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SARS-CoV-2 Delta variant

Source: Wikipedia, the free encyclopedia.

Countries with confirmed cases of Delta variant as of 10 August 2021 (GISAID)
Legend:
  10,000+ confirmed sequences
  5,000–9,999 confirmed sequences
  1,000–4,999 confirmed sequences
  100–999 confirmed sequences
  10–99 confirmed sequences
  1-9 confirmed sequence
  None or no data

The Delta variant[note 1] is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The Delta variant was named on 31 May 2021 and had spread to over 163 countries by 24 August 2021. The World Health Organization (WHO) indicated that the Delta variant is becoming the dominant strain globally.[when?]

It has mutations in the gene encoding the SARS-CoV-2 spike protein[1] causing the substitutions T478K, P681R and L452R,[2][3] 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.[4] It is thought to be one of the most transmissible respiratory viruses known.[5] In August 2021, Public Health England (PHE) reported secondary attack rate in household contacts of non-travel or unknown cases for Delta to be 10.8% vis-à-vis 10.2% for the Alpha variant;[6] the case fatality rate for those 386,835 people with Delta is 0.3%, where 46% of the cases and 6% of the deaths are unvaccinated and below 50 years old.[7] Immunity from previous recovery[8][9] or COVID-19 vaccines are effective in preventing severe disease or hospitalisation from infection with the variant.[10]

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);[11] the UK's SAGE using May data estimated a "realistic" possibility of being 50% more transmissible.[12] On 11 May 2021, the WHO also classified this lineage VOC, and said that it showed evidence of higher transmissibility and reduced neutralisation. On 15 June 2021, the Centers for Disease Control and Prevention (CDC) declared Delta a variant of concern.[13]

The variant is thought to be partly responsible for India's deadly second wave of the pandemic beginning in February 2021.[14][15][16] It later contributed to a third wave in Fiji, the United Kingdom[17][18][19] and South Africa,[20] and the WHO warned in July 2021 that it could have a similar effect elsewhere in Europe and Africa.[21][20] By late July, it had also driven an increase in daily infections in parts of Asia,[22] the United States,[23] Australia, and New Zealand.[24]

Classification

The Delta variant has mutations in the gene encoding the SARS-CoV-2 spike protein[1] causing the substitutions D614G, T478K, P681R and L452R.[25][3] It is identified as the 21A clade under the Nextstrain phylogenetic classification system.[26]

Names

The virus has also been referred to by the term "Indian Variant"[27] as it was originally detected in India. However, the Delta variant is only one of three variants of the lineage B.1.617, all of which were first detected in India.[28] 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.[29]

Other sublineages of B.1.617

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

B.1.617.1 (Kappa variant) 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.[30][31] 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".[32]

Mutations

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[34] Covariants.org[35]

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.[36] 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.[4]
  • T478K.[4][25] The exchange at position 478 is a threonine-to-lysine substitution.[37]
  • L452R. The substitution at position 452, a leucine-to-arginine substitution, confers stronger affinity of the spike protein for the ACE2 receptor[38] and decreased recognition capability of the immune system.[3][39]
  • 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".[40]

The E484Q mutation is not present in the B.1.617.2 genome.[40][41]

Delta variants

As of August 2021, Delta have been subdivided in the Pango lineage designation system into variants from AY.1 to AY.38. However, there are no information on whether such classification correlate with biological characteristic changes of the virus.[42] It is said that, as of August 2021, AY.4 to AY.11 are predominant in the UK, AY.12 in Israel, AY.2, AY.3, AY.13, AY.14, AY.25 in the US, AY.20 in the US and Mexico, AY.15 in Canada, AY.16 in Kenya, AY.17 in Ireland and Northern Ireland, AY.19 in South Africa, AY.21 in Italy and Switzerland, AY.22 in Portugal, AY.24 in Indonesia, and AY.23 in Indonesia, Singapore, Japan, and South Korea.[43]

As of 30 August 2021, the AY.4 variant accounted for approximately 59% of cases in the United States.[44]

"Delta plus" variant

Delta with K417N corresponds to lineages AY.1 and AY.2[45] and has been nicknamed "Delta plus" or "Nepal variant".[46] It has the K417N mutation,[47] which is also present in the Beta variant.[48] The exchange at position 417 is a lysine-to-asparagine substitution.[49]

As of mid-October 2021, the AY.3 variant accounted for a cumulative prevalence of approximately 5% in the United States, and 2% worldwide.[50] In mid-October the AY.4.2 Delta sublineage was expanding in England, and being monitored and assessed. It contains mutations A222V and Y145H in its spike protein, not considered of particular concern. It has been suggested that AY.4.2 might be 10-15% more transmissible than the original Delta variant. Mid-October 2021, AY.4.2 accounted for an estimated 10% of cases, and has lead to an additional growth rate rising to about 1% (10% of 10%) per generational time of five days or so. This additional growth rate would grow with increasing prevalence. Without AY.4.2 and no other changes, the number of cases in the UK would have been about 10% lower.[51] In the UK it was reclassified as a "variant under investigation" (but not "of concern") in late October 2021.[52]

Symptoms

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.[53][medical citation needed][54] In the United Kingdom, when the Delta variant accounted for 91 percent of new cases, one study found that the most reported symptoms were headache, sore throat, and runny nose.[55]

Prevention

Summary of Vaccine Protection against Delta
(WHO's update, 24 August 2021[56])
Disease or infection Severe: protection retained
Symptomatic: possibly reduced protection
Severe disease Steady: AstraZeneca-Vaxzevria(1), Moderna(1), Pfizer-BioNTech(2)
Symptomatic disease Steady to Neutral decrease: Pfizer-BioNTech(3)
Neutral decrease: Covaxin(1)
Neutral decreaseNeutral decrease: AstraZeneca-Vaxzevria(2)
Infection Neutral decrease: AstraZeneca-Vaxzevria(1), Pfizer-BioNTech(1)
Symbols indicate the magnitude of vaccine effectiveness (VE) reduction. Note that VE reduction doesn't mean loss of protection, because original high protection rate (such as 95%) with some reduction (such as 10%) would still retain protection (such as 85%). Enclosed in parentheses is the number of studies supporting the indication. Studies vary in population, outcome definitions, study design, etc., which may explain differences in VE estimates for a product in different studies. Also, the reductions represent VE estimates and do not represent uncertainties around the estimates which may vary substantially across studies. The VE reductions should be interpreted with these limitations.

Steady: VE reduces <10%, or VE >90% without comparator
Neutral decrease: VE reduces between 10 to <20%

Neutral decreaseNeutral decrease: VE reduces between 20 to <30%
Effects on Neutralization (fully vaccinated)[57]
Steady to Neutral decrease: Anhui-ZIFIVAX(2), Covaxin(3)
Neutral decrease: Janssen(3), Moderna(3), Covishield(2)
Neutral decrease to Neutral decreaseNeutral decrease: AstraZeneca-Vaxzevria(4), Pfizer-BioNTech(8)
Neutral decreaseNeutral decrease:Moderna & Pfizer-BioNTech(1)*
Neutral decrease to Neutral decreaseNeutral decreaseNeutral decrease: Coronavac(2)
Symbols indicate the magnitude of neutralization reduction with full vaccination. Enclosed in parentheses is the number of studies supporting the indication.

Steady: Neutralization reduces <2-fold
Neutral decrease: Neutralization reduces 2 to <5-fold
Neutral decreaseNeutral decrease: Neutralization reduces 5 to <10-fold
Neutral decreaseNeutral decreaseNeutral decrease: Neutralization reduces ≥ 10-fold
* Moderna & Pfizer-BioNTech were evaluated together.

WHO has not issued preventative measures against Delta specifically; non-pharmaceutical measures recommended to prevent wild type COVID-19 should still be effective. These would include washing hands, wearing a mask, maintaining distance from others, avoiding touching the mouth, nose or eyes, avoiding crowded indoor spaces with poor ventilation especially where people are talking, going to get tested if one develops symptoms and isolating if one becomes sick.[58] Public Health authorities should continue to find infected individuals using testing, trace their contacts, and isolate those who have tested positive or been exposed.[59] Event organizers should assess the potential risks of any mass gathering and develop a plan to mitigate these risks.[60] 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.[61]

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.[62]

Anthony Fauci, the Chief Medical Advisor to the President of the United States, 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.[63]

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.[64]

A study conducted by the Public Health England, has found that compared to those who were unvaccinated those who were vaccinated with either the Pfizer-BioNTech or AstraZeneca-Oxford had 33% less instances of symptomatic disease caused by the variant after the first dose. Among those who were two weeks after the receiving their second dose of the Pfizer-BioNTech vaccine 88% less subjects had symptomatic disease from the Delta variant versus those that were unvaccinated. Among those who were two weeks after the receiving their second dose of the AstraZeneca-Oxford vaccine 60% less subjects had symptomatic disease from the Delta variant versus those that were unvaccinated.[65][66]

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.[67][68]

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.[69][70]

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.[71][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.[72][73]

On 29 June 2021, the director of the Gamaleya Institute, Denis Logunov, said that Sputnik V is about 90% effective against the Delta variant.[74]

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.[75]

On August 2, several experts expressed concern that achieving herd immunity may not currently be possible because the Delta variant is transmitted among those immunized with current vaccines.[76]

On August 10, a study showed that the full vaccination coverage rate is correlated inversely to the SARS-CoV-2 delta variant mutation frequency in 16 countries (R-squared=0.878). Data strongly indicates that full vaccination against COVID-19 may slow down virus evolution.[77]

Treatment

In vitro experiments suggest that bamlanivimab may not be effective against Delta on its own.[78] At high enough concentrations, casirivimab, etesevimab and imdevimab appear to still be effective. A preprint study suggests that sotrovimab may also be effective against Delta.[79] Doctors in Singapore have been using supplemental oxygen, remdesivir and corticosteroids on more Delta patients than they did on previous variants.[80]

Epidemiology

Summary of impacts for Delta*
(WHO's update, 24 August 2021[56])
Transmissibility Increased transmissibility and secondary attack rate, similar transmissibility between vaccinated and unvaccinated individuals.
Virulence Increased risk of hospitalization
Reinfection Decreased neutralizing activity
Diagnostics No impacts yet reported
* Generalized finding compared to other strains, based on evidence including non-peer-reviewed publications.

Transmissibility

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).[81] Given that Alpha is already 150% as transmissible as the original SARS-CoV-2 strain that emerged in late 2019 in Wuhan,[81] and if Delta is 150% as transmissible as Alpha, then Delta may be 225% as transmissible as the original strain.[82] 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 first detected SARS-CoV-2 virus is 2.4-2.6, whereas Alpha's reproduction number is 4-5 and Delta's is 5–9.[83][84] These basic reproduction numbers can be compared to MERS (0.29-0.80[85]), seasonal influenza (1.2-1.4[86]), Ebola (1.4-1.8[87]), common cold (2-3[88]), SARS (2–4[89]), smallpox (3.5-6[90]), and chickenpox (10-12[91]). Due to Delta's high transmissibility even those that are vaccinated are vulnerable,[92] albeit to a lesser extent.[66]

A study[93] published online (not peer-reviewed) by Guangdong Provincial Center for Disease Control and Prevention may partly explain the increased transmissibility: people with Delta infection had 1,000 times 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.[94][95]

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.[96][97][98]

In India, the United Kingdom,[99] Portugal,[100] Russia,[101] Mexico, Australia, Indonesia,[102] South Africa, Germany,[103] Luxembourg,[104] the United States,[105] the Netherlands,[106] Denmark,[107] France[108] 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. As of July 20, this variant had spread to 124 countries,[57] and WHO had indicated that it was becoming the dominant strain, if not one already.[109]

In the Netherlands, the virus was still able to propagate significantly in the population with over 93.4% of blood donors being tested positive for Sars-Cov-2 antibodies after week 28, 2021. Many people there are not fully vaccinated, so those antibodies would have been developed from exposure to the wild virus or from a vaccine.[110]

A preprint found that the viral load in the first positive test of infections with the variant was on average ∼1000 times higher than with compared infections during 2020.[111][112] Preliminary data from a study with 100,000 volunteers in the UK from May to July 2021, when Delta was spreading rapidly, indicates that vaccinated people who test positive for COVID-19, including asymptomatic cases, have a lower viral load in average. Data from the US, UK, and Singapore indicate that vaccinated people infected by Delta may have viral loads as high as unvaccinated infected people, but might remain infectious for a shorter period.[113]

Infection age groups

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.[114]

Virulence

A few early studies suggest the Delta variant causes more severe illness than other strains.[115] 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.[116] On June 11, Public Health England released a report finding that there was "significantly increased risk of hospitalization" from Delta as compared with Alpha;[117] the risk was approximately twice as high for those infected with the Delta variant.[118] On June 14, researchers from Public Health Scotland found that the risk of hospitalization from Delta was roughly double that of from Alpha.[119] On July 7, a preprint study from epidemiologists at the University of Toronto found that Delta had a 120% greater – or more than twice as large – 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.[120] However, 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."[121] James McCreadie, a spokesperson for Public Health England, clarified "It is too early to assess the case fatality ratio compared to other variants."[122]

A Canadian study released on 5 October, 2021 revealed that the Delta variant caused a 108 percent rise in hospitalization, 235 percent increase in ICU admission, and a 133 percent surge in death compared to other variants. is more serious and resulted in an increased risk of death compared to previous variants, odds that are significantly decreased with immunization.[123][124]

Statistics

By 22 June 2021,[needs update] more than 4,500 sequences of the variant had been detected in about 78 countries.[125][126][127] Reported numbers of sequences in countries with detections are:

Cases by country
Country/Area Confirmed Delta variant cases:
(PANGOLIN)[128] as of 2 September
Confirmed cases
(GISAID)[125] as of 15 September
Cases (other sources)
as of 29 September 2021
First detection
 United Kingdom 239,594 418,611 669,401[129] 22 February 2021
 United States 86,350 302,001 99.4% of cases[130] 23 February 2021
 Fiji - - 47,639 [131][132][133] 19 April 2021
 India 15,693 24,877 5 October 2020
 Denmark 23,365 44,372 8 March 2021
 Canada 1,411 14,476 80,560[134] 15 March 2021
 Japan 1,374 12,840 1,583[135] L452R: 7,143[136] 28 March 2021
 Germany 9,252 36,505 1 March 2021
 Italy 8,027 15,031 2 April 2021
 Spain 6,443 15,332 22 April 2021
 France 10,063 28,077 21 February 2021
 Belgium 4,942 12,265 25 March 2021
 Portugal 4,151 6,908 5 April 2021
 Sweden 5,587 19,887 26 March 2021
 The Netherlands 7,886 16,028 6 April 2021
 South Africa 2,582 6,175 4[137] 30 April 2021
 Mexico 3,110 7,537 5 April 2021
 Ireland 4,461 10,559 26 February 2021
 Singapore 2,727 4,573 26 February 2021
 Russia 1,468 2,469 16[138] 21 April 2021
 Indonesia 1,623 2,613 3 April 2021
  Switzerland 5,150 13,105 29 March 2021
 Israel 2,460 3,375 41[139][140][141] 16 April 2021
 Australia 3,504 9,118 9,325[142] 16 March 2021
 Turkey 5,489 40,511 5[143] 28 April 2021
 Austria 1,578 3,622 17 April 2021
 Norway 1,241 4,273 1[144] 15 April 2021
 Botswana 196 468 2[145] 28 April 2021
 Bangladesh 283 702 9[146][147] 28 April 2021
 Qatar 121 179 19 April 2021
 DR Congo 19 228 5[148] 3 May 2021
 Finland 1,570 4,217 2,876[149][150][151][152] 18 March 2021
 Poland 491 1,690 16[153] 26 April 2021
 Thailand 236 420 2[154] 24 April 2021
   Nepal 100 138 9[155] 28 April 2021
 Luxembourg 1,153 1,227 15 April 2021
 China 86 307 24 April 2021
 Bahrain 117 618 5 April 2021
 New Zealand 92 1,008 107[156][157] 9 March 2021
 Angola 6 28 14 January 2021
 Hong Kong 153 10 22 April 2021
 South Korea 706 2,426 26 March 2021
 Jordan 5 19 21 April 2021
 Czech Republic 787 1,859 24 April 2021
 Greece 17 800 23 March 2021
 Guadeloupe - 149 10 March 2021
 Argentina 4 77 2[158] 24 April 2021
 Morocco 3 3 2[159] 3 May 2021
 Sint Maarten - 896 19 March 2021
 Algeria 17 18 6[160] 28 July 2021
 Aruba 90 1,285 16 April 2021
 Cambodia 171 243 5 April 2021
 Curacao - 234 23 April 2021
 Cyprus - 1 4[161] 19 May 2021
 Haiti - 1 (number unreported)[162] 27 July 2021
 Iran 11 11 3[163] 11 May 2021
 Kenya 256 694 5[148][164] 17 July 2021
 Kyrgyzstan - - (number unreported)[162] 16 May 2021[162]
 Malaysia 146 763 10 April 2021
 Nigeria 36 250 1[148] 7 August 2021
 Panama - - 1[165] April 2021
 Romania 294 504 26 April 2021
 Reunion 54 112 4 May 2021
 Slovenia - 2,973 20 April 2021
 Sri Lanka 117 467 1[166] 30 April 2021
 Uganda 134 163 1[167] 26 March 2021
 Philippines 11 12 3,366[168] 11 May 2021
 Uzbekistan 30 47 (number unreported)[162] 25 June 2021
 Vietnam 54 188 12[169][170] 18 April 2021
 Brazil 437 2,688 1051 [171][172] 20 May 2021[173][174][175][176][177]
 Guam - 14 26 April 2021
 Ghana 101 267 20 April 2021
 Pakistan 49 199 16 May 2021
 Lithuania 899 3,911 1[178] 17 June 2021
 Croatia 479 1,434 11 June 2021
 Monaco 34 48 15 May 2021
 Malawi 5 114 30 April 2021
 Slovakia 353 1,360 15 June 2021
 Myanmar 12 18 1 June 2021
 Barbados 3 23 24 May 2021
 Kuwait 108 161 5 June 2021
 Georgia 19 39 15 May 2021
 Malta 42 63 23 June 2021
 Senegal 13 33 6 May 2021
 Peru 6 104 10 June 2021
 Mauritius 15 17 8 May 2021
 Chile 64 231 13 June 2021
 Taiwan 3 5 14 June 2021
 Bulgaria 231 783 5 April 2021
 Anguilla - 7 20 April 2021
 Albania 11 11 13 July 2021
 Azerbaijan - 1 14 July 2021
 Bosnia and Herzegovina 31 31 26 July 2021
 Bonaire - 116 13 July 2021
 Burundi 3 3 31 May 2021
 Colombia - 21 3 July 2021
 Costa Rica 35 174 7 July 2021
 Crimea - 21 1 July 2021
 Ecuador 89 115 20 July 2021
 Gambia 42 82 12 July 2021
 French Guiana 53 132 22 July 2021
 Kosovo - 30 2 May 2021
 Latvia 22 22 27 May 2021
 Lebanon - 80 3 July 2021
 Maldives 6 168 31 July 2021
 Moldova 11 11 6 July 2021
 Namibia - 16 June 2021
 North Macedonia 6 38 11 July 2021
 Oman 8 113 17 May 2021
 Paraguay 4 8 8 July 2021
 Serbia 5 5 6 July 2021
 Södermanland - 1 7 July 2021
 South Sudan - 29 7 June 2021
 Tunisia - 1 21 May 2021
 United Arab Emirates - 28 23 June 2021
 Ukraine 13 34 24 June 2021
 Västra Götaland - 86 19 July 2021
 Zambia 82 82 29 May 2021
 East Timor - - 12[179] 8 August 2021
 Venezuela - 1 7 July 2021
 Northern Mariana Islands 2 19 7 July 2021
 Republic of Congo - 1 15 July 2021
 Dominican Republic - 1 3 May 2021
 Iraq 2 2 27 April 2021
 Rwanda 91 98 9 July 2021
 Liechtenstein - 20 15 July 2021
 Estonia - 460 21 July 2021
 Guatemala 4 86 29 July 2021
 Andorra - 12 17 July 2021
 Suriname - 17 3 August 2021
 Hungary - - 14[180] 22 July 2021
 Martinique 8 69 10 August 2021
 Iceland - 3,767 30 August 2021
 Gibraltar - 848 5 September 2021
 Mozambique - 66 16 July 2021
 Montenegro - 93 8 August 2021
 Jamaica - 10 23 July 2021
 Ethiopia - 8 16 August 2021
 Papua New Guinea - 8 10 August 2021
 Honduras - 2 31 July 2021
 Egypt - 1 15 July 2021
 Montserrat - 1 1 August 2021
 Liberia - 44 10 July 2021
 Antigua and Barbuda - 34 6 August 2021
 Armenia - 50 5 August 2021
 Brunei - 28 17 August 2021
 British Virgin Islands - 1 27 July 2021
 Cayman Islands - 11 30 July 2021
 Central African Republic - 17
 Gabon - 7 2 August 2021
 Grenada - 3 26 July 2021
 Saint Lucia - 4 26 July 2021
 Saint Vincent and the Grenadines - 2 8 August 2021
 Togo - 130 31 July 2021
 Trinidad and Tobago - 2 3 August 2021
 Turks and Caicos Islands - 4 12 July 2021
 Zimbabwe - 96 26 July 2021
 Burkina Faso - 21 21 April 2021
 Afghanistan - 20 24 May 2021
 Belize - 22 30 June 2021
 Saint Barthelemy - 3 17 August 2021
 Mali - 2 11 August 2021
 Benin - 47 23 July 2021
 Equatorial Guinea - 14 30 August 2021
 U.S. Virgin Islands - 184 18 August 2021
 Puerto Rico - 1,081 9 September 2021
 Sierra Leone - 8 8 September 2021
World (167 countries) Total: 471,067
(solely B.1.617.2)
Total: 1,119,561
(B.1.617.2+AY.1+AY.2+AY.3)
Total: 767,989

History

The first cases of the variant outside India were detected in late February 2021, including the United Kingdom on 22 February, the United States on 23 February and Singapore on 26 February.[181][36][125]

British scientists at Public Health England redesignated the B.1.617.2 variant on 7 May 2021 as "variant of concern" (VOC-21APR-02),[182] after they flagged evidence in May 2021 that it spreads more quickly than the original version of the virus.[17] Another reason was that they identified 48 clusters of B.1.617.2, some of which revealed a degree of community transmission.[183][184] 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.[185] 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.[186]

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.[187] Alberta reported a single case of the variant on 22 April 2021.[188] Nova Scotia reported two Delta variant cases in June 2021.[189]

Fiji also confirmed its first case of the variant on 19 April 2021 in Lautoka, and has since then climbed up to 47,000 cases and counting.[190] 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 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.[149]

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.[191]

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.[192]

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.[193][194] 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.[193]

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.[47] B.1.617.2.1 was detected in Europe in March 2021, and has since been detected in Asia and America.[47]

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%.[195] 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."[196] 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."[195] 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.[197][198]

Government responses

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.[199][200][201]

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.[202]

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.

From 16 May to 13 June 2021, as well as 22 July 2021 to 10 August 2021; Singapore entered lockdowns, known as "Phase 2 Heightened Alert", similar to 2020.

On 14 June, the British prime minister Boris Johnson announced that the proposed end of all restrictions on 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.[203] 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).[204]

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.[205]

On 25 June, Israel restored their mask mandate citing the threat of Delta.[206]

On 28 June, Sydney and Darwin in Australia went back into lockdown because of Delta outbreaks.[207] South Africa banned indoor and outdoor gatherings apart from funerals, imposed a curfew, and banned the sale of alcohol.[208]

On 3 July, the islands of Bali and Java in Indonesia went into emergency lockdown.[209]

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 23 July.[210]

On 9 July, Seoul, South Korea ramped up restrictions urging people to wear masks outdoors, and limiting the size of gatherings.[211]

On 12 July, French President Emmanuel Macron announced that all health care workers will need to be vaccinated by 15 September and that France will start using health passports to enter bars, cafés, restaurants and shopping centres from August.[212]

Los Angeles announced it will require masks indoors starting 17 July 2021.[213]

The United Kingdom lifted most COVID-19 restrictions on 19 July, despite a surge in cases as the Delta variant became dominant. The government cited the protection and wide coverage of the COVID-19 vaccination programme, although health experts expressed concern at the move.[214][215]

On 23 July, Vietnam extended its lockdown of Ho Chi Minh City to 1 August, and announced lockdown restrictions would be put in place in Hanoi, affecting a third of the country's population. The Delta variant had brought upon the country's largest outbreak to date, after mostly successful containment measures throughout 2020.[216][217]

On 17 August, New Zealand went into an alert level 4 lockdown, following a positive case being reported in Auckland. More cases soon followed in the Coromandel Peninsula.[218] This was the first reported community transmission case in the country in 170 days (since February 2021).[219]

See also

Notes

  1. ^ For other names, see § Names.

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