SARS-CoV-2 lineage B.1.617

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Lineage B.1.617 is a lineage of SARS-CoV-2, the virus that causes COVID-19. [1] It first came to international attention in late March 2021 after the newly established INSACOG performed genome sequencing on positive samples throughout various Indian states. Analysis of samples from Maharashtra had revealed that compared to December 2020, there was an increase in the fraction of samples with the E484Q and L452R mutations. [2] Lineage B.1.617 later came to be dubbed a double mutant by news media. [3]

Contents

Lineage B.1.617 has three sublineages according to the PANGO nomenclature:

Mutations

SARS-CoV-2 'spike' protein Novel Coronavirus SARS-CoV-2 Spike Protein (49583626473).jpg
SARS-CoV-2 'spike' protein

Here are some of the common mutations present in the spike protein of lineage B.1.617. Not all sublineages of B.1.617 share the same mutations:

History

The first B.1.617 genome sequence was submitted to GISAID in fall 2020 according to one source. [12] The team at PANGO behind manually curating the phylogenetic tree of SARS-CoV-2 noted the earliest sequence was from 7 December 2020. They proposed a new designation for the variant containing the mutations at the spike protein including G142D, L452R, E484Q, D614G, P681R among others and this variant went to be assigned PANGO lineage B.1.617 on 1 April 2021. [13] They revised the phylogenetic tree to include three sublineages of B.1.617 on 21 April 2021 after noticing that not all genome sequences being assigned by the PANGOLIN tool contained the same set of mutations. [14]

Up until mid-April 2021, India submitted the most B.1.617 genomes, followed in frequency by UK and the US. Based on genome information, lineage B.1.617 was first detected in the UK on 22 February 2021, and in the US on 23 February 2021. [12]

After detecting 77 cases of lineage B.1.617 in the UK in mid-April 2021, Public Health England designated the lineage as a variant under investigation. [15] In less than two months, the Delta variant would go on to become the dominant variant in the UK with researchers stating early evidence suggested there may be an increased risk of hospitalization for Delta compared to the previously dominant Alpha variant. [16]

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National Centre for Disease Control Indian medical health government agency

The National Centre for Disease Control is an institute under the Indian Directorate General of Health Services, Ministry of Health and Family Welfare. It was established in July 1963 for research in epidemiology and control of communicable diseases and to reorganize the activities of the Malaria Institute of India. It has eight branches at Alwar, Bengaluru, Trivandrum, Calicut, Coonoor, Jagdalpur, Patna, Rajahmundry and Varanasi to advise the respective state governments on public health. The headquarters are in Sham Nath Marg, in New Delhi.

Severe acute respiratory syndrome coronavirus 2 Virus that causes COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is the virus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. Also colloquially known simply as the coronavirus, it was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019. First identified in the city of Wuhan, Hubei, China, the World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. As described by the US National Institutes of Health, it is the successor to SARS-CoV-1, the virus that caused the 2002–2004 SARS outbreak.

SARS-CoV-2 Alpha variant Variant of SARS-CoV-2, the virus that causes COVID-19

The Alpha variant, also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several variants of concern, the variant is estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. It was first detected in November 2020 from a sample taken in September in the United Kingdom, and began to spread quickly by mid-December, around the same time as infections surged. This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant is also notable for having more mutations than normally seen.

SARS-CoV-2 Beta variant Variant of the SARS-CoV-2 virus

Beta variant, also known as lineage B.1.351, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa in October 2020, which was reported by the country's health department on 18 December 2020. Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay area in July or August 2020.

COVID-19 Genomics UK Consortium

The COVID-19 Genomics UK Consortium (COG-UK) is a group of public health agencies and academic institutions in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the Wellcome Sanger Institute. The consortium is known for first identifying the SARS-CoV-2 Alpha variant in November 2020. As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to the GISAID sequencing database originated from COG-UK.

Variants of SARS-CoV-2 Notable variants of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them.

SARS-CoV-2 Gamma variant Variant of the SARS-Cov-2 virus

Gamma variant, also known as lineage P.1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the World Health Organization, P.1 has been labeled Gamma variant, and is currently considered a variant of concern.

Phylogenetic Assignment of Named Global Outbreak Lineages SARS-CoV-2 lineage nomenclature

The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by members of the laboratory of Andrew Rambaut, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. Its purpose is to implement a dynamic nomenclature to classify genetic lineages for SARS-CoV-2, the virus that causes COVID-19. A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage. Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available genomes obtained from the COVID-19 Genomics UK Consortium and from those submitted to GISAID. It is named after the pangolin.

Variant of concern Newly emerged variant of a virus with transmissibility and virulence that causes concerns

The term variant of concern (VOC) for severe acute respiratory syndrome coronavirus 2 is a category used when mutations in Receptor Binding Domain (RBD) substantially increase binding affinity in RBD-hACE2 complex, while also being linked to rapid spread in human populations.

SARS-CoV-2 Iota variant Variant of the SARS-Cov-2 virus first identified in New York City

Iota variant, also known as lineage B.1.526, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in New York City in November 2020. The variant has appeared with two notable mutations: the E484K spike mutation, which may help the virus evade antibodies, and the S477N mutation, which may help the virus bind more tightly to human cells.

SARS-CoV-2 Delta variant COVID-19 virus variant

The 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. It was first detected in India in late 2020. The World Health Organization (WHO) named it the Delta variant on 31 May 2021.

SARS-CoV-2 Theta variant Variant of the SARS-CoV-2 virus

Theta variant, also known as lineage P.3, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. The variant was first identified in the Philippines on February 18, 2021, when two mutations of concern were detected in Central Visayas. It was detected in Japan on March 12, 2021, when a traveler from the Philippines arrived at Narita International Airport in Tokyo.

INSACOG is the forum set up under the Ministry of Health and Family Welfare by the Government of India on 25 December 2020, to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India. Initially it was tasked to study the virus variant Lineage B.1.1.7 earlier found in United Kingdom in December 2020. INSACOG works as a consortium of 28 national laboratories for genome sequencing located in different parts of India. All these 10 laboratories are required to share 5% of positive samples to INSACOG for further research and studies. A National Centre for Disease Control (NCDC) nodal unit maintain a database of all samples of the new variants. Two national genomic sequencing database centers are appointed 1) National Institute of Biomedical Genomics and 2) CSIR Institute of Genomics and Integrative Biology. In its early research INSACOG identefied virus variant Lineage B.1.617 referred to as a double mutation variant.

SARS-CoV-2 Kappa variant COVID-19 virus variant

Kappa variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It is one of the three sublineages of Pango lineage B.1.617. The SARS-CoV-2 Kappa variant is also known as lineage B.1.617.1 and was first detected in India in December 2020. By the end of March 2021, the Kappa sub-variant accounted for more than half of the sequences being submitted from India. On 1 April 2021, it was designated a Variant Under Investigation (VUI-21APR-01) by Public Health England.

SARS-CoV-2 Lambda variant COVID-19 virus variant

Lambda variant, also known as lineage C.37, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Peru in August 2020. On 14 June 2021, the World Health Organization (WHO) named it Lambda variant and designated it as a variant of interest. It has spread to at least 30 countries around the world and is known to be more resistant to neutralizing antibodies compared to other strains. It is also suggested that the Lambda variant could be more infectious and resistant to vaccines than the Alpha and/or Gamma variant.

SARS-CoV-2 Epsilon variant Variant of the SARS-Cov-2 virus

Epsilon variant, also known as CAL.20C and referring to two PANGO lineages B.1.427 and B.1.429, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in California, USA in July 2020.

SARS-CoV-2 Zeta variant Variant of the SARS-Cov-2 virus

Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.

SARS-CoV-2 Eta variant Variant of the SARS-Cov-2 virus

The Eta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. The Eta variant or lineage B.1.525, also called VUI-21FEB-03 by Public Health England (PHE) and formerly known as UK1188, 21D or 20A/S:484K, does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion as found in Alpha, N439K variant and Y453F variant.

Coronavirus spike protein Glycoprotein spike on a viral capsid or viral envelope

Spike (S) protein is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into trimers that form large structures, called spikes or peplomers, that project from the surface of the virion. The distinctive appearance of these spikes when visualized using negative stain transmission electron microscopy, "recalling the solar corona", gives the virus family its name.

SARS-CoV-2 Mu variant Variant of the SARS-CoV-2 virus

The Mu variant, also known as lineage B.1.621 or VUI-21JUL-1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Colombia in January 2021 and was designated by the WHO as a variant of interest on August 30, 2021. The WHO said the variant has mutations that indicate a risk of resistance to the current vaccines and stressed that further studies were needed to better understand it. Outbreaks of the Mu variant were reported in South America and Europe. The lineage B.1.621 has a sublineage, labeled B.1.621.1 under the PANGO nomenclature, which has already been detected in more than 20 countries worldwide.

References

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  2. "Genome Sequencing by INSACOG shows variants of concern and a Novel variant in India". Press Information Bureau Government of India. 24 March 2021.
  3. "Covid-19: Double mutation variant fuels fears". The Telegraph online. 17 March 2021.
  4. "Lineage B.1.617.3". cov-lineages.org. Retrieved 10 July 2021.
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  7. Koshy, Jacob (8 April 2021). "Coronavirus | Indian 'double mutant' strain named B.1.617". The Hindu. Retrieved 19 April 2021. Though these mutations have individually been found in several other coronavirus variants, the presence of both these mutations together have been first found in some coronavirus genomes from India.
  8. Greenwood, Michael (30 March 2021). "SARS-CoV-2 mutation T478K spreading at alarming speed in Mexico". Medical News. Retrieved 6 September 2021. The T478K mutation constitutes the exchange of the non-charged amino acid threonine with the positively charged lysine at position 478...
  9. Delphine Planas (8 July 2021). "Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization". Nature. 596 (7871): 276–280. doi: 10.1038/s41586-021-03777-9 . PMID   34237773. S2CID   235775860 . Retrieved 6 September 2021. The T478K mutation in the RBD is unique to the Delta variant...
  10. 1 2 Haseltine, William. "An Indian SARS-CoV-2 Variant Lands In California. More Danger Ahead?". Forbes. Retrieved 20 April 2021.
  11. "SARS-CoV-2 variants of concern as of 3 June 2021". European Centre for Disease Prevention and Control. Archived from the original on 3 June 2021.
  12. 1 2 "Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK". Science Media Centre. Retrieved 20 April 2021.
  13. "Proposed new B.1 sublineage circulating in India #38". GitHub. Retrieved 2 April 2021.
  14. "Potential sequences that should be included in B.1.617 #49". GitHub. Retrieved 28 February 2021.
  15. "Confirmed cases of COVID-19 variants identified in UK". www.gov.uk. 15 April 2021. Archived from the original on 16 April 2021. UKOpenGovernmentLicence.svg  This article incorporates text published under the British Open Government Licence  v3.0:
  16. "Confirmed cases of COVID-19 variants identified in UK". www.gov.uk. 3 June 2021. Archived from the original on 4 June 2021. UKOpenGovernmentLicence.svg  This article incorporates text published under the British Open Government Licence  v3.0: