While there are a lot of Avian Leukosis Virus (ALV) sequences in databases, there are fewer from Rous Sarcoma viruses (RSV). ALV is grouped within subgroups A to K except F, G, H and I.
RSV is a similar virus whose biggest difference when compared with ALV is the addition of the oncogenic src gene.
I could only find sequences for ALV-A, B, E, J and K in databases while the only sequences noted as C or D apperently correspond to RSV. My confusion increases when I find a sequence mentioned as ALV-B in a paper but that is instead RSV because it has a src gene.
The only way I can make sense of this is that because subgroup is assigned by similarity of env gene gp85 and both viruses are really similar (prone to recombination even), they have been confused in literature. And while some authors distinguish between ALV and RSV, others might use ALV as a term to encapsulate both.
Could anyone clarify this for me?
Because I couldnt answer this question on my own.
I am not an expert in viruses but brief search in Wikipedia indicated towards the answer. Please refer to the wiki of both and cited references.
* Both are members of same genus, so this is relationship.
* Databases are not always correct and often have errors. The information submitted to database are generally derived from the research articles. Research articles can also have incorrect information (at the time of publication), and newer articles/research might have proven it wrong. Thus is the probable reason for the wrong data/annotations in databases/articles.
Abhijeet Singh
I mean, Im asking this because all the sequences I have seen referred as ALV-C and ALV-D in papers are instead RSV sequences, in all papers, be it recent or old.
For example, in Liang, X., Gu, Y., Chen, X., Li, T., Gao, Y., Wang, X., Fang, C., Fang, S., & Yang, Y. (2019). Identification and characterization of a novel natural recombinant avian leucosis virus from Chinese indigenous chicken flock. Virus Genes, 55(5), 726–733. https://doi.org/10.1007/s11262-019-01695-7
The strain table is titled ALV strains while it contains C subgroup representants that are RSV.
Same here Meng, F., Li, Q., Zhang, Y., Zhang, Z., Tian, S., Cui, Z., Chang, S., & Zhao, P. (2018). Characterization of subgroup J avian Leukosis virus isolated from Chinese indigenous chickens. Virology Journal, 15(1), 1–7. https://doi.org/10.1186/s12985-018-0947-1
And similar occurrences happen in any paper that I found that mentions a reference number for ALV C or D subgroups. Also notable that there isnt any reference sequence for ALV-C or D that doesnt have src (thus becoming RSV instead).
There is a taxa however that ought to contain both, ALV and RSV, which is ASLV (Avian Sancoma and Leukosis Virus) and I think both terms are being used indistinctively.
I presume there is confusion in this virus classification or I was unable to understand it. As I previously said, I am not in virology, still I tried to read few articles, the ones you suggested and other related to alphavirus classification. Unfortunately, I could not find any article (in my brief search) which clearly give summarized information of something which is easily understandable. In addition to your confusion, I was even more confused when I saw Avian leukosis virus (ALV-A) was names as RSA. I think I need to invest significant time in understanding this classification. So, I feel not able to help in solving your problem.
Sergio Fandiño González
It is part of confusing nomenclature in retrovirus field especially to people new to the field. Essentially RSV is same virus as ALV. When Avian Leukosis Virus infects a cell and by chance integrates close to src gene, the resulting virus contain part of src gene and hence called Rous sarcoma virus. Similarly when ALV integrates near other protooncogenes and resulting virus contain part of these genes, they might be referred as AMV (mob gene- avian myeloblastosis virus), mic gene- Avian myelocytoma virus etc. All these virus have same gag, pol and env sequence. Please search for some old reviews to get more information or checkout the Retrovirus Textbooks.
I believe it is easier (and correct) to refer to them collectively as ASLVs.
RSV is the least helpful term, because vast majority of people would immediately confuse it with Respiratory Syncytial Virus. AMV is not even replication-competent. Both are not the original viral species, as they both contain host cell genomic material. The terms persist for historical reasons, and arose before modern phylogeny.
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