Lineage P.1, also known as 20J/501Y.V3, Variant of Concern 202101/02 (VOC-202101/02) or colloquially known as the Brazil(ian) variant, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named P.1 lineage and has 17 unique amino acid changes, 10 of which in its spike protein, including these 3 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), 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.
It has caused widespread infection in the city of Manaus, despite the fact that the city had already experienced widespread infection in May with a study indicating high seroprevalence of antibodies for SARS-CoV-2. P.1 has also been called 'B.126.96.36.199', although strictly only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation 'P.1'. P.1 comprises the two distinct sub variants 28-AM-1 and 28-AM-2, which both carry the K417T, E484K, N501Y mutations, and both developed independently of each other within the same Brazilian Amazonas region. P.1 is notably different from the other Brazilian P.2 lineage (also called 'B.188.8.131.52' or 'VUI-202101/01', which originated from Rio de Janeiro). In particular, P.2 only carries the E484K mutation and has neither of the other two concerning N501Y and K417T mutations.
On 12 January 2021, the Brazil–United Kingdom CADDE Centre confirmed 13 local cases of the P.1 lineage in Manaus, Amazonas state, largest city of the Amazon rainforest. The new lineage was absent in samples from March to November from Manaus, but it was identified in 42% of the samples from December 2020 collected in the same city, suggesting a recent increase in frequency.
A preprint of a paper by Carolina M Voloch et al. describes relationships between Brazilian samples sequenced during 2020 and identified a novel lineage of SARS-CoV-2, 'B.1.1.248', in circulation in Brazil, which originated from B.1.1.28. It describes it as first emerging in July and first detected by themselves in October, but as of publishing (December 2020), although significantly increased in frequency, it was still largely (61% of cases) confined to the state capital of Rio de Janeiro. In May the majority of their samples had been of lineage B.1.1.33, whereas by September there was significant spread of B.1.1.28, and during October and November P.1 predominated over respectively 3 and 4 other classifications using the Pangolin tool. The paper identifies the change E484K (present in both B.1.1.28 and P.1) as "widely spread" across the samples (for example, 36 out of the 38 samples in one set).
As well as having eight mutations (four of these synonymous genetic mutations) in its open reading frames (ORF1a and ORF1b)- one of which is a set of deletions- Lineage P.1 has 10 defining mutations in its spike protein, including N501Y and E484K. It also has two mutations- one an insertion- in its ORF8 region and one in its N region.