SARS-CoV-2 Delta Variant

The Delta variant (B.1.617.2) was 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 179 countries by 22 November 2021. The World Health Organization (WHO) indicated in June 2021 that the Delta variant was becoming the dominant strain globally.

It has mutations in the gene encoding the SARS-CoV-2 spike protein causing the substitutions T478K, P681R and L452R, 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. 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; 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. Immunity from previous recovery or COVID-19 vaccines are effective in preventing severe disease or hospitalisation from infection with the variant.

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); the UK's SAGE using May data estimated a "realistic" possibility of being 50% more transmissible. 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.

The variant is thought to be partly responsible for India's deadly second wave of the pandemic beginning in February 2021.WHO labels a Covid strain in India as a 'variant of concern' — here's what we know
CNBC, 11 May 2021."WHO says India Covid variant of 'global concern
BBC News, 11 May 2021. It later contributed to a third wave in Fiji, the United Kingdom and South Africa, and the WHO warned in July 2021 that it could have a similar effect elsewhere in Europe and Africa. By late July, it had also driven an increase in daily infections in parts of Asia, the United States, Australia, and New Zealand.

Classification

The Delta variant has mutations in the gene encoding the SARS-CoV-2 spike protein causing the substitutions D614G, T478K, P681R and L452R. It is identified as the 21A, 21I, and 21J clades under the Nextstrain phylogenetic classification system.

Names

The virus has also been referred to by the term "Indian Variant" 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. 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.

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. 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".

Mutations

File:SARS-CoV-2 Delta variant.svg, Amino acid mutations of SARS-CoV-2 Delta variant plotted on a genome map of SARS-CoV-2 with a focus on Spike.

The Delta/ B.1.617.2 genome has 13 mutations (15 or 17 according to some sources, depending on whether more common mutations are included) which produce alterations in the amino-acid sequences of the proteins it encodes.

The list of spike protein mutations is: 19R, (G142D), Δ156-157, R158G, L452R, T478K, D614G, P681R, D950N according to GVN, or T19R, G142D, del 156–157, R158G, L452R, T478K, D614G, P681R according to Genscript 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.
* T478K. The exchange at position 478 is a threonine-to-lysine substitution.
* 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.
* 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".

The E484Q mutation is not present in the B.1.617.2 genome.

Lineages

As of August 2021, Delta variants have been subdivided in the Pango lineage designation system into variants from AY.1 to AY.28. However, there is no information on whether such classification correlates with biological characteristic changes of the virus. 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.

"Delta plus" variant

Delta with K417N originally corresponded to lineages AY.1 and AY.2, subsequently also lineage AY.3, and has been nicknamed "Delta plus" or "Nepal variant". It has the K417N mutation, which is also present in the Beta variant. The exchange at position 417 is a lysine-to-asparagine substitution.

As of mid-October 2021, the AY.3 variant accounted for a cumulative prevalence of approximately 5% in the United States, and 2% worldwide. 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 led 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. AY.4.2 grows about 15% faster per week. In the UK it was reclassified as a "variant under investigation" (but not "of concern") in late October 2021. In Denmark, after a drop in AY.4.2 cases, a new fast surge was detected and monitored, but was not yet considered a cause of concern.

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. 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.

Prevention

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. Public Health authorities should continue to find infected individuals using testing, trace their contacts, and isolate those who have tested positive or been exposed. Event organizers should assess the potential risks of any mass gathering and develop a plan to mitigate these risks. 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.

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.

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:

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.

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.

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.

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.

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.

In a study of the University of Sri Jayewardenepura in July 2021 found the Sinopharm BIBP 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.

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

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.

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.

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.

Treatment

In vitro experiments suggest that bamlanivimab may not be effective against Delta on its own. 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. Doctors in Singapore have been using supplemental oxygen, remdesivir and corticosteroids on more Delta patients than they did on previous variants.

Epidemiology

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). cited Given that Alpha is already 150% as transmissible as the original SARS-CoV-2 strain that emerged in late 2019 in Wuhan, and if Delta is 150% as transmissible as Alpha, then Delta may be 225% as transmissible as the original strain. BBC
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