PONE-D-21-09819

Increased diversity with absence of site-specific selection bias in SAR-CoV-2 genomes from the early pandemic period in Pakistan

PLOS ONE

Dear Dr. Zahra,

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PLOS ONE

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Partly

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: In this manuscript, 32 SARS-CoV-2 strains were isolated, of which 21 were complete genome and 11 partial. Complete genome sequences have been submitted to Genbank. Phylogenic, SNP and selection analyses have been performed for these genomes.

Comments:

(1) This manuscript was not well-organized and the English writings need to be improved, such as typos and misuse of punctuation.

(2) There should be more details about SARS-CoV-2 cases, epidemiology and evolution in Pakistan in the background part.

(3) There are 57 complete and high coverage genome sequences available from Pakistan at Sep. 31, 2000 in the GISAID EpiCoV database. These genomes need to be added for phylogenetic analyses. Moreover, other genome sequences used in analyses need description. E.g., the choose of the 449 full-length sequences, and the 6523 global complete sequences. By the way, the "supplemtary file 1" is not available.

(4) HyPHY SLAC is not adequate for selection pressure analysis. More methods need to be applied. And the gene/cds used for the analysis need to be indicated.

(5) High-resolution figures for Fig. 1 and 2 need to be provided. Phylogenetic tree should be displayed in rectangular, rather than circular.

(6) A clear conclusion need be provided. The difference and relationship of first and second wave should be discussed.

(7) Some references were not cited properly.

Reviewer #2: This manuscript presents a meaningful and useful result, and futher increases our understanding of SAR-CoV-2 in Pakistan.

However, the genomic analysis of this manuscript is not deep enough.

For example, in Fig1 and Fig2, the clades and isolate date are needed to shown in figures and analysis, the additional analysis may make the conclusion of this manuscript more credible.

Page16: Figure 3.

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Reviewer #1: No

Reviewer #2: No

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Higher entropy observed in SAR-CoV-2 genomes from the first COVID-19 wave in Pakistan

PONE-D-21-09819R1

Dear Dr. Hasan,

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

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Kind regards,

Sagheer Atta, Ph.D

Academic Editor

PLOS ONE

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Reviewers' comments: