grinch | global report investigating novel coronavirus haplotypes

P.1 report 2021-01-18



Description

Brazilian lineage with variants of biological significants E484K, N501Y and K417T, described in recent virological posts: here and here. P.1 lineage is an alias of lineage B.1.1.28.1. As described in Rambaut et al., 2020 when the lineage heirarchy reaches a certain depth (length of 5) lineage names are given an alias to prevent them from becoming infinitely long.

Data source and processing

This report is recent as of 2021-01-18 19:03 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.7, pangoLEARN version 2021-01-11.

Pangolin assigns P.1 to sequences with more than 10 of the 17 defining P.1 SNPs – described here and here

Table 1 | Summary of sequence data

Lineage Country count Country Sequence count Earliest sequence Travel history
P.1 2 Brazil 11, Japan 4 15 2020-12-16

Lineage P.1

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table P.1 | Lineage P.1

Statistic Information
Sequence count 15
Countries with sequences 2
Countries reported 3
Likely origin Brazil
SNPs aa:orf1ab:S1188L
aa:orf1ab:K1795Q
del:11288:9
aa:S:L18F
aa:S:T20N
aa:S:P26S
aa:S:D138Y
aa:S:R190S
aa:S:K417T
aa:S:E484K
aa:S:N501Y
aa:S:H655Y
aa:S:T1027I
aa:orf3a:G174C
aa:orf8:E92K
aa:N:P80R

Figure 1 | Cumulative sequence count over time P.1

2021-01-18T20:32:29.298605 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 2 | Date of earliest P.1 detected

2021-01-18T20:32:28.543143 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/