RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.

Question

[jimmysibandah]

Hi everyone,

Does anyone know where I can find RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values?

Regarding to fitness it can be either of the following ( Epidemiological fitness, Adaptation Fitness, Immune Evasion Fitness, Transmission Fitness, Replication Fitness.

Epidemiological Fitness: This refers to the ability of an RNA virus strain to spread within a population.

Adaptation Fitness: This relates to the ability of an RNA virus to adapt to changing environmental conditions, including host immune responses or changes in host populations.

Immune Evasion Fitness: This refers to how effectively an RNA virus can evade or suppress the host immune response.

Transmission Fitness: This measures how efficiently an RNA virus can be transmitted from one host to another.

Replication Fitness: This refers to the ability of an RNA virus to replicate within a host cell. It includes factors such as the efficiency of viral genome replication, the production of viral proteins, and the assembly of new virus particles.

Thanks in advance!

[Ram]

This question was also asked on Bioinformatics SE: https://bioinformatics.stackexchange.com/questions/22656/rna-virus-hiv-hcv-influenza-or-sars-cov-2-datasets-with-corresponding-fitne

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[jimmysibandah]

Thanks for flagging this , I am still new on these platforms so I might violate some rules unintentionally .

Answer 1

[ehaag]

Check out the NIAID Data Ecosystem, which aggregates datasets related to RNA viruses including HIV, Influenza, and SARS-CoV-2: https://data.niaid.nih.gov/

You can explore datasets that include virological and host response data, often with variables tied to immune evasion, viral replication, and transmission. Just to see, I tried searching for "SARS-CoV-2 immune evasion" and found lots of relevant datasets. You can then filter it down by "Variable Measured," "Host Species,"" or something else. I also tried "HIV replication" and got thousands, but again you can then narrow it down using filters (e.g. it reduces the results to only a few by selecting "Longitudinal study" under "Measurement Technique"). Hope it helps!