SARS-CoV-2 Theta variant

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The Theta variant (P.3) was a SARS-CoV-2 variant of interest. [1] It was first identified in the Philippines on February 18, 2021, [2] and shortly thereafter detected in Japan on March 12, 2021. [3]

Contents

The variant is distinct from those first discovered in the United Kingdom, South Africa, and Brazil, and is thought to pose a similar threat. It is more resistant to neutralizing antibodies, including those gained through vaccination, like how the South African and Brazilian variants appear to be. [4]

Under the standardized nomenclature system established by the World Health Organization (WHO), lineage P.3 has been labeled Theta and was classified as a variant of interest rather than a variant of concern. As of July 2021, Theta is no longer considered a variant of interest by the WHO. [1]

Classification

The Theta variant corresponds to PANGO lineage P.3 (B.1.1.28.3), which stems from B.1.1.28, the same parental lineage as P.1 (Gamma) and P.2 (Zeta). [5] It also belongs to Nextstrain clade 21E and GISAID clade GR/1092K.V1. [1] On March 17, 2021, it was designated as a variant under investigation (VUI) labeled VUI-21MAR-02 by Public Health England (PHE). [6] On March 24, 2021, the World Health Organization (WHO) classified it as a variant of interest (VOI) and assigned it the Greek-letter name Theta. Then, on July 6, 2021, it was reclassified as a variant under monitoring (VUM), and again on August 17, 2021, as a previously circulating VOI because it no longer poses a major additional risk to global public health. [1]

Mutations

A total of 14 amino acid replacements were observed in all samples (labeled in red below), including seven spike protein mutations. Among the spike protein mutations, four have been previously associated with lineages of concern (i.e., E484K, N501Y, D614G, and P681H), while three additional replacements were observed towards the C-terminal region of the protein (i.e., E1092K, H1101Y, and V1176F). A single amino acid replacement at the N-terminus of ORF8 (i.e., K2Q) was also found in all samples. Three other mutations were seen in 32 of the 33 samples (labeled in green), including a three-amino acid deletion at the spike protein positions 141 to 143. Lastly, five synonymous mutations (labeled in gray) were also detected in all of the cases. [8]

Mutation profile of Theta variant
Gene Amino acid
ORF1ab F924F
D1554G
S2433S
L3201P
D3681E
N3928N
L3930F
P4715L
A5692V
S LGV141_143del
E484K
N501Y
G593G
D614G
P681H
S875S
E1092K
H1101Y
V1176F
ORF8 K2Q
N R203K
G204R
Characteristic mutations of Theta variant [9]
Gene Amino acid
ORF1a D1554G
S2625F
D2980N
L3201P
D3681E
L3930F
ORF1b P314L
L1203F
A1291V
S LGV141_143del
E484K
N501Y
G593G
D614G
P681H
S875S
E1092K
H1101Y
V1176F
ORF8 K2Q
N R203K
G204R

History

On February 18, 2021, the Department of Health (Philippines) confirmed the detection of two mutations of COVID-19 in Central Visayas after samples from patients were sent to undergo genome sequencing. The mutations, later named as E484K and N501Y, were detected in 37 out of 50 samples, with both mutations co-occurrent in 29 of these cases. There were no official names for the variants at the time, and the full sequence had yet to be identified. [2] Japan then detected the variant when a traveler from the Philippines arrived at Narita International Airport in Tokyo on March 12, 2021. [3] The following day, March 13, 2021, the Department of Health of the Philippines confirmed that these mutations constituted a new variant, which was designated as lineage P.3. On the same day, it also confirmed the country's first case of lineage P.1. Although lineages P.1 and P.3 stem from the same B.1.1.28 lineage, the department said that the impact of lineage P.3 on vaccine efficacy and transmissibility is yet to be ascertained. [10]

On March 17, 2021, the United Kingdom confirmed its first two cases, [11] while on April 30, 2021, Malaysia detected 8 cases of lineage P.3 in Sarawak. [12]

Statistics

Confirmed cases by country (as of January 24, 2022)
Country PANGOLIN [13] outbreak.info [9] Regeneron [14] Other sources
Flag of the Philippines.svg Philippines455513516461 [15]
Flag of the United States.svg USA172017
Flag of Germany.svg Germany111111
Flag of Malaysia.svg Malaysia10101013 [16]
Flag of the United Kingdom.svg United Kingdom99910 [17]
Flag of Japan.svg Japan788
Flag of the Netherlands.svg Netherlands7774 [18]
Flag of Canada (Pantone).svg Canada555
Flag of Australia (converted).svg Australia334
Flag of Belgium (civil).svg Belgium333
Flag of the People's Republic of China.svg China [a] 31414
Flag of Guam.svg Guam3–3
Flag of New Zealand.svg New Zealand333
Flag of Norway.svg Norway333
Flag of Singapore.svg Singapore333
Flag of Angola.svg Angola222
Flag of South Korea.svg South Korea222
Flag of Sweden.svg Sweden222
Flag of Brazil.svg Brazil111
Flag of Finland.svg Finland111
 Total550620624488

See also

Notes

  1. ↑ Cases in Hong Kong.

References

  1. 1 2 3 4 "Tracking SARS-CoV-2 variants". who.int. World Health Organization.
  2. 1 2 "DOH confirms new COVID-19 mutations in Central Visayas". CNN Philippines. February 18, 2021. Archived from the original on November 26, 2021. Retrieved May 2, 2021.
  3. 1 2 "New coronavirus variant found in traveler from Philippines: Japan". Kyodo News. March 12, 2021. Retrieved May 2, 2021.
  4. ↑ "Japanese authorities discover a new coronavirus variant in traveler from Philippines". The Japan Times. March 12, 2021. Archived from the original on May 4, 2021. Retrieved May 2, 2021.
  5. ↑ Chadha, Jatin; Khullar, Lavanya; Mittal, Nidhi (2021). "Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease‑19 pandemic". Environmental Microbiology. 24 (6): 2615–2629. doi:10.1111/1462‑2920.15687. PMC   8441773 . PMID   34320263.
  6. ↑ "Variants: distribution of cases data". gov.uk . Government Digital Service.
  7. ↑ "Spike Variants: Theta variant, aka B.1.128". covdb.stanford.edu. Stanford University Coronavirus Antiviral & Resistance Database. 1 July 2021. Retrieved 2021-07-05.
  8. ↑ Center, Philippine Genome (13 March 2021). "PGC SARS-CoV-2 Bulletin No. 7: Detection and characterization of a new SARS-CoV-2 lineage P.3, with spike protein mutations E484K, N501Y, P681H and LGV 141–143 deletion, from samples sequenced through the intensified UP-PGC, UP-NIH and DOH biosurveillance program". Philippine Genome Center.
  9. 1 2 "P.3 Lineage Report". outbreak.info.
  10. ↑ "DOH confirms new COVID-19 variant first detected in PH, first case of Brazil variant". ABS-CBN. March 13, 2021. Retrieved May 2, 2021.
  11. ↑ "England reports 2 cases of new COVID-19 variant found in Philippines". Rappler. March 17, 2021. Retrieved May 2, 2021.
  12. ↑ "Covid-19: Sarawak detects variant reported in the Philippines". April 30, 2021. Retrieved April 30, 2021.
  13. ↑ "PANGO lineages". cov-lineages.org. Archived from the original on 2021-05-05. Retrieved 2021-05-02.
  14. ↑ "Regeneron COVID-19 Dashboard". covid19dashboard.regeneron.com. Retrieved August 27, 2021.
  15. ↑ Lopez, Virgil (September 29, 2021). "DOH detects additional 339 Delta variant cases". GMA News. Retrieved October 1, 2021.
  16. ↑ Pei Pei, Goh (July 8, 2021). "Delta variant detected in Sarawak" . Retrieved July 13, 2021. He said for the Theta variant, six cases had been detected in Kuching and seven in Kota Samarahan
  17. ↑ "Variants: distribution of case data, 13 August 2021". August 13, 2021. Retrieved August 13, 2021.
  18. ↑ "Variants in the Netherlands". rivm.nl. Retrieved July 16, 2021.
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