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Theta variant, also known as lineage P.3,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. It was detected in Japan on March 12, 2021, when a traveler from the Philippines arrived at Narita International Airport in Tokyo.
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.
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.
As of July 2021, Theta is no longer considered as a variant of interest by the WHO.
On March 17, 2021, Public Health England (PHE) named Lineage P.3 VUI-21MAR-02.
On June 1, 2021, the World Health Organization (WHO) named lineage P.3 as Theta variant.
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.
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.
On March 12, 2021, Japan detected the variant on a traveler from the Philippines.
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.
On March 17, 2021, the United Kingdom confirmed its first two cases, where Public Health England (PHE) termed it VUI-21MAR-02.
On April 30, 2021, Malaysia detected 8 cases of lineage P.3 in Sarawak.
The Philippine Genome Center (PGC) is a multi-disciplinary research facility in Quezon City, Metro Manila, Philippines which specializes in genomics.
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), also known as the coronavirus, is the virus that causes COVID-19, the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019. First identified in the city of Wuhan, Hubei, China, the World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. As described by the US National Institutes of Health, it is the successor to SARS-CoV-1, the virus that caused the 2002–2004 SARS outbreak.
The COVID-19 pandemic in the Philippines is part of the worldwide pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2. The first case in the Philippines was identified on January 30, 2020, and involved a 38-year-old Chinese woman who was confined at San Lazaro Hospital in Metro Manila. On February 1, a posthumous test result from a 44-year-old Chinese man turned out positive for the virus, making the Philippines the first country outside China to record a confirmed death from the disease.
"Cluster 5", also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI), is a variant of SARS-CoV-2, the virus that causes COVID-19, that is believed to be extinct. It was discovered in North Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of North Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic.
The Alpha variant, also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several variants of concern, the variant is estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. It was first detected in November 2020 from a sample taken in September in the United Kingdom, and began to spread quickly by mid-December, around the same time as infections surged. This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant is also notable for having more mutations than normally seen.
Beta variant, also known as lineage B.1.351, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa in October 2020, which was reported by the country's health department on 18 December 2020. Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay area in July or August 2020.
The COVID-19 Genomics UK Consortium (COG-UK) is a group of public health agencies and academic institutions in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the Wellcome Sanger Institute. The consortium is known for first identifying the SARS-CoV-2 Alpha variant in November 2020. As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to the GISAID sequencing database originated from COG-UK.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them.
Gamma variant, also known as lineage P.1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the World Health Organization, P.1 has been labeled Gamma variant, and is currently considered a variant of concern.
The term variant of concern (VOC) for severe acute respiratory syndrome coronavirus 2 is a category used when mutations in Receptor Binding Domain (RBD) substantially increase binding affinity in RBD-hACE2 complex, while also being linked to rapid spread in human populations.
Iota variant, also known as lineage B.1.526, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in New York City in November 2020. The variant has appeared with two notable mutations: the E484K spike mutation, which may help the virus evade antibodies, and the S477N mutation, which may help the virus bind more tightly to human cells.
The Delta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The Delta variant was named on 31 May 2021 and had spread to over 163 countries by 24 August 2021. The World Health Organization (WHO) indicated that the Delta variant is becoming the dominant strain globally.
Kappa variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It is one of the three sublineages of Pango lineage B.1.617. The SARS-CoV-2 Kappa variant is also known as lineage B.1.617.1 and was first detected in India in December 2020. By the end of March 2021, the Kappa sub-variant accounted for more than half of the sequences being submitted from India. On 1 April 2021, it was designated a Variant Under Investigation (VUI-21APR-01) by Public Health England.
Lineage B.1.617 is a lineage of SARS-CoV-2, the virus that causes COVID-19. It first came to international attention in late March 2021 after the newly established INSACOG performed genome sequencing on positive samples throughout various Indian states. Analysis of samples from Maharashtra had revealed that compared to December 2020, there was an increase in the fraction of samples with the E484Q and L452R mutations. Lineage B.1.617 later came to be dubbed a double mutant by news media.
Lambda variant, also known as lineage C.37, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Peru in August 2020. On 14 June 2021, the World Health Organization (WHO) named it Lambda variant and designated it as a variant of interest. It has spread to at least 30 countries around the world and is known to be more resistant to neutralizing antibodies compared to other strains. There is evidence that suggests the Lambda variant is both more infectious and resistant to vaccines than the Alpha and/or Gamma variant.
Epsilon variant, also known as CAL.20C and referring to two PANGO lineages B.1.427 and B.1.429, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in California, USA in July 2020.
Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.
The Eta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. The Eta variant or lineage B.1.525, also called VUI-21FEB-03 by Public Health England (PHE) and formerly known as UK1188, 21D or 20A/S:484K, does not carry the same N501Y mutation found in Alpha, Beta and Gamma, but carries the same E484K-mutation as found in the Gamma, Zeta, and Beta variants, and also carries the same ΔH69/ΔV70 deletion as found in Alpha, N439K variant and Y453F variant.
Spike (S) protein is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into trimers that form large structures, called spikes or peplomers, that project from the surface of the virion. The distinctive appearance of these spikes when visualized using negative stain transmission electron microscopy, "recalling the solar corona", gives the virus family its name.
The Mu variant, also known as lineage B.1.621 or VUI-21JUL-1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. It was first detected in Colombia in January 2021 and was designated by the WHO as a variant of interest on August 30, 2021. The WHO said the variant has mutations that indicate a risk of resistance to the current vaccines and stressed that further studies were needed to better understand it. Outbreaks of the Mu variant were reported in South America and Europe. The B.1.621 lineage has a sublineage, labeled B.1.621.1 under the PANGO nomenclature, which has already been detected in more than 20 countries worldwide.
He said for the Theta variant, six cases had been detected in Kuching and seven in Kota Samarahan