Katana VentraIP

SARS-CoV-2 Gamma variant

The Gamma variant (P.1)[a] was[6][7] one of the variants of SARS-CoV-2, the virus that causes COVID-19.[8] This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T.[4][9] It 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.[4][10] It was subsequently declared to be in circulation in Brazil.[4] Under the simplified naming scheme proposed by the World Health Organization, P.1 was labeled Gamma variant, and was considered a variant of concern until March 2022, when it was largely displaced by the delta and omicron variants.[11]

Not to be confused with Gammacoronavirus.

General details

Gamma

20J/501Y.V3, Variant of Concern 202101/02 (VOC-202101/02),[1] Brazilian variant or Brazil variant'[2][3][4]

P.1

Tokyo, Japan

6 January 2021 (2021-01-06)

Gamma caused widespread infection in early 2021 in the city of Manaus, the capital of Amazonas, although the city had already experienced widespread infection in May 2020,[12] with a study[13] indicating high seroprevalence of antibodies for SARS-CoV-2.[14] A research article published in Science Journal indicate that P.1 infected people have a greater chance of transmissibility and death than B.1.1.28 infected ones.[15]


The Gamma variant comprises the two distinct subvariants 28-AM-1 and 28-AM-2, which both carry the K417T, E484K, N501Y mutations, and which both developed independently of each other within the same Brazilian Amazonas region.[16]


Gamma is notably different from the Zeta variant (lineage P.2) which also circulated strongly in Brazil. In particular, Zeta only carries the E484K mutation and has neither of the other two mutations of concern, N501Y and K417T.[16][9]

History[edit]

On 12 January 2021, the Brazil–United Kingdom CADDE Centre confirmed 13 local cases of lineage P.1 in Manaus, Amazonas state, the largest city of the Amazon rain forest.[4] The new lineage was absent in 27 samples collected from March to November 2020 from Manaus, but it was identified for the same city in 42% (n=13/31) of the samples collected 15–23 December 2020, followed by 52.2% (n=35/67) during 15–31 December 2020 and 85.4% (n=41/48) during 1–9 January 2021. Most notably, the P.2 was rapidly outcompeted by P1 going from the second half of December to 1–9 January, where the lineage P.2 share for Manaus decreased from 25.4% to 6.3%.[4][89]


A study of 180 sequenced Brazilian samples collected in the state of Rio de Janeiro during 2020, identified emergence of the novel lineage P.2 of SARS-CoV-2 (originating from B.1.1.28). P.2 was first detected by genome sequencing in October 2020, but it was estimated to have emerged in early July 2020.[27] As of December 2020, although having significantly increased in frequency throughout the state, it was still largely confined to the state capital Rio de Janeiro. In May 2020 the main lineages behind the COVID-19 positives were B.1.1.33 (70%) and B.1.1.28 (20%), whereas by September the main lineages were B.1.1.33 (50%) and B.1.1.28 (40%), with no detected presence of P.2, while during October and November P.2 was the most common lineage with a share close to 50% (according to the Pangolin tool).[90] The study also found the E484K mutation as "widely spread" across all analysed P.2 samples (36 out of 38).[90]


Researchers at the Oswaldo Cruz Foundation published a preprint genomic epidemiology study of 250 collected genomes from different places in Amazonas and found that P.1 infections can produce nearly 10 times more viral load than in other COVID-19-infected persons involving lineages B.1.1.28 and B.1.195. The lineage also showed 2.2 times higher transmissibility with the same ability to infect both adults (18–59 years old) and older persons (60 years old and higher), suggesting P.1 and its sublineages are more successful at infecting younger humans with no gender differential.[91]


The Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) produced another journal article of samples collected in Manaus between November 2020 and January 2021. The study indicated lineage P.1 to be about 2.0 times (50% CrI, 1.72.4 times) more transmissible and was shown to be capable of evading about 32% (50% CrI, 2146%) of inherited immunity from previous coronavirus diseases, leading to the possibility of reinfection. These increased statistics also had the same reflection in fatality, in that P.1 infections can be about 50% (50% CrI, 2090%) more lethal.[92][93][94] As part of ongoing research, the variant's capacity to neutralise antibodies has been evaluated by scientists in a published preprint work demonstrating that 8 CoronaVac-immunised persons had a poor blood plasma response against lineage P.1. Since the study only had a small number of participants, it was not possible to establish any statistical conclusion as a larger number of vaccinated people would need to be studied.[95] Scientists at MIT, Harvard and Cambridge, and hospitals physicians in Boston, corroborated that people fully vaccinated with Pfizer and Moderna vaccines have significantly decreased neutralisation with P.1—in a preprint work.[96]

Extinction[edit]

In March 2022, the World Health Organization listed the Alpha, Beta and Gamma variants as previously circulating citing lack of any detected cases in the prior weeks and months.[11]

: Alpha, Beta, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, Mu, Omicron

Variants of SARS-CoV-2

PANGO lineages: New variant report -Report on global distribution of 3 variants including P.1, a descendent of B.1.1.28

COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK