SARS-CoV-2 Theta variant

Lineage P.3, also known as the P.3 Variant, VUI(Variant Under Investigation)-21MAR-02, Lineage B.1.1.28.3 and colloquially known as the Philippines variant is one of the Variants of SARS-CoV-2, the virus that causes COVID-19. This variant was first identified in the Philippines on 18 February 2021 when two mutations of concern detected in Central Visayas^[1]. This variant was detected in Japan on 12 March 2021 when a traveler from the Philippines arrived in Narita Airport, Tokyo^[2]. This variant is distinct from those first discovered in Britain, South Africa and Brazil, and is thought to pose a similar threat. The Philippine variant may be more resistant to neutralizing antibodies, including those gained through vaccination, like the South African and Brazilian variants appear to be.^[3]

Detection

On 18 February 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 12 March 2021, Japan detects new coronavirus variant found in traveler from the Philippines.^[2]

On 13 March 2021, the Department of Health confirmed the mutations constitutes a variant which was designated as lineage P.3. On the same day, it also confirmed its first case of Lineage P.1 variant of Covid-19 in the country. Although the P.1 and P.3 variants stem from the same lineage B.1.1.28, the department said that P.3 variant's impact on vaccine efficacy and transmissibility is yet to be ascertained.^[4]

On 17 March 2021, the United Kingdom confirmed its first two cases, where PHE termed it VUI-21MAR-02.^[5]

On 30 April 2021, Malaysia detected 8 cases of P.3 variant in Sarawak.^[6]

Mutations

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. ^[7]

Mutation profile of P.3 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

Statistics

Cases by country (As of May 4, 2021)
Country	Confirmed cases	References
Philippines	157	^[8]^[9]
Japan	3	^[10]
United Kingdom	5	^[10]
Germany	7	^[10]
Australia	2	^[10]
Netherlands	6	^[10]
Norway	2	^[10]
United States of America	2	^[10]
New Zealand	2	^[10]
China	1	^[10]
Singapore	1	^[10]
South Korea	1	^[10]
Malaysia	8	^[11]
World (13 countries)	Total: 197	Total as of 4 May 2021