants.org[30]

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.[31]
  • T478K.[31][23] The exchange at position 478 is a threonine-to-lysine substitution.[32]
  • L452R. The substitution at position 452, a leucine-to-arginine substitution, confers stronger affinity of the spike protein for the ACE2 receptor[33] and decreased recognition capability of the immune system.[7][34] These mutations, when taken individually, are not unique to the variant; rather, their simultaneous occurrence is.[7][35]
  • 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".[36]

The E484Q mutation is not present in the B.1.617.2 genome.[36][37]

"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[38] and has been nicknamed "Delta plus" or "Nepal variant". It has the K417N mutation[39] which is also present in the Beta variant.[40] The exchange at position 417 is a lysine-to-asparagine substitution.[41]

As of 15 July 2021, the AY.3 variant accounted for approximately 21% of cases in the United States.[42]

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.[43][better source needed][44] 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.[45]

Prevention

See also: Oxford–AstraZeneca COVID-19 vaccine § Effectiveness, Pfizer–BioNTech COVID-19 vaccine § Effectiveness, Sputnik V COVID-19 vaccine § Variants, and Covaxin § Efficacy

Non-pharmaceutical measures recommended to prevent wild type COVID-19 should still be effective for Delta. These would include washing your hands, wearing a mask, maintaining distance from others, avoiding touching your mouth, nose or eyes, avoiding crowded indoor spaces with poor ventilation especially where people are talking or exhaling, going to get tested if you develop symptoms and isolating if you become sick.[46] Public Health Authorities should continue to search out infected individuals using testing, trace their contacts, and isolate those who have tested positive or been exposed.[47] Event organizers should assess the potential risks of any mass gathering and develop a plan to mitigate these risks.[48] See also Non-pharmaceutical intervention (epidemiology).

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.[49]

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.[50]

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.[51]

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.[52]

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".[53] 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.[54][55]

A study by 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 compared to the original COVID-19 strain.[56][57]

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.[58][59]

On July 3, researchers from the universities of Toronto and Ottawa in Ontario, Canada released a preprint study suggesting that the Moderna vaccine may be effective against death or hospitalization from the Delta variant.[60][unreliable medical source?]

In a study of the University of Sri Jayewardenepura in July 2021 found the Sinopharm BBIBP-CorV vaccine caused seroconversion in 95% of individuals studied that had received both doses of the vaccine. The rate was higher in 20-39 age group (98.9%) but slightly lower in the over 60 age group (93.3%). Neutralising antibodies were present among 81.25% of the vaccinated individuals studied.[61][62]

On July 21, researchers from Public Health England published a study finding that the Pfizer vaccine was 93.7% effective against symptomatic disease from Delta after 2 doses, while the Astrazeneca vaccine was 67% effective.[63]

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.

Epidemiology

UK scientists have said that the Delta variant is between 40% and 60% more transmissible than the previously-dominant Alpha variant, which was first identified in the UK (as the Kent variant).[64] Given that Alpha is already 150% as transmissible compared to the original Wuhan strain,[64] and if Delta is 150% as transmissible compared to Alpha, then Delta may be 225% as transmissible compared to the original strain.[65] BBC reported that  – basic reproduction number, or the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection – for the original Wuhan virus to be 2.4-2.6, for Alpha 4-5, and for Delta 5-8;[66] these can be compared to seasonal influenza (1.2-1.4[67]), common cold (2-3[68]), smallpox (3.5-6[69]), and chickenpox (10-12[70]).

NPR reported on an a study[71] published online (not peer-reviewed) by Guangdong Provincial Center for Disease Control and Prevention that may partly explain the increased transmissibility: people with Delta infection had 1,000 time more copies of the virus in the respiratory tracts than those with Wuhan strain infection; and it took on average 4 days for people infected with Delta for the virus to be detectable compared to 6 days with the Wuhan strain.[72]

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.[73]

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.[74][75][76]

In India, the United Kingdom,[77] Portugal,[78] Russia,[79] Mexico, Australia, Indonesia,[80] Russia,[81] South Africa, Germany,[82] Luxembourg,[83] the United States,[84] the Netherlands,[85] Denmark,[86] France[87] and probably many other countries the Delta variant had become the dominant strain by July 2021. There is typically a three-week lag between cases and variant reporting.

On 7 June 2021, researchers at the National Centre for Infectious Diseases in Singapore posted a paper suggesting that patients testing positive for Delta are more likely to develop pneumonia and/or require oxygen than patients with wild type or Alpha.[88]

On June 14, researchers from Public Health Scotland found that the risk of hospitalization from Delta was roughly double that of from Alpha.[89]

On June 11, Public Health England released a report finding that there was "significantly increased risk of hospitalization" from Delta as compared with Alpha.[90]

On July 9, Public Health England reported that the Delta variant in England had a case fatality rate (CFR) of 0.2%, while the Alpha variant's case fatality rate was 1.9%, although the report warns that "case fatality rates are not comparable across variants as they have peaked at different points in the pandemic, and so vary in background hospital pressure, vaccination availability and rates and case profiles, treatment options, and impact of reporting delay, among other factors. "[91] James McCreadie, a spokesperson for Public Health England, clarified "It is too early to assess the case fatality ratio compared to other variants."[92]

On 12 July, a preprint study from epidemiologists at the University of Toronto, Canada found that Delta had a 120% greater risk of hospitalization, 287% greater risk of ICU admission and 137% greater risk of death compared to non-variant of concern strains of SARS-COV-2.[93]

Statistics

By 22 June 2021, more than 4,500 sequences of the variant had been detected in about 78 countries.[2][94][95] Reported numbers of sequences in countries with detections are:

Cases by country
Country/Area Confirmed Delta variant cases:
(PANGOLIN)[96] as of 14 July 		Confirmed cases
(GISAID)[2] as of 22 July 		Cases (other sources)
as of 22 July 2021 		First detection
 United Kingdom 124,991 153,862 253,049[97] 22 February 2021
 United States 12,499 17,650 83.2% of variant cases[98] 23 February 2021
 Fiji - - (15,686 active cases of COVID-19) [99][100][101] 19 April 2021
 India 10,584 13,575 5 October 2020
 Canada 315 2,365 7.782[102] 15 March 2021
 Denmark 2,534 7,022 8 March 2021
 Japan 448 577 918[103] L452R: 4,349[104] 28 March 2021
 Germany 2,679 3,609 1 March 2021
 Spain 1,399 2,789 22 April 2021
 Italy 1,346 2,534 2 April 2021
 Portugal 1,846 2,495 5 April 2021
 Sweden 1,725 2,442 26 March 2021
 France 1,109 1,871 21 February 2021
 Belgium 1,077 1,841 25 March 2021
 The Netherlands 821 1,249 6 April 2021
 South Africa 382 1,201 4[105] 30 April 2021
 Mexico 382 1,198 5 April 2021
 Ireland 602 1,194 26 February 2021
 Singapore 1,038 1,083 26 February 2021
 Russia 783 985 16[106] 21 April 2021
 Indonesia 580 797 3 April 2021
  Switzerland 418 675 29 March 2021
 Israel 644 670 41[107][108][109] 16 April 2021
 Australia 583 643 332[110] 16 March 2021
 Turkey - 611 5[111] 28 April 2021
 Austria 370 554 17 April 2021
 Norway 347 411 1[112] 15 April 2021
 Botswana - 233 2[113] 28 April 2021
 Bangladesh 43 204 9[114][115] 28 April 2021
 Qatar - 184 19 April 2021
 DR Congo - 182 5[116] 3 May 2021
 Finland 126 1 60[117][118][119] 18 March 2021
 Poland 82 106 16[120] 26 April 2021
 Thailand 94 100 2[121] 24 April 2021
   Nepal - 88 9[122] 28 April 2021
 Luxembourg 51 52 15 April 2021
 China - 41 24 April 2021
 Bahrain - 36 5 April 2021
 New Zealand - 23 9 March 2021
 Angola - 8 14 January 2021
 Hong Kong - 10 22 April 2021
 South Korea - 20 26 March 2021
 Jordan - 5 21 April 2021
 Czech Republic - 79 24 April 2021
 Greece - 10 23 March 2021
 Guadeloupe - 3 10 March 2021
 Argentina - 1 2[123] 24 April 2021
 Morocco - 1 2[124] 3 May 2021
 Sint Maarten - 4 19 March 2021
 Algeria - - 6[125] April 2021
 Aruba - 3 16 April 2021
 Cambodia - 25 5 April 2021
 Curacao - 1 23 April 2021
 Cyprus - - 4[126] 19 May 2021
 Haiti - - (number unreported)[127]
 Iran - 6 3[128] 11 May 2021
 Kenya - 37 5[116][129] May 2021
 Kyrgyzstan - - (number unreported)[127]
 Malaysia - 24 10 April 2021
 Nigeria - - 1[116] May 2021
 Panama - - 1[130] April 2021
 Romania - 32 26 April 2021
 Reunion - 2 4 May 2021
 Slovenia - 6 20 April 2021
 Sri Lanka - 6 1[131] 30 April 2021
 Uganda - 38 1[132] 26 March 2021
 Philippines - 12 64[133][134][135][136][137][138][139][140] 11 May 2021
 Uzbekistan - - (number unreported)[127]
 Vietnam 54 72 12[141][142] 18 April 2021
 Brazil - 16 10 [143][144] 20 May 2021[145][146][147]
 Guam - 1 26 April 2021
 Ghana - 5 20 April 2021
 Pakistan - 9 16 May 2021
 Lithuania - 10 1[148] 17 June 2021
 Croatia - 28 11 June 2021
 Monaco - 16 15 May 2021
 Malawi - 14 30 April 2021
 Slovakia - 5 15 June 2021
 Myanmar - 5 1 June 2021
 Barbados - 4 24 May 2021
 Kuwait - 4 5 June 2021
 Georgia - 4 15 May 2021
 Malta - 3 23 June 2021
 Senegal - 2 6 May 2021
 Peru - 2 10 June 2021
 Mauritius - 2 8 May 2021
 Chile - 1 13 June 2021
 Taiwan - 1 14 June 2021
 Bulgaria - 1 5 April 2021
 Anguilla - 1 20 April 2021
World (90 countries) Total: 170,661
(solely B.1.617.2)		 Total: 181,129
(B.1.617.2+AY.1+AY.2)		 253,029

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.[149][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),[150] 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.[151][152] 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.[153] 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.[154]

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.[155] Alberta reported a single case of the variant on 22 April 2021.[156] Nova Scotia reported two Delta variant cases in June 2021.[157]

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.[158] 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.[117]

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.[159]

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.[160]

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.[161][162] 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.[161]

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.[39] B.1.617.2.1 was detected in Europe in March 2021, and has since been detected in Asia and America.[39]

On 9 July 2021, Public Health England issued Technical Briefing 18 on SARS-CoV-2 variants, documenting 112 deaths among 45,136 UK cases of SARS-CoV-2 Delta variant with 28 days follow-up with a fatality rate of 0.2%.[163] Briefing 16 notes that "[M]ortality is a lagged indicator, which means that the number of cases who have completed 28 days of follow up is very low – therefore, it is too early to provide a formal assessment of the case fatality of Delta, stratified by age, compared to other variants."[164] Briefing 18 warns that "Case fatality is not comparable across variants as they have peaked at different points in the pandemic, and so vary in background hospital pressure, vaccination availability and rates and case profiles, treatment options, and impact of reporting delay, among other factors."[163] The most concerning issue is the logistic growth rate of 0.93/week relative to Alpha. This means that per week, the number of Delta samples/cases is growing by a factor of exp (0.93)=2.5 with respect to the Alpha variant. This results, under the same infection prevention measures, in a much greater case load over time until a large fraction of people have been infected by it.[165][166]

Government response

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.[167][168][169]

In May 2021, residents of two tower blocks in Velbert, Germany were quarantined after a woman in the building tested positive for the Delta variant.[170]

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,[171][172] and that the increase in COVID-19 cases came from the Delta variant.[172]

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.[173] UK scientists have said that the Delta variant is between 40% and 60% more transmissible than the previously-dominant Alpha variant, which was first identified in the UK (as the Kent variant).[174]

On 23 June, the province of Ontario in Canada accelerated 2nd dose vaccine appointments for people living in Delta hot spots such as Toronto, Peel and Hamilton.[175]

On 25 June, Israel restored their mask mandate citing the threat of Delta.[176]

On 28 June, Sydney and Darwin in Australia went back into lockdown because of Delta outbreaks.[177] South Africa banned indoor and outdoor gatherings apart from funerals, imposed a curfew, and banned the sale of alcohol.[178]

On 3 July, the islands of Bali and Java in Indonesia went into emergency lockdown.[179]

On 8 July, Japanese Prime Minister Yoshihide Suga announced that Tokyo would once again enter a state of emergency, and that most spectators would be barred from attending the Olympics set to start there on July 23.[180]

On 9 July, Seoul, Korea ramped up restrictions urging people to wear masks outdoors, and limiting the size of gatherings.[181]

On 12 July, French President Emmanuel Macron announced that all health care workers will need to be vaccinated by September 15 and that France will start using health passports to enter bars, cafés, restaurants and shopping centres from August.[182]

Los Angeles announced it will require masks indoors starting 17 July 2021.[183]

See also

References

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External links

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