SARS-CoV-2 Theta variant

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Theta variant, also known as lineage P.3, [lower-alpha 1] 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. [1] It was detected in Japan on March 12, 2021, when a traveler from the Philippines arrived at Narita International Airport in Tokyo. [2]

Contents

It is distinct from those first discovered in the United Kingdom, South Africa, and Brazil, and is thought to pose a similar threat. The variant is more resistant to neutralizing antibodies, including those gained through vaccination, like how the South African and Brazilian variants appear to be. [3]

Under the simplified naming scheme proposed by the World Health Organization, P.3 has been labeled Theta variant, and is considered a variant of interest (VOI), but not yet a variant of concern. [4]

As of July 2021, Theta is no longer considered as a variant of interest by the WHO. [4]

Classification

Naming

On March 17, 2021, Public Health England (PHE) named Lineage P.3 VUI-21MAR-02. [5]

On June 1, 2021, the World Health Organization (WHO) named lineage P.3 as Theta variant. [6]

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). Interestingly, 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 of the 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 were later named as E484K and N501Y, which were detected in 37 out of 50 samples, with both mutations co-occurrent in 29 out of these. There were no official names for the variants and the full sequence was yet to be identified. [1]

On March 12, 2021, Japan detected the variant on a traveler from the Philippines. [2]

On March 13, 2021, the Department of Health confirmed the mutations constituted a new variant, which was designated as lineage P.3. On the same day, it also confirmed its first case of lineage P.1 in the country. Although the lineages P.1 and P.3 stem from the same lineage B.1.1.28, 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, where Public Health England (PHE) termed it VUI-21MAR-02. [11]

On April 30, 2021, Malaysia detected 8 cases of lineage P.3 in Sarawak. [12]

Statistics

Cases by country (as of October 16, 2021)
CountryConfirmed cases
PANGOLIN [13] outbreak.info [9] Regeneron [14] Other sources
Flag of the Philippines.svg  Philippines 248298298461 [15]
Flag of the United States.svg  United States 171717
Flag of Germany.svg  Germany 111111
Flag of Malaysia.svg  Malaysia 10101013 [16]
Flag of the United Kingdom.svg  United Kingdom 99910 [17]
Flag of Japan.svg  Japan 788
Flag of the Netherlands.svg  Netherlands 7774 [18]
Flag of Canada (Pantone).svg  Canada 555
Flag of Australia (converted).svg  Australia 344
Flag of Belgium (civil).svg  Belgium 333
Flag of the People's Republic of China.svg  China [lower-alpha 2] 31418
Flag of Guam.svg  Guam 333
Flag of New Zealand.svg  New Zealand 333
Flag of Norway.svg  Norway 333
Flag of Singapore.svg  Singapore 333
Flag of Angola.svg  Angola 222
Flag of South Korea.svg  South Korea 222
Flag of Sweden.svg  Sweden 222
Flag of Finland.svg  Finland 111
Flag of Italy.svg  Italy 1
Total:342405410488

See also

Notes

  1. Other names include:
    VUI-21MAR-02
    Lineage B.1.1.28.3
    Philippine variant
  2. Cases in Hong Kong.

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References

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  14. "Regeneron COVID-19 Dashboard". covid19dashboard.regeneron.com. Retrieved August 27, 2021.
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