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. 2021 Jul 19;15(7):e0009591. doi: 10.1371/journal.pntd.0009591

Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil

Stephane Tosta 1,2,#, Marta Giovanetti 1,3,*,#, Vanessa Brandão Nardy 2, Luciana Reboredo de Oliveira da Silva 2, Marcela Kelly Astete Gómez 2, Jaqueline Gomes Lima 2, Cristiane Wanderley Cardoso 4, Tarcisio Oliveira Silva 5, Marcia São Pedro Leal de Souza 6, Pedro Henrique Presta Dia 7, Vagner Fonseca 1,8,9, Tulio de Oliveira 9, José Lourenço 10, Luiz Carlos Junior Alcantara 1,3,*, Felicidade Pereira 2,*,#, Arabela Leal 2,*
Editor: Colleen B Jonsson11
PMCID: PMC8321350  PMID: 34280196

Abstract

Tracking the spread of SARS-CoV-2 variants of concern is crucial to inform public health efforts and control the ongoing pandemic. Here, we report genetic evidence for circulation of the P.1 variant in Northeast Brazil. We advocate for increased active surveillance to ensure adequate control of this variant throughout the country.

Author summary

In recent months’ variants of SARS-CoV-2 that have more mutations on the Spike protein has brought concern all over the world. These have been called ‘variants of concern’ (VOC) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. The P.1 variant, also known as 20J/501Y.V3, was first identified in travelers from Brazil during routine airport screening in Tokyo, Japan, in early January 2021. This VOC has 17 amino acid changes, ten of which are in its spike protein, including three designated to be of particular concern: N501Y, E484K and K417T. Since its first detection, despite it has presented sustained transmission worldwide, much is still unknown about its circulation into Brazilian regions. Here, through an active monitoring conducted by public health authorities of the Bahia state (Northeast Brazil), we report genetic evidence for circulation of the P.1 variant into the state. Our findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of the circulating and co-circulating SARS-CoV-2 variants, which might help to attenuate their public health impact worldwide.

Introduction

Since the emergence of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, the combination between the unprecedented number of cases and more than 500K genomes generated has allowed the identification of hundreds of circulating genetic variants during the pandemic [1]. Currently, three variants (B.1.1.7 or VOC202012/01, B.1.351 or 20H/501Y.V2 and P.1) carrying several mutations in the receptor-binding domain (RBD) of the spike (S) protein, raise concerns about their potential to shift the dynamics and public health impact of the pandemic [2–5]. They appear potentially associated with (i) increased transmissibility, (ii) propensity for re-infection, (iii) escape from neutralizing antibodies, and (iv) increased affinity for the human ACE2 receptor [6–8].

First identified in January 2021 in travelers from the Amazonas state (North of Brazil) who arrived in Japan, the P.1 variant (alias of B.1.1.28.1) [9], harbors a constellation of 17 unique mutations, including three in the receptor binding domain of the spike protein (K417T, E484K, and N501Y). It thus immediately raised concerns to public health authorities over the risk of its unknown potential of faster spreading and/or worsening of coronavirus disease (COVID-19) clinical outcomes. In view of its rapid spread in Brazil and elsewhere [1,4,5] the public health authorities of the Bahia state (Northeast Brazil) conducted an active monitoring for a rapid detection of this variant in the state.

Here, we report genetic evidence of the circulation of the P.1 variant in Bahia, by generating 11 SARS-CoV-2 complete genomes from travelers returning from the Amazonas state (North of Brazil).

Material and methods

Ethics statement

This research was approved by the Ethics Review Committee of the Pan American Health Organization (PAHOERC.0344.01) and the Federal University of Minas Gerais (CEP/CAAE: 32912820.6.1001.5149). The availability of these samples for research purposes during outbreaks of national concern is allowed to the terms of the 510/2016 Resolution of the National Ethical Committee for Research–Brazilian Ministry of Health (CONEP—Comissão Nacional de Ética em Pesquisa, Ministério da Saúde), that authorize, without the necessity of an informed consent, the use of clinical samples collected in the Brazilian Central Public Health Laboratories to accelerate knowledge building and contribute to surveillance and outbreak response.

Sample collection and RT-qPCR diagnosis

In mid-January 2021, routine genomic surveillance in the Central Laboratory of Health of the Bahia state (LACEN-BA), started an extensive screening of COVID-19 patients and their contacts reporting a travel history to/from the Amazonas state, resulting in eleven suspected SARS-CoV-2, P.1 infections.

Viral RNA was extracted from nasopharyngeal swabs using an automated protocol on the King Fisher platform using the MagMax Kit (Thermofisher Scientific) and tested for SARS-CoV-2 by multiplex real-time PCR assays: i) Allplex 2019-nCoV Assay (Seegene) targeting the envelope (E), the RNA dependent RNA polymerase (RdRp) and the N genes and ii) the Charité: SARS-CoV2 (E/RP) assay (Biomanguinhos) targeting the E gene, supplied by the Brazilian Ministry of Health. Samples were selected based on the Ct value ≤ 32. Associated epidemiological data, such as symptoms, travel history and municipality of residency, were collected from medical records accompanying the collected samples provided by LACEN-BA.

Library preparation

Samples with RT-PCR–positive were submitted to the Ion GeneStudio S5 Plus System (Life Technologies, USA) to viral genomic amplification and subsequent sequencing according to the manufacturer’s instructions.

Generation of consensus sequences

Raw files were basecalled using Guppy v3.4.5 and barcode demultiplexing was performed using qcat v.1.1.0. Consensus sequences were generated by de novo assembling using Genome Detective (https://www.genomedetective.com/) [10].

Phylogenetic analysis

We explored the genetic relationship of the newly sequenced P.1 genomes to those of other isolates by phylogenetic inference. To do so, we combined the eleven new isolates (Accession numbers EPI_ISL_1067728—EPI_ISL_1067738) with all Brazilian SARS-CoV-2 (n = 1663) genomes, including recently released P.1 genomes [4,5] available on GISAID (https://www.gisaid.org/) up to February 21st, 2021 (a fully annotated tree can be found in the S1 Fig). Only genomes >29,000bp and <1% of ambiguities were considered (n = 1663). Sequences were aligned using MAFFT v.7 [11] and submitted to IQ-TREE 2 for maximum likelihood (ML) phylogenetic analysis [12]. The ML phylogenetic tree was inferred under the GTR+F+I+G4 nucleotide substitution model as selected by the ModelFinder application and the branch support was assessed by the approximate likelihood-ratio test based on the bootstrap and the Shimodaira–Hasegawa-like procedure (SH-aLRT) with 1,000 replicates. Lineages assessment was conducted using Phylogenetic Assignment of Named Global Outbreak Lineages tool available at https://github.com/hCoV-2019/pangolin [1].

Results

In mid-January 2021, samples from (clinically) suspected cases and their contact reporting a travel history to/from the Amazonas state were screened at the Central Laboratory of Health of the Bahia state (LACEN-BA). A total of 11 RT-qPCR positive samples were screened. All samples tested, contained sufficient DNA (≥2ng/μL) to proceed to library preparation. For those positive samples, PCR cycle threshold (Ct) values for common target (E gene) ranged from ≈16 to ≈30 (Table 1). We next subjected the qRT-PCR–positive samples to viral genomic amplification and sequencing using the Ion GeneStudio™ S5 Plus Ion Torrent (Life Technologies, USA), according to the manufacturer’s instructions. A total of 13,234,814 mapped reads were obtained, resulting in a sequencing mean depth of 4824 and a coverage of 98% (Table 1). The new whole genome sequences generated were assigned, according to the Pangolin [1] lineage classification, as the recently identified P.1 Brazilian VOC. All patients had recently recorded travel from the city of Manaus in Amazonas back to the Bahia state. Four patients were from the same family and the others had no other known connection between them. The data from the eleven patients are described in (Table 1).

Table 1. Information from patients with travel history from Manaus, Amazonas to state of Bahia.

GISAID ID ID Colection Date Sex Age Municipality Symptoms Protocol Cycle threshold (ct) Reads Coverage Depth of Coverage
EPI_ISL_1067737 BA491 2021-01-26 M 7 Salvador Assymptomatic Allplex 2019-nCoV Assay (Seegene) CI -16.8
E—18.1
N—20.8
RdRp—26.5		 1659219 99.8 10179.3
EPI_ISL_1067730 BA501 2021-01-26 F 31 Salvador Sore throat, cough, fever Allplex 2019-nCoV Assay (Seegene) CI -28.7
E—25.7
N—25.6
RdRp—28.4		 594545 99.8 3706.8
EPI_ISL_1067738 BA511 2021-01-26 M 66 Salvador Sore throat, cough, fever Allplex 2019-nCoV Assay (Seegene) CI -27.0
E—24.9
N—23.8
RdRp—25.6		 412507 82.2 2869
EPI_ISL_1067731 BA521 2021-01-26 F 37 Salvador Sore throat, cough, fever Allplex 2019-nCoV Assay (Seegene) CI -27.5
E -24.5
N—25.5
RdRp -26.8		 1047634 99.2 6779
EPI_ISL_1067735 BA 561 2021-01-16 M 37 Salvador Sore throat, cough, fever Allplex 2019-nCoV Assay (Seegene) CI -25.2
E -24.9
N—25.7
RdRp -26.6		 862894 99.8 5438.3
EPI_ISL_1067729 BA 54 2021-01-23 F 56 Irecê Sore throat, cough, fever, fatigue, dyspnea, coriza, dyspnea, diarrhea, respiratory distress, O2 saturation = 92% Allplex 2019-nCoV Assay (Seegene) CI -15.4
E -16.9
N—16.8
RdRp -27.2		 625085 99.8 3982.5
EPI_ISL_1067734 BA 55 2021-01-23 M 52 João Dourado Fever, headache Allplex 2019-nCoV Assay (Seegene) CI -27.0
E -22.3
N—23.7
RdRp -24.4		 1848679 99.8 11278.1
EPI_ISL_1067733 BA 53 2021-01-23 M 19 João Dourado Assymptomatic Charité: SARS-CoV2 (E/RP) (Bio Manguinhos) E—22.9
RP—26.6		 1131609 99.8 6979.9
EPI_ISL_1067736 BA57 2021-01-23 M 42 Salvador Fever, headache Allplex 2019-nCoV Assay (Seegene) CI -25.5
E -17.2
N—18.9
RdRp -19.2		 1416051 99.8 8970.8
EPI_ISL_1067728 BA58 2021-01-08 F 53 Salvador Fever, headache Allplex 2019-nCoV Assay (Seegene) CI -27.8
E -29.0
N—29.7
RdRp -30.0		 2343392 98 14635.7
EPI_ISL_1067732 BA59 2021-01-18 M 57 Salvador Fever, headache Allplex 2019-nCoV Assay (Seegene) CI -26.7
E -30.0
N—30.0
RdRp -30.0		 1293199 99.8 8105.2
Open in a new tab

1Patients from the same familiy

Phylogenetic analysis strongly supported placement of the isolates from Bahia within the Brazilian P.1 clade (Fig 1A) (Bootstrap = 1.0, SH-aLTR = 1.0).

Fig 1. Genomic detection of the SARS-CoV-2 P.1 variant of concern in Bahia state, Northeast Brazil.

Fig 1

Open in a new tab

a) Maximum likelihood (ML) phylogenetic tree including the 11 new isolates obtained in this study plus n = 1663 SARS-CoV-2 Brazilian strains collected up to February 21st, 2021. b) Map of Brazil (generated in R using the “get_brmap” package available at: https://rdrr.io/cran/brazilmaps/man/get_brmap.html) showing the number of P.1 SARS-CoV-2 sequences available by region and state (updated up to when this surveillance was done—February 21st, 2021). North region (blue): AM = Amazonas state, RR = Roraima state and RO = Rondônia state; Midwest region (dark green): GO = Goiás state; Southeast region (lilac): SP = São Paulo and South region: SC (light green): Santa Catarina state and RS = Rio Grande do Sul state and Northeast region (red): BA = Bahia state. c) Representation of the zoom of the Brazilian P.1 clade. Branch support (Bootstrap = 1.0, SH-aLTR = 1.0) is shown at key nodes. d) Variant maps of the P.1 lineage-defining-mutations were mapped against the SARS-CoV-2 genome structure. Most common mutations defined as mutations present in more than 90% of the genomes in that group. Mutations of international concern: i) K417T (22812A>C); ii) E484K (23012G>A) and iii) N501Y (23063A>T), among the RDB domain are highlighted in red.

Our results further highlighted that most of our new isolates formed two well supported monophyletic clusters (Fig 1C). One of those clusters (Cluster i), included samples from the capital city of Salvador, isolated from individuals from the same family (BA49, 50, 51 and 52) plus the sample BA57 (Bootstrap = 1.0, SH-aLTR = 1.0). And a second cluster (Cluster ii) which included samples BA53, 54 and 55 that were isolated from patients from the municipalities of João Dourado and Irecê (Bootstrap = 1.0, SH-aLTR = 1.0). Moreover, samples BA56 and BA58 and BA59 appeared to be interspersed among P.1 strains from the North and Southeast Brazil. By combining all the P.1 strains already available from distinct Brazilian regions (Fig 1B and 1C) our analysis further revealed that this variant was already detected in the majority of Brazilian regions (starting from the North to Midwest, Northeast, Southeast and South Brazil) highlighting the high connectivity of the country and reinforcing the need of active monitoring to follow the local real-time spread of this new variant of international concern. Finally, among the eleven new genomes, we also identified lineage-specific mutations, including the ones of international concern among the RDB domain: K417T (22812A>C), E484K (23012G>A) and the N501Y (23063A>T) (Fig 1D).

Discussion

This report describes the early detection of the SARS-CoV-2 P.1 variant in the Northeast of Brazil (Bahia state) and provides evidence regarding the P.1 circulation across all Brazilian macro-regions that would have occurred within the past two months. The P.1 variant is now known to have emerged in the Amazonas state, but was first detected in travelers arriving in Japan from Brazil. The latter is a testimony for the currently scarce genomic surveillance in Brazil, which has failed to detect the variant before it became a public health emergency in the Amazonas state. Moreover, the eleven individuals here described to carry the P.1 variant in the Bahia state were only detected after a unique active screening initiative that focused on travelers and their recent contacts. This case study should serve as an example of the effectiveness of active surveillance to monitor the importation of genetic variants of importance for public health. Since such initiatives are not only critical to monitor the ongoing spread of known variants but are also necessary to detect the possible emergence of new ones in the near future, continual and revamped investment is needed and will be necessary for adequate public health policy in Brazil.

Supporting information

S1 Table. GISAID acknowledgment table.

(PDF)

Click here for additional data file. (72KB, pdf)
S1 Fig. Fully annotated Maximum likelihood (ML) phylogenetic tree including the 11 new isolates obtained in this study plus n = 1663 SARS-CoV-2 Brazilian strains collected up to February 21st, 2021.

(TIF)

Click here for additional data file. (1.3MB, tif)

Acknowledgments

We thank the “Centro e Informações Estratégicas de Vigilância em Saúde” (CIEVS) in the municipality of Salvador, Bahia and Pan American Health Organization PAHO/WHO. We also would like to thank all the authors who have kindly deposited and shared genome data on GISAID. A table with genome sequence acknowledgments can be found in S1 Table.

Data Availability

Newly generated SARS-CoV-2 sequences have been deposited in GISAID under accession numbers EPI_ISL_1067728 to EPI_ISL_1067738 and are already available at: https://www.gisaid.org/.

Funding Statement

This work was financed by Laboratório Central de Saúde Pública da Bahia (LACEN-BA) and Secretaria da Saúde do Estado da Bahia (SESAB). ST is supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. MG is supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). JL is supported by a lectureship from the Department of Zoology, University of Oxford. This work was support in part through National Institutes of Health USA grant U01 AI151698 for the United World Arbovirus Research Network (UWARN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

References

PLoS Negl Trop Dis. doi: 10.1371/journal.pntd.0009591.r001

Decision Letter 0

Colleen B Jonsson, Emma Wise

7 May 2021

Dear Dr. Giovanetti,

Thank you very much for submitting your manuscript "Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil" for consideration at PLOS Neglected Tropical Diseases. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

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Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Colleen B Jonsson, PhD

Associate Editor

PLOS Neglected Tropical Diseases

Emma Wise

Deputy Editor

PLOS Neglected Tropical Diseases

***********************

Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: (No Response)

Reviewer #2: na

--------------------

Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: (No Response)

Reviewer #2: The data is clearly presented

--------------------

Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: (No Response)

Reviewer #2: (No Response)

--------------------

Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

Reviewer #2: The manuscript “Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil” provides a brief report resulting from the analyses of 11 viral genomes. While the dataset is limited, it comes from an epidemiologically interesting region at an important time in the dispersal of the P.1 variant. As such, the manuscript provides information that will be of general interest. The message is simple and clearly presented by the authors. Some minor comments for the authors consideration follow.

1. Ln 78. The authors state that eleven suspected P1 infections resulted from the massive screening program. It is a little unclear exactly what this means. Were only 11 positive samples detected through this screening (I suspect this is not what is meant)? It might be clearer if the number of tests conducted and the number of positive PCR tests were provided. If more than 11 samples were positive, how were these particular samples selected?

2. Ln 129. What was the rationale for using two PCR assays on each sample?

3. Ln 136. Did all four family members travel, or was there evidence of within household spread?

4. It would be of interest to know the spectrum of disease experienced by these individuals.

Editorial suggestions

1. Ln 133. “generated where assigned” should be “generated were assigned”

2. Ln 135. “recently record travel” should be “recently recorded travel”

3. Ln 136. “back into the” should be “back to the”

4. Ln 136-137. “and the other others had” should be “and the others had”

--------------------

Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: Tosta et.al. present the manuscript entitled “Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil” described a pilot study in the northern region of brazil to recover the 11 SARS-COV2 genomes contain P.1 variant, which is of the active public health concern strain. As P1 variants is the important for public health on the active COVID19 pandemic right now, the manuscript will be interested in researchers of the closely related filed. However, the manuscript needs to be improved, especially in the method section. The inconsistency between method and result needs to be clarified.

Comments

1. The P.1 variant need to be defined in detail at first in the Author summary section.

2. Please provide version of the software used in the study: Guppy, qcat, MAFFT, IQ_TREE

3. As Phylogenetic tree analysis is very important result of the study, I recommend the author give the reader more details how to construct the tree such as what is the parameter used, what is the evolutionary model used. Boot strapping is highly recommended to perform and report as confident of the tree result.

4. It is very inconsistency in the method and result! The authors mentioned that they use Oxford Nanopore sequencing of PCR product from ARCTIC primer set, but the first paragraph of the result mentioned that Ion torrent sequencer was used. The authors need to clarify experimental procedures in a better detail.

5. Figure 1A need to be improved. The annotation of different clades based on known linages need to be reported on the figure. Readers will not gain any knowledge from the figure without the annotation of leakages. By using “Others” is meaningless. Standard tree file format such as newick format need to be shared as a supplementary for the readers.

6. The label on y-axis of Figure 1D is missing.

7. Raw sequence data need to be deposited and shared for the research community in a public database such as NCBI SRA database.

8. For reproducible and transparency of the result, I recommended the authors share the computational notebook or chunk of code used in the study.

Reviewer #2: (No Response)

--------------------

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Reviewer #2: Yes: Richard J Webby

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PLoS Negl Trop Dis. doi: 10.1371/journal.pntd.0009591.r003

Decision Letter 1

Colleen B Jonsson, Emma Wise

23 Jun 2021

Dear Dr. Giovanetti,

We are pleased to inform you that your manuscript 'Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil' has been provisionally accepted for publication in PLOS Neglected Tropical Diseases.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

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IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Neglected Tropical Diseases.

Best regards,

Colleen B Jonsson, PhD

Associate Editor

PLOS Neglected Tropical Diseases

Emma Wise

Deputy Editor

PLOS Neglected Tropical Diseases

***********************************************************

Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

Reviewer #2: (No Response)

**********

Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: The author improved the manuscript and addressed my comments.

Reviewer #2: my concerns have been addressed

**********

PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Richard Webby

PLoS Negl Trop Dis. doi: 10.1371/journal.pntd.0009591.r004

Acceptance letter

Colleen B Jonsson, Emma Wise

15 Jul 2021

Dear Dr. Giovanetti,

We are delighted to inform you that your manuscript, "Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil," has been formally accepted for publication in PLOS Neglected Tropical Diseases.

We have now passed your article onto the PLOS Production Department who will complete the rest of the publication process. All authors will receive a confirmation email upon publication.

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Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Neglected Tropical Diseases.

Best regards,

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. GISAID acknowledgment table.

    (PDF)

    Click here for additional data file. (72KB, pdf)
    S1 Fig. Fully annotated Maximum likelihood (ML) phylogenetic tree including the 11 new isolates obtained in this study plus n = 1663 SARS-CoV-2 Brazilian strains collected up to February 21st, 2021.

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    Data Availability Statement

    Newly generated SARS-CoV-2 sequences have been deposited in GISAID under accession numbers EPI_ISL_1067728 to EPI_ISL_1067738 and are already available at: https://www.gisaid.org/.

    Articles from PLoS Neglected Tropical Diseases are provided here courtesy of PLOS

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