SARS-CoV-2 Theta variant

Theta variant, also known as lineage P.3,^[a] 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]

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 may be more resistant to neutralizing antibodies, including those gained through vaccination, like 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]

Detection[edit]

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.^[5]

On March 17, 2021, the United Kingdom confirmed its first two cases, where Public Health England (PHE) termed it VUI-21MAR-02.^[6]

On April 30, 2021, Malaysia detected 8 cases of lineage P.3 in Sarawak.^[7]

Naming[edit]

On March 17, 2021, PHE named Lineage P.3 VUI-21MAR-02.^[8]

On June 1, 2021, the World Health Organization (WHO) named Lineage P.3 as the Theta variant.^[9]

Mutations[edit]

A total of 14 amino acid replacements were observed in all samples (labeled in red), 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.^[10]

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
N	G204R

Characteristic mutations of Theta Variant^[11]
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
N	G204R

Statistics[edit]

Cases by country (as of June 22, 2021)
Country	Cases	Ref.
Philippines	163	^[12]^[13]^[14]^[15]^[16]
United States	14	^[17]
Malaysia	12	^[18]^[19]
Germany	9	^[17]
Netherlands	7	^[17]
United Kingdom	7	^[17]
Japan	4	^[17]
Hong Kong	3	^[17]
New Zealand	3	^[17]
Singapore	3	^[17]
Angola	2	^[17]
Australia	2	^[17]
Norway	2	^[17]
China	1	^[17]
South Korea	1	^[17]
Total	233