Review 1: "The emergence of new lineages of the Monkeypox virus could affect the 2022 outbreak"

RR:C19 Evidence Scale rating by reviewer:

• Reliable. The main study claims are generally justified by its methods and data. The results and conclusions are likely to be similar to the hypothetical ideal study. There are some minor caveats or limitations, but they would/do not change the major claims of the study. The study provides sufficient strength of evidence on its own that its main claims should be considered actionable, with some room for future revision.

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Review:

The claims in this preprint are generally supported by the data and methods used. Decision-makers should consider the claim in this study actionable with limitations.

Summary and Strengths:

The present work describes the changes in the MPXV genome of the current outbreak, focusing on some selected viral genes related to immune evasion or host response. The analysis by the authors revealed some synonymous nucleotide changes, but also a discrete set of potentially interesting amino acid changes. The aim of this work is the identification of such mutations rather than determining their relevance or impact on virus infection. Regardless of the degree of novelty, the findings from this work encourage the implementation of genomic MPXV surveillance and future studies to link mutations with viral transmissibility, pathogenesis, or virulence. I find this point correct and very valuable.

Limitations:

Some of the claims or findings from this manuscript confirm the previous work on MPXV, such as the absence of the C3L gene from the less virulent variants (Chen et al 2005). This is somewhat expected since from the start of the current outbreak, MPXV genomes seemed to match Western African isolates (clades 2 and 3), rather than the most virulent ones from Congo (clade 1) with an intact C3L. Also, the authors highlight the mutations found in structural protein B5R and viral DNA ligase A50R mutations, while additional mutations related to C7L, C12L and H5R are just included in the Table, but not discussed. I suppose the reason is that these mutations do not map in a characterized protein domain. This should be further explained or discussed. Other changes are synonymous mutations, with an unknown impact. For these reasons, in my opinion, these findings do not refute the current understanding.

Although the work is concise, well-written, and clearly presented, in my opinion, a better description of the current MPXV lineages/clades in the introduction would improve the understanding of the manuscript by a broader audience. Also, some discussion about the mutation affecting host range factor C7L is missing. Could this represent the changes in C7L an adaptation to a new host?

The manuscript properly selects and cites the current literature, with the exception of the first work analyzing an MPXV genome from the 2022 outbreak, which is missing from the MS: Isidro, J.et al. Nat Med (2022). https://doi.org/10.1038/s41591-022- 01907-y.

Minor limitations:

A50R and B5R are referred as A50L and B5L in the text, and a couple of sentences are not complete.