<p>You should sit down with a viral epidemiologist, immunologist, or virologist to identify the phenotypes and viruses you are targeting.</p>
<p>I personally would approach the question from phylogenetic &quot;positive selection&quot; analysis and then look at correlating phenotypes involving epidemiology, immunology and virology (<em>in vitro</em> replication). Again you need cross-functional support for this approach to be effective.</p>
<p>For SARS-CoV-2 the NCBI database contains all the relevant epidemiologic and virulence data in a singular (presumably SQL) database with a nice GUI frontend. It is really cool and thats the way to solve that virus. Check my post history for the exact location of the database on NCBI. With expert help with the interpretation of the vast outputs of NCBI's SARS-CoV-2 metadata thats absolutely doable in generic fitness landscapes, epistasis and all that. I have used NCBI SARS-CoV-2 database, not specifically in fitness landscapes/phenomena, but related genetic behaviour and it is fabulous. The speed this was unfurled in response to the epidemic was a credit to the NCBI.</p>

CC BY-SA 4.0
2024-07-02T19:00:29.897Z
Thank you very much for this detailed response
user20708
CC BY-SA 4.0
2024-07-03T02:26:54.600Z
@user20708 thanks, however "accepts" and upvotes are much more appreciated than notes of thanks.
M__
CC BY-SA 4.0
2024-07-01T14:50:35.220Z
2024-07-01T15:07:27.320Z
2024-07-01T15:07:27.320Z
M__
<p><a href="https://www.biostars.org/p/9597885/" rel="nofollow noreferrer">Cross-posted on biostars</a></p>
<p>Does anyone know where I can find RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values?</p>
<p>The dataset must contain genotypes and annotated .</p>
<p>I am interested in RNA viruses that affects humans .</p>
<p>Regarding to fitness it can be either of the following ( Epidemiological fitness, Adaptation Fitness, Immune Evasion Fitness, Transmission Fitness, Replication Fitness.</p>
<p>I want to visualise the dataset(s) using fitness landscape(s).</p>
<p>Thanks in advance!</p>

CC BY-SA 4.0
2024-06-27T18:26:48.940Z
Please [edit] your question and give us more detail about what you need. What would the dataset include? Genomes? Virus species names? Genes? And what do you mean by fitness? Replicative fitness? In what host? Transmission fitness? Are you only thinking of viruses that affect humans? Any RNA virus?
terdon
CC BY-SA 4.0
2024-06-27T18:44:02.160Z
Thanks Terdon , for raising this , I have tried to give more info. I am still new to the field so my knowledge is limited.
user20708
CC BY-SA 4.0
2024-06-27T19:15:46.393Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2024-06-28T08:09:19.013Z
When you say "genotypes" what do you mean? And annotated how? With what information?
terdon
CC BY-SA 4.0
2024-06-28T10:08:52.687Z
Genotype in this context I am refereeing to data representing the genetic makeup of the RNA viruses.
Annotations for the genotype provide additional context and information about the genetic data. These annotations can include functional impacts of mutations, related phenotypic data, references to known databases, and more.
user20708
CC BY-SA 4.0
2024-07-01T15:03:36.570Z
I've worked on this stuff and a key part is identifying epistasis against selection pressure
M__
<rna-seq>
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values
# RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values

(Asked by: username_0 on 2024-06-27)

[Cross-posted on biostars](https://www.biostars.org/p/9597885/)

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

The dataset must contain genotypes and annotated .

I am interested in RNA viruses that affects humans .

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

I want to visualise the dataset(s) using fitness landscape(s).

Thanks in advance!

**Tags:** rna-seq
> **Comments:**
> **username_1**: Please [edit] your question and give us more detail about what you need. What would the dataset include? Genomes? Virus species names? Genes? And what do you mean by fitness? Replicative fitness? In what host? Transmission fitness? Are you only thinking of viruses that affect humans? Any RNA virus?  
> **username_0**: Thanks Terdon , for raising this , I have tried to give more info. I am still new to the field so my knowledge is limited.  
> **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_1**: When you say "genotypes" what do you mean? And annotated how? With what information?  
> **username_0**: Genotype in this context I am refereeing to data representing the genetic makeup of the RNA viruses. Annotations for the genotype provide additional context and information about the genetic data. These annotations can include functional impacts of mutations, related phenotypic data, references to known databases, and more.  
> **username_3**: I've worked on this stuff and a key part is identifying epistasis against selection pressure  

---

## 1 answers

### Answer by username_3 on 2024-07-01. Score: 0

You should sit down with a viral epidemiologist, immunologist, or virologist to identify the phenotypes and viruses you are targeting.

I personally would approach the question from phylogenetic "positive selection" analysis and then look at correlating phenotypes involving epidemiology, immunology and virology (*in vitro* replication). Again you need cross-functional support for this approach to be effective.

For SARS-CoV-2 the NCBI database contains all the relevant epidemiologic and virulence data in a singular (presumably SQL) database with a nice GUI frontend. It is really cool and thats the way to solve that virus. Check my post history for the exact location of the database on NCBI. With expert help with the interpretation of the vast outputs of NCBI's SARS-CoV-2 metadata thats absolutely doable in generic fitness landscapes, epistasis and all that. I have used NCBI SARS-CoV-2 database, not specifically in fitness landscapes/phenomena, but related genetic behaviour and it is fabulous. The speed this was unfurled in response to the epidemic was a credit to the NCBI.

> **Comments:**
> **username_0**: Thank you very much for this detailed response  
> **username_3**: @user20708 thanks, however "accepts" and upvotes are much more appreciated than notes of thanks.  

---

