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 2021-01-22 17:25 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	4	Brazil 24, Japan 4, Faroe_Islands 1, South_Korea 1	30	2020-12-04

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	30
Countries with sequences	4
Countries reported	6
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 9 | Air traffic from Brazil by destination

The number of ticketed origin-to-destination journeys from Braziliann airports to countries outside Brazil during October 2020.

Colours indicate numbers of published genomes of P.1 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published P.1 sequences on GISAID. White bars indicate countries with no reports of B.1.351.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >100 passengers.

Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased. Also, this data will not reflect volume of traffic over land or other modes of transport.

Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer

Table 2 | Reported P.1 imports.

Country count: 6

Country	Earliest report	Date local transmission	Local transmission	Method of surveillance	Source
Brazil	2020-12-15	2020-12-15	1	community_sequencing	https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
Japan	2021-01-12		0	travellers	https://www.niid.go.jp/niid/en/2019-ncov-e/10108-covid19-33-en.html
Italy	2021-01-17		0	travellers	https://www.business-standard.com/article/current-affairs/italy-bans-flights-from-brazil-after-covid-variant-detected-in-4-passengers-121011700080_1.html
South Korea	2021-01-10		0	travellers	GISAID
Germany	2021-01-22		0	travellers	https://www.faz.net/aktuell/rhein-main/nachweis-in-frankfurt-neue-corona-mutation-in-deutschland-17159476.html
Faroe Islands	2021-01-12		0	travellers	https://local.fo/in-a-first-european-case-brazilian-coronavirus-variant-confirmed-in-the-faroe-islands/

Table 3 | Raw data for figures in the report.

Country	Earliest sequence	Number of variant sequences	Total sequences since first variant sequence
Faroe Islands	2021-01-12	1	1
Brazil	2020-12-04	24	79
Japan	2021-01-02	4	4
South Korea	2021-01-10	1	1