Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

Abstract

On the February 2020, the very first case was an American female from Diamond Princess cruise ship. Since, we have confirmed 136 patients infected with coronavirus disease 2019 (COVID-19) until February 2021. Here, we conducted the whole genome sequencing analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on samples from 70 of 136 patients (51.5%). These patients were infected in Diamond Princess cruise ship (n=1), Africa (n=2), Japan (n=66) and Brazil (n=1). The viral genome sequence of a patient on the Diamond Princess cruise ship in February 2020 was similar to that of original strain found in Wuhan, China (19A clade). Four patients, including two returnees from Africa and two lived in Japan, confirmed at the end of March 2020 had sequences similar to those of lineage with D614G mutation, which was endemic in Europe (20A [n=3] and 20B [n=1] clade). The 64 Japanese patients confirmed from September 2020 to January 2021 had sequences similar to those of the currently prevalent lineage (20B [n=58] and 20C clade [n=6]). Subsequent analysis revealed three mutations (K417T/ E484K / N501Y) in the receptor binding domain of the spike protein in a man in his 40s. The sequence was identical to the P.1 lineage (also known as 20J/501Y.V3) reported in Brazil. This is the first report of SARS-CoV-2 P.1 lineage identified in the city, Japan.

Recent highlights on Omicron as a new SARS-COVID-19 variant: evolution, genetic mutation, and future perspectives

“…This strain indicated three major changes within the receptor-binding domain on N501Y, K417T, and E484K that mimic the beta (β) strain found in South Africa. An experiment was performed with different monoclonal antibodies (MAB) to check the responses of gamma variant and results obtained were noted as: (1) most MABs were not able to neutralise the P.1 variant, (2) Adagio antibodies were found to be superior among other in terms of neutralisation of gamma variant, (3) zero neutralisation was found with bamlanivimab [ 18 , 30 ]. Moderna and Pfizer-BioNTech vaccinated sera were not able to neutralise gamma (γ) strain as like beta (β) strain [ 29 ].…”

Immune dynamics of SARS-CoV-2 virus evolution

“…The variant is associated with increased transmissibility and decreased neutralization efficacy by neutralizing antibodies. [2] It has been traced by the molecular clocking method to 6 th November 2020 as the emergent P.1 mutant in Manaus, Brazil, [15] which was also discovered in Japan. [16] Delta (B.1.617.2 lineage -Indian variant-21A): The variant B.1.617.2 holds the following S glycoprotein mutations -T19R (Threonine to Arginine substitution mutation at position 19), R158G (Arginine to Glycine), L452R (RBD substitution mutation reported to allow a stronger binding to the ACE2 receptor while also facilitating immune escape), [17] T478K (Threonine to Lysine substitution mutation predicted to increase transmission), D614G (Aspartic acid to Glycine), P681R (Proline to Arginine), and D950N (Aspartic acid to Asparagine) while also displaying a deletion at the 156 and 157 amino acid positions within the spike proteins.…”

“…In the case of SARS-CoV-2 variants such as the Beta (B.1.351) variant, wherein the antibodies generated from the previous strains show less efficacy, scientists are now diverting toward the use of killer T-cells, which is, CD8+ lineage. This is because killer T-cells can recognize a wider range of epitopes from COVID-19 proteins in terms of number (15)(16)(17)(18)(19)(20) and types (not only spike protein but also other expressed proteins with a slower mutation rate) which proves that they can potentially be a much better alternative than antibodies to deal with the emerging COVID-19 variants. The logic for the latter fact is that these cells recognize processed and presented viral antigens on the surface of infected host cells.…”

Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North America

“…A second new variant, known as 501Y.V3 or P.1, carries three mutations in the S-RBD domain (K417T, E484K, and N501Y) and was discovered for the first time in Brazil [9]. It was then detected in other countries including the U.S. [10,11]. A third variant, called 202012/01 (also known as 501Y.V1 or B.1.1.7) was first identified in the United Kingdom (U.K.) [12], and soon after became the primary emerging variant in many countries [13][14][15][16][17][18].…”