Molecular Aspects of the Emergence of Monkeypox Virus Clades
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThis is a very interesting paper on monkeypox but there are several shortcomings that need to be addressed.<
1) There is a discussion about cowpox but there is no phylogenetic tree that includes cowpox. There should be at least one that includes cowpox, monkeypox, horse pox, vaccinia and smallpox.This can show how close the viruses are.
2) There is very little discussion about smallpox. There are many reasons that a more elaborate discussion is needed in this paper. Firstly, smallpox is a cousin that had inflicted untold sufferings and deaths to humans for centuries and is therefore important. Secondly, smallpox is extremely contagious among humans and the objective of this paper is understand why the more recent monkeypox isolates are more contagious. Therefore, it would have been wise if the authors have chosen to compare the genome of smallpox to the mutations of monkeypox. Theoretically mpox genome should become more similar to that of smallpox.
3) There is very little discussion about Virion physiology of the various viruses, The discussion pertaining to proteins should be made with respect to their locations in the Virion. If the protein is found at the surface of the virus, it could mean that the protein is involved in viral entry or immune escape.
https://www.sciencedirect.com/science/article/pii/S1876034123000345
4) There should be a comparative analysis of the viral proteins among cowpox, smallpox and monkeypox. This is related to (2)
https://www.ncbi.nlm.nih.gov/books/NBK230917/
5) One major problem with phylogenetic studies is that the algorithm cannot handle recombination well. For this reason, you may want to use phylogenetic trees of individual proteins like OPG173 or OPG027
Posada, D. How does recombination affect phylogeny estimation? Trends Ecol Evol 2000, 15, 489-490, doi:10.1016/s0169-5347(00)02027-9.
6) It is not good English to start a sentence with "So". as in Line 12
6) It is not good English to start a sentence with "So". as in Line 12
Author Response
Response to Reviewer 1
We would like to thank you for your valuable recommendations and comments that undoubtedly improved our manuscript. Please find the detailed responses below and the corresponding revisions highlighted in yellow in the resubmitted file.
Comment 1: There is a discussion about cowpox but there is no phylogenetic tree that includes cowpox. There should be at least one that includes cowpox, monkeypox, horse pox, vaccinia and smallpox. This can show how close the viruses are.
Response 1: We have added Figure 2.: Phylogenetic tree for the highly conserved central genome region of the orthopoxviruses was generated using the maximum-likelihood method. We agree that this analysis can show how close the viruses are.
Comment 2: There is very little discussion about smallpox. There are many reasons that a more elaborate discussion is needed in this paper. Firstly, smallpox is a cousin that had inflicted untold sufferings and deaths to humans for centuries and is therefore important. Secondly, smallpox is extremely contagious among humans and the objective of this paper is understand why the more recent monkeypox isolates are more contagious. Therefore, it would have been wise if the authors have chosen to compare the genome of smallpox to the mutations of monkeypox. Theoretically mpox genome should become more similar to that of smallpox.
Comment 4: (related to Comment 2) There should be a comparative analysis of the viral proteins among cowpox, smallpox and monkeypox. This is related to (2)
Response 2/4: Thanks for the interesting recommendations. Indeed, we should not forget about smallpox, which has caused a huge number of deaths around the world. The evolution of viruses is an intriguing mystery of the development of these pathogens. Despite the fact that MPXV and VARV belong to different species within the genus orthopoxviruses, these pathogens pose a threat to humans. It's amazing how it appears that the CPXV-like virus with a wide range of hosts became the progenitor of three highly specialized viruses: VARV, CMLV, and TATV.
The main task of this manuscript was to determine which factors played a significant role in the origin of MPXV from its precursor. The question of the further evolution of MPXV and its increase in human contagiousness is very interesting. To date, several publications have appeared evaluating mutations in the MPXV genome and their role in the adaptation of this virus to a new host (human). From this point of view, it would be interesting to compare them all with the mutations in the VARV genome that appeared during its origin from CPXV-like precursor. At the same time, the repertoire of the used MPXV and VARV immunomodulatory genes differs and their evolutionary trajectories cannot completely coincide. However, all this applies to future analysis.
We conducted a comparative analysis of the viral proteins among orthopoxviruses described in the work: Figure 4. Maximum likelihood phylogenetic trees of the Old World orthopoxviruses proteins coding OPG027 (A) and t OPG173 (B). An interesting fact is that the MPXV protein encoded by OPG027 is closest to VARV proteins.
Thank you for your professional comments. We believe that a more detailed comparison of the evolution paths of MPXV and VARV can be presented in a future publication.
Comment 3: There is very little discussion about Virion physiology of the various viruses, the discussion pertaining to proteins should be made with respect to their locations in the Virion. If the protein is found at the surface of the virus, it could mean that the protein is involved in viral entry or immune escape. https://www.sciencedirect.com/science/article/pii/S1876034123000345
Response 3: Dear reviewer, thank you for pointing out the issue. We have supplemented the manuscript with information: “All of the above proteins are not included in either extracellular enveloped virus or intracellular mature virus, with the exception of viral hemagglutinin. The hemagglutinin is a glycoprotein found on the envelope of extracellular virus.” For most of the described proteins, their ability to suppress the innate immune response does not affect viral replication in cell culture or in vivo.
Comment 5: One major problem with phylogenetic studies is that the algorithm cannot handle recombination well. For this reason, you may want to use phylogenetic trees of individual proteins like OPG173 or OPG027.
Response 5: Indeed, recombination and the long passage history of the virus on cell culture or CAM are the major problems of phylogenetic studies. For analysis, we selected the strains without long passage history and used the nucleotide sequences of the central region of the genome. The nucleotide sequences of the central region of the genome were used since it is known that recombination rearrangements that can interfere with phylogenetic studies occur only in variable terminal regions of the orthopoxvirus genomes. We have added this information to the text.
Besides, we conducted a comparative analysis of the viral proteins among orthopoxviruses described in the work: Figure 4. Maximum likelihood phylogenetic trees of the Old World orthopoxviruses proteins encoding by OPG027 (A) and OPG173 (B).
Comment 6: It is not good English to start a sentence with "So". as in Line 12
Response 6: Corrected.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript entitled „Molecular aspects of the emergence of monkeypox virus clades” focuses on the evolution of MPXV clades responsible for the recent mpox outbreak. The Authors in the well-designed studies presented an analysis of the gene panels that allowed for assessing the virus adaptation for human-to-human transmission. MPXV, for many years, was considered the infectious agent responsible for zoonotic diseases. Thus far, the reservoir of the virus has not been established. The current MPXV outbreak raises numerous questions, one of which is what is responsible for the accelerated transmission of the virus from person to person. The Authors focused on the evolutionary analysis of the MPXV genome, indicating target genes that can be of value in further analysis. The obtained data are well-discussed and presented comprehensively. The manuscript is informative and will contribute to elucidating the immunobiology of MPXV.
Minor remarks:
The Authors should include a schematic of the MPXV genome, indicating the areas evaluated for genes. It will lead to a better understanding of the presented data.
The Authors should be consistent in their use of virus abbreviations. Once the abbreviation (VARV) is used, the full name of the virus (variola virus) should not be used throughout the manuscript.
Lines 53-56: The Authors mentioned the sporadic zoonotic transmission to other continents. In the case of MPXV, the most notable transmission was the accidental introduction of the virus to the USA, along with establishing the reservoir, the prairie dogs. Martin Enserink's paper should be added.
Author Response
Response to Reviewer 2
Thank you for your positive review. We considered all your comments and recommendations to improve our manuscript. Please find the detailed responses below and the revisions highlighted in yellow in the resubmitted file.
Comment 1: The Authors should include a schematic of the MPXV genome, indicating the areas evaluated for genes. It will lead to a better understanding of the presented data.
Response 1: We have added Figure 1 with schematic representation of the MPXV genome. We agree that this scheme can help to better understand the information presented.
Comment 2: The Authors should be consistent in their use of virus abbreviations. Once the abbreviation (VARV) is used, the full name of the virus (variola virus) should not be used throughout the manuscript.
Response 2: Corrected.
Comment 3: Lines 53-56: The Authors mentioned the sporadic zoonotic transmission to other continents. In the case of MPXV, the most notable transmission was the accidental introduction of the virus to the USA, along with establishing the reservoir, the prairie dogs. Martin Enserink's paper should be added.
Response 3: The article is added.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsImprovements seen in this version
Comments on the Quality of English Language6) It is not good English to start a sentence with "So". as in Line 12
