PONE-D-19-29145

Persistence of Chikungunya ECSA genotype and local outbreak in an upper medium class neighbourhood in Northeast, Brazil.

PLOS ONE

Dear Dr Luiz Carlos Junior Alcantara,

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This work was supported by the ZiBRA2 project supported by the Brazilian Ministry of Health (SVS- MS) and the Pan American Organization (OPAS) and founded by Decit/SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); by CAPES (88887.130716/2016-00, 88881.130825/2016-00 and 88887.130823/2016-00); by EU’s Horizon 2020 Programme through ZIKAlliance (PRES-005-FEX-17-4-2-33). The Virology and Experimental Therapy Laboratory (LaVite) at Aggeu Magalhães Institute (IAM) FIOCRUZ-PE is supported by Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco (FACEPE) [grant number APQ-0078-2.02/16].

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LCJA: This research was funded by CNPq grant number (440685/2016-8); CAPES grant number (88887.130716/2016-00).

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Reviewer #2: Yes

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Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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Reviewer #1: Goes de Jesus et al., in this research article report evidence of the persistence of CHIKV ECSA genotype and shed light on a local outbreak raised in the Serraria Brasil, an upper medium class neighbourhood within FS in 2016, two years after the lineage introduction in the locality.

Although there have now been many papers documenting various portions of the Chikungunya virus outbreak in Brazil, this manuscript benefits from the fact that no genomic data have been generated in 2016 in Bahia state, contributing to add knowledge regarding the persistence as well as the transmission dynamics of these virus in Brazil. This manuscript does not provide a large conceptual advance in our understanding of the Chikungunya virus outbreak in the Americas, but it does tell a nice story. With some minor changes, I think it would be suitable for publication in Plos One.

Comments:

- Please revise carefully the English used.

- What was the considerations for using 2 x 75 bp NGS reagent? Why not using larger read length such as 2 x 150 bp? Longer reads may decrease gaps.

- Figure 1. Is the zoom representing the city of Feira de Santana or the Serraria Brasil neighnorhood? Please state this and add the hype in the map.

- In the method section, could the authors add more information regarding the Library prep sequencing for Illumina, this is really fundamental in the field. Did the author used barcode? Have been this barcode pooled in an equimolar fashion after the amplification?

Reviewer #2: Goes de Jesus et al., in this research article, report evidence of the persistence of CHIKV ECSA genotype and shed light on a local outbreak raised in the Serraria Brasil, an upper medium class neighbourhood within FS in 2016, two years after the lineage introduction in the locality.

Bahia was the introductory point of CHIKV-ECSA in the Americas and it is the region in Brazil that seems to have the highest genetic diversity of this genotype. Since the first registered cases in 2014, no new genomic surveillance data had been released. Authors provide new genomic data from this state from 2016, and this is, in my point of view the main benefits of the present research article.

Despite these considerations I have a main concern:

The Authors state, in lines 347-349 that these data improve intervention strategies. How? Please provide strong evidence.

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Reviewer #1: No

Reviewer #2: No

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Persistence of Chikungunya ECSA genotype and local outbreak in an upper medium class neighbourhood in Northeast, Brazil.

PONE-D-19-29145R1

Dear Dr. Luiz Carlos Junior Alcantara,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Massimo Ciccozzi

Academic Editor

PLOS ONE

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