Novel coronavirus complete genome from the Wuhan outbreak available in GenBank

Human cell nuclei produce mRNA from DNA, which then makes it's way to the ribosome to be expressed as a chain of amino acids, or a protien. On it's way to the ribosome, it needs protection from the cell's RNA cleanup enzymes, so it leaves the nucleus with a 5' cap and a poly-A tail.

Therefore, it makes sense that a virus that wishes to hijack human ribosomes would end in a poly-A tail (a bunch of As) in order to not get destroyed by human cells.

Is a good start.

    from Bio import Entrez
    import time
    from urllib.error import HTTPError
    
    DB = 'nucleotide'
    QUERY = '("pneumoviridae"[Organism] OR "Coronaviridae"[Organism])'
    
    Entrez.email = 'your.email@provider.com'
    handle = Entrez.esearch(db=DB, term=QUERY, rettype='fasta')
    record = Entrez.read(handle)
    
    handle = Entrez.esearch(db=DB, term=QUERY, retmax=count, rettype='fasta')
    record = Entrez.read(handle)

    id_list = record['IdList']
    count = len(id_list)
    post_xml = Entrez.epost(DB, id=",".join(id_list))
    search_results = Entrez.read(post_xml)
    
    webenv = search_results['WebEnv']
    query_key = search_results['QueryKey']

    batch_size = 200
    with open('viruses.fasta', 'w') as out_handle:
        for start in range(0, count, batch_size):
            end = min(count, start+batch_size)
            print(f"Going to download record {start+1} to {end}")
            attempt = 0
            success = False
            while attempt < 3 and not success:
                attempt += 1
                try:
                    fetch_handle = Entrez.efetch(db=DB, rettype='fasta',
                                                 retstart=start, retmax=batch_size,
                                                 webenv=webenv, query_key=query_key)
                    success = True
                except HTTPError as err:
                    if 500 <= err.code <= 599:
                        print(f"Received error from server {err}")
                        print("Attempt {attempt} of 3")
                        time.sleep(15)
                    else:
                        raise
            data = fetch_handle.read()
            fetch_handle.close()
            out_handle.write(data)

https://www.biorxiv.org/content/10.1101/2020.01.22.914952v1....

So even if China did ban it, would other countries have to as well for it to be effective?

https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequen...

The human genome is 3 Gbp, which is 100,000 times the size of the coronavirus at 30 kbp.

It's quite compact. What would be interesting to know, is the percentage of programs still running when a few bits are modified, to know how sharp is the search space.

Exploring living programs space, you probably can use some advance neural network techniques, like GPT-2 to explore it more efficiently, directly in its compressed representation to provide an high level interface with slider controlling the high-level properties.

Hepatitis B is 800 bytes for comparison.

Side not: I'm always concerned when we're put in a situation like this where we're pressured to put out a vaccine quickly because it opens the door for a less than optimal solution to become a mainstay. For example since it's an emergency you may put forward a solution, have it go through human trials, find some side effect, but given the current circumstance say that it's "good enough" and give it the green light of approval. Now I understand that in such an urgent circumstance that this may be justified, but after the urgency is over it's my understanding that this solution that may or may not be approved under regular circumstances will remain approved.

https://blogs.sciencemag.org/pipeline/archives/2020/01/27/co...

https://news.ycombinator.com/item?id=22169593

They launch with near absolute MVP. Design is not the priority here; the information is. When it comes to dealing with a pandemic, every minute counts.

The default theme is a sign that someone who knows software and project management is working on it.

https://www.who.int/emergencies/diseases/novel-coronavirus-2...

https://www.nature.com/articles/d41586-020-00180-8

When you cook something, it tends to kill the virus and germs. Or at least makes it safer to consume. But, you can still get sick from the fluidic contact, like getting salmonella from handling raw chicken.

Let’s take a look at some scientific evidence.

Ebola was theorized to come from bat feces, that might have fallen on a toy, and a girl put it into her mouth. She didn’t eat the bat. (This is only a theory, as they don’t know the true origin.)

The MERS virus from the Middle East, was thought to come from sick camel. I haven’t heard of the locals there eating camel, so it must have transmitted via fluidic contact. (Again, this is only a theory, as they don’t know the true origin.)

SARS was theorized to come from bats as the carrier, but the vector was a civet. Maybe the infected fluids of the civet jumped to humans. (And again, this is only a theory, as they really don’t know the true origin.)

This 2019-nCoV is again thought to come from bats, but the vector is currently unknown.

So with all that, I think perhaps, a bat was a carrier, and got some other animal sick, which became the vector. And when they slaughtered the sick animal, the infected fluid must’ve infected a worker, who got sick. And this worker might’ve infected an old person, who has a weaker immune system, and got sick, who then transmitted it to others, and got them sick, and now we have a full-blown pandemic.

So, the true cause here, might not be that people ate the wild animal, but that the humans came into contact with infected fluids from wild animals. And the presence of bats and wild animals, at this Wuhan market, just increased the probability that an outbreak like this could happen.

As a thought experiment, in Texas, there are a bunch of bats in Austin. What if one of these bats are also a carrier of some disease, and they fly over a nearby chicken farm, and poops on the chicken, which gets the chickens sick. The chickens are now the vector. And now, these sick chickens are handled by humans, and the above scenario plays out in Texas. And then, a pandemic spreads out from Texas. Would you think that Americans are disgusting for consuming chickens here, if this theoretical scenario were to happen?

Is that not also a possible source of infection?

//edit// A slightly similar case from the UK: https://www.theguardian.com/uk/2008/oct/17/footandmouth-rura...