Lineage B.1.617

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Total number of B.1.617 sequences by country as of 21 April 2021[1]
Legend:
  100+ confirmed sequences
  2–99 confirmed sequences
  1 confirmed sequence
  None or no data available
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Lineage B.1.617, also known as VUI-21APR-01,[2] is one of the known variants of SARS-CoV-2, the virus that causes COVID-19.[3] It was first identified in Maharashtra, India[4] on 5 October 2020[5] and has been referred to as a "double mutation" variant.[1][6][7] "Double mutation" refers to B.1.617's mutations in the SARS-CoV-2 spike protein's[8] coding sequence at E484Q and L452R.[9] However, infectious disease scientist Professor Kristian Andersen[10] told reporters at NPR that "SARS-CoV-2 mutates all the time. So there are many double mutants all over the place. The variant in India really shouldn't be called that."[11]. It is identified within the 20A clade under the Nextstrain phylogenetic classification system.[12]

Characteristics[edit]

Emerging research suggests the variant may be more transmissible than previously evolved ones.[13] Whether the effectiveness of currently-deployed vaccines is affected remains under investigation.[14][15][16]

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 20-39 bracket increased to 25.5% from 23.7% earlier. The data also showed a higher proportion of asymptomatic patients were admitted during the second wave, with more complaints of breathlessness.[17]

First detection and international spread[edit]

Despite its name, B.1.617.3 was the first sublineage of this variant to be detected, in October 2020 in India. This sublineage has remained relatively uncommon compared to the two other sublineages, B.1.617.1 and B.1.617.2, both of which were first detected in December 2020.[18] There were few known cases of B.1.617 (of all sublineages) until early February 2021 when there was a significant increase.[1]

In other countries, 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.[1][5][4]

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.[19] Alberta reported a single case of the variant 22 April 2021.[20]

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.[21] The variant has been identified as a super-spreader and has lead 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.

Mutations[edit]

Defining mutations in B.1.617
Gene Nucleotide Amino acid
ORF1ab T749I
T77A
P323L
M429I
K259R
T93M
Spike G142D
E154K
L452R
E484Q
D614G
P681R
Q1071H
H1101D
orf3a S26L
orf6 I33T
orf7a V82A
Source: Haseltine/ Forbes[22]

The B.1.617 genome has 13 mutations (15 or 17 according to some sources,[which?] depending on whether more common mutations are included) which produce alterations in its coding.[23] Three of them, all of which are in the virus's spike protein code, are of great concern:

  • E484Q. The mutation at position 484, a glutamic acid-to-glutamine substitution, confers the variant stronger binding potential to hACE2 (the human ACE2 receptor), as well as better ability to evade hosts' immune systems, to B.1.617 in comparison to other variants.[9][verification needed]
  • L452R. The mutation 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.[9][24] These mutations, when taken individually, are not unique to the variant; rather, their simultaneous occurrence is.[9][6]
  • P681R. This is a mutation 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".[22]

There are three sublineages of B.1.617, which have some differences in their exact mutations. Notably, B.1.617.1 and B.1.617.3 have the E484Q mutation, but B.1.617.2 does not.[18] On 29 April 2021, PHE added two further variants, VUI-21APR-02 and VUI-21APR-03, which share the same parent lineage (B.1.617) as VUI-21APR-01.[25]

Vaccine efficacy[edit]

ICMR found that convalescent sera of the COVID-19 cases and recipients of Bharat Biotech's BBV152 (Covaxin) were able to neutralize VUI B.1.617 although with a lower efficacy.[26]

Anurag Agrawal, the Director of the Institute of Genomics and Integrative Biology (IGIB), said the study on effectiveness of the available vaccines on the B.1.617 variant of SARS-CoV2 suggests that post vaccination, the infections are milder. He tweeted: 

Initial positive neutralization studies of B.1.617, with both post-Covaxin or Covishield sera, are correlatable with milder disease during post-vaccination breakthrough infections. This is a positive while we get quantitative data for better understanding of infection protection.[27]

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

This is something where we're still gaining data on a daily basis. 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[28]

Another study by the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad found Covishield vaccinated sera offers protection against the B.1.617 variant. Rakesh Mishra, the Director of CCMB, said in a tweet:

Very preliminary but encouraging result: #Covishield protects against #B1617. Early results using in vitro neutralization assay show that both convalescent (prior infection) sera and Covishield vaccinated sera offer protection against the B.1.617 variant, aka #DoubleMutant[29]

International reactions[edit]

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 premier Boris Johnson cancelled his visit to India twice, while Japanese Prime Minister Yoshihide Suga postponed his April trip.[30][31][32]

Statistics[edit]

By 3 May 2021, 1,815 sequences of the variant had been detected in 28 countries.[1] Countries with detections are:

Cases by country (As of 3 May 2021)
Country Confirmed cases
(GISAID)[4] as of 5 May 		Confirmed cases
(PANGOLIN)[1] as of 3 May 		Cases (other sources) First detection
 India 1,306 781 5 October 2020
 United Kingdom 844 522 22 February 2021
 USA 270 215 23 February 2021
 Singapore 145 121 26 February 2021
 Canada 5 - 77[33][19][34][35] April 2021
 Germany 58 18 1 March 2021
 Australia 68 47 16 March 2021
 Fiji - - 42[36] 28 April 2021
 Israel - - 41[37][38][39] 16 April 2021
 Denmark 39 - 29[40][41] March 2021
 Bahrain 22 22 5 April 2021
 Poland 5 - 16[42] -
 New Zealand 13 11 9 March 2021
  Switzerland 11 10 -
 Ireland 17 10 -
 Belgium 14 9 -
 China 12 - -
 Hong Kong - 8 -
 Portugal 7 5 -
 The Netherlands 6 6 -
 South Korea 5 5 -
 Turkey - - 5[43] 28 April 2021
 Sweden 7 4 -
 Greece 3 2 -
 Italy 3 2 -
 Jordan 3 3 -
 Russia 3 3 -
 Spain 5 3 -
 Czech 2 - -
 Guadeloupe 2 2 -
 Indonesia 2 1 2[44][45] 3 May 2021
 Morocco - - 2[46] 3 May 2021
 Sint Maarten 2 - -
 Aruba 1 1 -
 Austria 1 - 17 April 2021
 Cambodia 1 1 -
 France 13 - -
 Malaysia 1 1 -
 Mexico 1 1 -
 Norway - - 1[47] 16 April 2021
 Romania 1 1 -
World (41 countries) Total: 2,898 Total: 1,815
incl. B.1.617.1, B.1.617.2, and B.1.617.3		 215 Total as of 3 May 2021.

See also[edit]

References[edit]

  1. ^ a b c d e f "PANGO lineages Lineage B.1.617". cov-lineages.org. Retrieved 3 May 2021.
  2. ^ "Variants: distribution of cases data". GOV.UK. Public Health England. This article contains OGL licensed text This article incorporates text published under the British Open Government Licence v3.0:
  3. ^ "Confirmed cases of COVID-19 variants identified in UK". www.gov.uk. 15 April 2021. Retrieved 20 April 2021.
  4. ^ a b c "Tracking of Variants". gisaid.org. GISAID. 26 April 2021. Retrieved 3 May 2021.
  5. ^ a b "Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK". Science Media Centre. Science Media Centre. Retrieved 20 April 2021.
  6. ^ a b 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.
  7. ^ Cuff, Madeleine (19 April 2021). "Indian variant: Cases of new 'double mutation' Covid strain thought to be spreading in UK". i. London. Retrieved 20 April 2021.
  8. ^ Shang, Jian; Yushun, Wan; Lou, Chuming; Ye, Gang; Geng, Qibin; Auerbach, Ashley; Fang, Li (2020). "Cell entry mechanisms of SARS-CoV-2". Proceedings of the National Academy of Sciences. 117 (21): 11727–11734. doi:10.1073/pnas.2003138117.
  9. ^ a b c d Starr, Tyler N.; Greaney, Allison J.; Dingens, Adam S.; Bloom, Jesse D. (April 2021). "Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016". Cell Reports Medicine: 100255. doi:10.1016/j.xcrm.2021.100255.
  10. ^ Professor Kristian Andersen, PhD www.scripps.edu
  11. ^ "People Are Talking About A 'Double Mutant' Variant In India. What Does That Mean?". NPR.org. Retrieved 27 April 2021.
  12. ^ "Genomic epidemiology of novel coronavirus - Global subsampling (Filtered to B.1.617)". nextstrain.org. Retrieved 5 May 2021.
  13. ^ Deng, Xianding; Garcia-Knight, Miguel A.; Khalid, Mir M.; Servellita, Venice; Wang, Candace; Morris, Mary Kate; Sotomayor-González, Alicia; Glasner, Dustin R.; Reyes, Kevin R.; Gliwa, Amelia S.; Reddy, Nikitha P.; Martin, Claudia Sanchez San; Federman, Scot; Cheng, Jing; Balcerek, Joanna; Taylor, Jordan; Streithorst, Jessica A.; Miller, Steve; Sreekumar, Bharath; Chen, Pei-Yi; Schulze-Gahmen, Ursula; Taha, Taha Y.; Hayashi, Jennifer; Simoneau, Camille R.; Kumar, G. Renuka; McMahon, Sarah; Lidsky, Peter V.; Xiao, Yinghong; Hemarajata, Peera; Green, Nicole M.; Espinosa, Alex; Kath, Chantha; Haw, Monica; Bell, John; Hacker, Jill K.; Hanson, Carl; Wadford, Debra A.; Anaya, Carlos; Ferguson, Donna; Frankino, Phillip A.; Shivram, Haridha; Lareau, Liana F.; Wyman, Stacia K.; Ott, Melanie; Andino, Raul; Chiu, Charles Y. (20 April 2021). "Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant". Cell. 0 (0). doi:10.1016/j.cell.2021.04.025. ISSN 0092-8674. Retrieved 26 April 2021.
  14. ^ "Gupta Lab, Cambridge on Twitter". Twitter.
  15. ^ "Gupta Lab, Cambridge on Twitter". Twitter.
  16. ^ Doucleff, Michaeleen (24 April 2021). "People Are Talking About A 'Double Mutant' Variant In India. What Does That Mean?". NPR.org. NPR.
  17. ^ Dey, Sushmi. "Covid second wave in India: Percentage of young infected in second wave same, but more serious". The Times of India. Retrieved 27 April 2021.
  18. ^ a b "Weekly epidemiological update on COVID-19 - 27 April 2021". World Health Organization. 27 April 2021. Retrieved 28 April 2021.
  19. ^ a b Carrigg, David (21 April 2021). "COVID-19: Double mutant virus first identified in India is now in B.C." Vancouver Sun. Retrieved 28 April 2021.
  20. ^ "First case of B.1.617 variant confirmed in Alberta". edmonton.citynews.ca.
  21. ^ "Fiji fears a coronavirus 'tsunami' after outbreak found to be Indian variant". SBS News. 28 April 2021. Retrieved 28 April 2021.
  22. ^ a b Haseltine, William. "An Indian SARS-CoV-2 Variant Lands In California. More Danger Ahead?". Forbes. Retrieved 20 April 2021.
  23. ^ "Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK | Science Media Centre". Science Media Centre. Retrieved 26 April 2021.
  24. ^ Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Sincuir Martinez, Jorge M.; Plummer, Jasmine T.; Vail, Eric (6 April 2021). "Emergence of a Novel SARS-CoV-2 Variant in Southern California". JAMA. 325 (13): 1324. doi:10.1001/jama.2021.1612.
  25. ^ "Confirmed cases of COVID-19 variants identified in UK (see: Two VUIs added to B.1.617 group)". www.gov.uk. 29 April 2021. Retrieved 1 May 2021.
  26. ^ Yadav, Pragya D; Sapkal, Gajanan N. "Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees" (PDF). doi:10.1101/2021.04.23.441101. Retrieved 24 April 2021.
  27. ^ "Covishield Covaxin effective against 'Indian strain' of coronavirus study suggests". The Week. Retrieved 27 April 2021.
  28. ^ "Covaxin found to neutralise 617 variant of COVID-19, says Dr. Fauci". The Hindu. 28 April 2021.
  29. ^ "Covishield, Covaxin effective against 'Indian strain' of coronavirus, study suggests - ET HealthWorld". ETHealthworld.com. The Economic Times. 28 April 2021.
  30. ^ report, Web. "India Covid crisis: 20 countries that have imposed travel bans, suspensions". Khaleej Times. Retrieved 1 May 2021.
  31. ^ "Countries enact travel bans to contain India's COVID variant—and protect against 'a global resurgence all over again'". Fortune. Retrieved 1 May 2021.
  32. ^ "Countries that have put India in red list due to rising COVID-19 cases". Times of India Travel. Retrieved 1 May 2021.
  33. ^ "Updates on COVID-19 Variants of Concern". National Collaborating Centre for Infectious Diseases. University of Manitoba. 27 April 2021. Retrieved 2 May 2021.
  34. ^ "Alberta reports 1,857 COVID-19 cases, identifies B.1.617 variant infection". CTV News Edmonton. 22 April 2021. Retrieved 28 April 2021.
  35. ^ "Public Health Ontario reports 36 cases of COVID-19 variant first identified in India". CP24. 23 April 2021. Retrieved 28 April 2021.
  36. ^ "Fiji fears a coronavirus 'tsunami' after outbreak found to be Indian variant". SBS News. 28 April 2021. Retrieved 28 April 2021.
  37. ^ Soni, Parul (30 April 2021). "Israel Is The Most Vaccinated Country, But The B.1.617 Is Threatening It Now". International Business Times. IBT Media.
  38. ^ "Israel logs Indian COVID-19 variant, sees some vaccine efficacy against it". Reuters. 20 April 2021. Retrieved 24 April 2021.
  39. ^ "זוהו 41 מקרים של הזן (הווריאנט) ההודי, מתוכם 24 חוזרים מחו"ל" [41 cases of the Indian variety have been identified, of which 24 are from abroad]. GOV.IL (in Hebrew). Retrieved 29 April 2021.
  40. ^ "Der har været 11 tilfælde af indisk dobbeltmutation i Danmark, bekræfter SSI" [There have been 11 cases of Indian double mutation in Denmark, confirms SSI]. TV2. 18 April 2021. Retrieved 28 April 2021.
  41. ^ "29 tilfælde af indisk variant fundet i Danmark - Statens Serum Institut er ikke bekymret" [29 cases of Indian variant found in Denmark - Statens Serum Institut is not worried]. Sundhedspolitisk Tidsskrift. 27 April 2021. Retrieved 28 April 2021.
  42. ^ "Minister zdrowia: mamy kolejne dwa ogniska związane z mutacją indyjską koronawirusa" [Health Minister: We have two more outbreaks related to the Indian mutation of the coronavirus]. tvn24.pl (in Polish). 4 May 2021. Retrieved 4 May 2021.
  43. ^ "Coronavirus live news, 16:54, 28 April 2021". The Guardian. 28 April 2021. Retrieved 28 April 2021.
  44. ^ Widianto, Stanley (3 May 2021). "Indonesia records two cases of Indian COVID-19 variant in Jakarta". Reuters. Retrieved 3 May 2021.
  45. ^ Nugraheny, Dian Erika (3 May 2021). Galih, Bayu (ed.). "Kemenkes: Varian B.1.1.7, B.1.617, dan B.1.351 Sudah Masuk Indonesia" (in Indonesian). Kompas. Retrieved 3 May 2021.
  46. ^ Yabiladi.com. "Morocco : Two cases of the Indian variant of Covid-19 confirmed in Casablanca". en.yabiladi.com (in French). Retrieved 3 May 2021.
  47. ^ "Indisk virusvariant påvist i Norge" [Indian virus variant detected in Norway]. dagbladet.no. 16 April 2021. Retrieved 28 April 2021.

External links[edit]

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