Detection and genetic characterization of Uukuvirus lihanense, (Uukuvirus, Phenuiviridae) in hard ticks from the Colombian Caribbean.
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Ticks are arthropod vectors that transmit pathogens important to human and animal health. The Objective of this work was to identify Uukuvirus lihanense in the metatranscriptome of hard ticks. Between October 2022 and June 2023, ticks were collected from rural areas of the Colombian Caribbean area of the departments of Córdoba and Cesar. High-throughput sequencing (NGS) was performed using MGI's DNBSEQ-G50RS. Bioinformatics analyses were performed in Galaxy, DIAMOND, and IQtree2. A total of 766 ticks were collected; 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus sanguineus and 3.0% (23/766) Amblyomma dissimile. Complete and partial L and S segments of Uukuvirus lihanense (LITV) were detected in the metatranscriptome of A. dissimile, D. nitens, and R. microplus. The LITV sequences found are phylogenetically related to those detected in R. sanguineus and A. variegatum from the French Antilles, in R. microplus from Trinidad and Tobago, and R. microplus from Brazil. LITV was identified in D. nitens and R. microplus; the first report was in A. dissimile. Although LITV is not considered necessary in public health, The virus belongs to the Phenuiviridae family, which includes viruses of public health importance, such as Dabie bandavirus and Bandavirus heartlandense. The data indicate the wide range of tick species that LITV can infect, with the potential for spread to other vectors.
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Dear Dr Mattar, Thank you for your submission. Two independent reviews have been obtained and these review comments are below. I have selected minor amendments with this in mind. Please address these comments and return by the noted data. Best wishes, John.
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Comments to Author
This study reports the detection and genetic characterization of Uukuvirus lihanense (LITV) in hard ticks (Amblyomma dissimile, Dermacentor nitens, and Rhipicephalus microplus) from Colombia, including the first identification in A. dissimile. The work contributes to the understanding of tick-borne viral diversity and highlights the need for surveillance of understudied Phenuiviridae viruses. Major comment 1. Classification Method Clarification: The manuscript fails to adequately describe the methodology used for tick species identification. While the classification appears to be based on morphological characteristics, this approach is inherently subjective and vulnerable to observer bias. Given the critical importance of accurate species identification in this study, it is essential that the authors …
Comments to Author
This study reports the detection and genetic characterization of Uukuvirus lihanense (LITV) in hard ticks (Amblyomma dissimile, Dermacentor nitens, and Rhipicephalus microplus) from Colombia, including the first identification in A. dissimile. The work contributes to the understanding of tick-borne viral diversity and highlights the need for surveillance of understudied Phenuiviridae viruses. Major comment 1. Classification Method Clarification: The manuscript fails to adequately describe the methodology used for tick species identification. While the classification appears to be based on morphological characteristics, this approach is inherently subjective and vulnerable to observer bias. Given the critical importance of accurate species identification in this study, it is essential that the authors supplement their morphological analyses with molecular biological evidence (such as COI or 16S rRNA). 2. Bioinformatic Method Clarification: The bioinformatics approach described in this manuscript is highly problematic, as the methods are insufficiently detailed. For instance, while the text mentions that genome sequences of different tick species were discarded through reference mapping using Bowtie2 v.2.5.0, critical details remain unclear: which specific reference genome was used for subtracting tick reads, and what parameters guided the assembly and alignment steps. Furthermore, the manuscript employs multiple annotation methods (DIAMOND-MEGAN6, BLASTx, nBLASTp) for contig analysis without clarifying the methodological differences between these approaches or justifying this pipeline design. The authors must provide explicit parameters and rationales for each analytical step. 3. Comparative Genomic Analyses: The manuscript reports the identification of multiple LITV strains from different tick groups. Although the authors have conducted comparisons between the newly identified LITV strains and known variants, the genetic relationships among these novel strains remain uncharacterized. To strengthen the study, identification of potential genetic variations among these newly detected strains should be included. 4. Discussion Enhancements: The consistent absence of the M segment in all detected LITV strains warrants further discussion regarding its biological implications. Consider whether this reflects a conserved genomic feature of LITV or the presence of defective viral particles, and how this might influence the virus's biology and host interactions. Other comment 1. Line 43: "confirma" should be "confirm" 2. Line 104-115: Version numbers must be provided for all software tools to ensure methodological reproducibility. 3. Line 155-157: The statement that "It is known that the difference between Bandavirus and Uukuvirus is based on the fact that the M segment is absent in the Uukuvirus genus" is factually incorrect. The prototype Uukuvirus species (Unkuniemi virus) possesses all three genomic segments. 4. Table 1: Consider adding a column for viral load estimates (reads per million) to enable cross-sample comparisons
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
General: Overall, I liked this paper, it was short but to the point, I only have some small corrections, it would have been nice if there was a section in the intro that explained how this paper was a spin-off of another, using a cohort of ticks to look for the virus. I didn't realise this was the case until I got to the results section so it would have been nice to have some context! There are also a lot of similarities writing wise, so be careful not to plagiarise yourself! Also please add supplementary with the details of pools, it was quite difficult to guess what each tick pool consisted of. Line 30: typo: 'The' instead of 'the' Line 37: Missing full stop after concern Line 43: typo: 'confirma' Line 59: a hyphen might be better than a full stop here Line 85: Don't use chemical formula Line 86: …
Comments to Author
General: Overall, I liked this paper, it was short but to the point, I only have some small corrections, it would have been nice if there was a section in the intro that explained how this paper was a spin-off of another, using a cohort of ticks to look for the virus. I didn't realise this was the case until I got to the results section so it would have been nice to have some context! There are also a lot of similarities writing wise, so be careful not to plagiarise yourself! Also please add supplementary with the details of pools, it was quite difficult to guess what each tick pool consisted of. Line 30: typo: 'The' instead of 'the' Line 37: Missing full stop after concern Line 43: typo: 'confirma' Line 59: a hyphen might be better than a full stop here Line 85: Don't use chemical formula Line 86: how were the ticks taxonomically identified Line 86: no need to have gender in the sentence when you have already said sex Line 86-90: could be clearer, I think it needs to be reworded so because you pooled ticks pre extraction and then again post extraction? If so, after extraction how many ticks per pool, how many total pools etc. Line 87: uses 12 as a number, line 95 uses thirteen as a word, stick to one way Line 90: how many pools? This would be useful as supplementary data Legends on figures and tables should be at the bottom. Figure 1. Include what you used to make the map in the legend and the lettering is unclear on the figure, might be too small Line 95: What qubit kit did you use? And you should put manufacturers details after kits and reagents Line 96: was there only 13 pools? If you didn't test all the pools how did you choose which ones and why did you not test them all? Line 98: Sentence beginning doesn't really make sense Line 102: how long was the sequencing process, any parameters used? Line 118: I don't think its necessary to put the reference to the other paper in the results, I would just stick to introducing this earlier in the paper and keeping the results for this paper in this section. Line 125: typo (missing words or brackets between 53aa and Table 1) Line 126: Typo- LIVT in title Table 1: Don't let this table be split up over two pages. The legend for this needs to be more detailed, and **aa Aminoacid should be in the legend (all at the bottom of the table). Its not clear how many ticks are in each of the pools, please provide supplementary material with the details on this. Mix of languages in the host column Line 127: just aa Aminoacid supposed to be a table annotation? Line 128- 138: this doesn't read very easily 133. Put 'Fig 2' in brackets Legend for Fig 2: The lettering (A, B) should be in brackets: [A] [B], and as said before the legend should be underneath the figure Figure 2: also quite small, could do as its own page, failed to omit low bootstrap values, as is convention Line 157: grammar/translation issue, sentence needs rephrasing Line 159: this feels like an incomplete sentence Discussion: some repetitions, try to combine these to make it more snappy Line 186: "Within this family" sentence could maybe do with some examples. Line 196- typo- "design" should be "designed". Line 198- análisis. Conclusion: virus only found in ticks, first report in Ambylomma dissimile, although authors aren't sure if its pathogenic, suggest follow up study in cell culture and animal models, which is fair.
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
Yes: Its very similar to the paper published last year (same authors) but in parasites and vectors https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-024-06362-x
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: I put no, because this was not outlined in the manuscript
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