Title: Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage
and diversification within P.2 clade in Brazil
Alessandra P Lamarca
1
, Luiz G P de Almeida
1
, Ronaldo da Silva Francisco Jr
1
, Lucymara
Fassarella Agnez Lima
2
, Kátia Castanho Scortecci
2
, Vinícius Pietta Perez
3
, Otavio J. Brustolini
1
,
Eduardo Sérgio Soares Sousa
4
, Danielle Angst Secco
5
, Angela Maria Guimarães Santos
5
, George
Rego Albuquerque
6
, Ana Paula Melo Mariano
6
, Bianca Mendes Maciel
6
, Alexandra L Gerber
1
,
Ana Paula de C Guimarães
1
, Paulo Ricardo Nascimento
7
, Francisco Paulo Freire Neto
7
, Sandra
Rocha Gadelha
6
, Luís Cristóvão Porto
5
, Eloiza Helena Campana
4
, Selma Maria Bezerra
Jeronimo
7,8
, Ana Tereza R Vasconcelos
#1
1
Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis,
Brazil.
2
Laboratório de Biologia Molecular e Genômica, Universidade Federal do Rio Grande do Norte,
Natal, Brazil.
3
Laboratório de Endemias, Núcleo de Medicina Tropical, Centro de Ciências da Saúde,
Universidade Federal da Paraíba, João Pessoa, Brazil.
4
Laboratório de Biologia Molecular, Centro de Ciências Médicas, Universidade Federal da
Paraíba, João Pessoa, Brazil.
5
Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de
Janeiro, Rio de Janeiro, Brazil.
6
Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa
Cruz, Ilhéus, Brazil.
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NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
7
Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do
Norte, Natal, Brazil.
8
Departamento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do
Norte, Natal, Brazil.
# corresponding author: atrv@lncc.br
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is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted March 26, 2021. ; https://doi.org/10.1101/2021.03.21.21253418doi: medRxiv preprint
Abstract
The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the
ongoing SARS-CoV-2 pandemic. Novel SARS-CoV-2 lineages P.1 and P.2, first identified
respectively in Manaus and Rio de Janeiro, have been associated with potentially higher
transmission rates and antibody neutralization escape. In this study, we performed a whole-genome
sequencing of 185 samples isolated from three out of the five Brazilian regions, including
Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de
Janeiro (Southeast region) aiming to identify SARS-CoV-2 mutations that could be involved in
the surge of COVID19 cases in Brazil. Here, we showed a widespread dispersion of P.1 and P.2
across Brazilian regions. Except for Manaus, P.2 was the predominant lineage identified country-
wise. P.2 lineage was estimated to have originated in February, 2020 and has diverged into new
clades. Interstate transmission of P.2 was detected since March, but reached its peak in December,
2020 and January, 2021. Transmission of P.1 was also high in December. P.1 origin was inferred
to have happened in August 2020. We also confirmed the presence of the variant under
investigation (VUI) NP13L, recently described in the southernmost region of Brazil, to have spread
across the Northeastern states. P.1, P.2 and NP13L are descended from the ancient B.1.1.28 strain,
although during the first phase of the pandemic in Brazil presence of B.1.1.33 strain was also
reported. We investigate here the possible occurrence of a new variant of interest descending from
B.1.1.33 that also carries the E484K mutation. Indeed, the recurrent report of many novel SARS-
CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting
in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the
critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted March 26, 2021. ; https://doi.org/10.1101/2021.03.21.21253418doi: medRxiv preprint
of the SARS-CoV-2 isolates worldwide in order to early identify novel variants of interest and to
monitor for vaccine effectiveness.
Keywords: COVID-19; coronavirus; pandemic; viral genomics; phylogenomics, time tree
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted March 26, 2021. ; https://doi.org/10.1101/2021.03.21.21253418doi: medRxiv preprint
Introduction
One year after identifying the first case of SARS-CoV-2 infection in Brazil, the country is in a
catastrophic situation with 11 million cases of COVID-19 and 265,000 deaths
(https://coronavirus.jhu.edu/map.html). The initially dominant lineages B.1.1.28 and B.1.1.33 [1]
have been gradually replaced by the new variant of concern P.1 and variant of interest P.2
harboring harmful mutations [2–4]. P.2 was firstly reported in November 2020 in samples from
the state Rio de Janeiro and was estimated in previous works to have emerged in late July [3]. By
December 2020, it was already prevalent in samples in Rio Grande do Sul, which borders the
countries Uruguay and Argentina [5]. P.1, on the other hand, was first detected in the city of
Manaus, north region of Brazil in early January 2021 [2,4], with a proposed emergence between
April and mid/late December. Both lineages evolved within the B.1.1.28 clade carrying the E484K
mutation in the receptor-binding domain (RBD) of the Spike protein. In addition to E484K, P.1
also harbors N501Y and K417T mutations in the RBD region, and both shared with the new
variants of concern from the United Kingdom (B.1.1.17) and South Africa (B.1.351). Those three
mutations are suggested to allow the viral escape from previous hosts' immune responses [6–8].
This hypothesis is supported by the explosive spread of P.1 cases in Manaus and reports of
reinfection involving both lineages.
During the first phase of the COVID-19 pandemic in Brazil, national long-distance travels from
large urban centers in the Southeast region to North and Northeast states was attributed to be the
source of the explosion of cases across the country [1]. Since mid-November, there has been an
expected and dramatic surge in new COVID-19 cases, supposedly caused by a reduction of social
distance levels due to end-of-the-year holidays and summer vacations (from December to
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted March 26, 2021. ; https://doi.org/10.1101/2021.03.21.21253418doi: medRxiv preprint