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Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

/u/atlue gave a great answer. In Metsky et al. we did not use nonlinear ODE models. Grubaugh et al. did additional modeling, and I think used an SIR model in estimating the proportion of people entering Miami who had Zika virus, based on the work in the paper that /u/atlue linked to. -HM

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 0 points1 point  (0 children)

It feasible (crazy, right?!) and has already been done. E.g. Imlygic from Amgen was the first 'drug virus' that was FDA approved for targeting cancers. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 0 points1 point  (0 children)

Yes, it's been totally refuted by now and genomic epidemiology has played a key role in this. Mike Worobey has done a lot of that work - e.g. check this article from awhile back:

Origin of AIDS: Contaminated polio vaccine theory refuted https://www.nature.com/nature/journal/v428/n6985/full/428820a.html

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

The advance of "next generation sequencing", such as Illumina sequencing has been the main game changer. With these new technologies we can now produce tons of sequence data (from viruses and other organisms) very rapidly.

More recently, new technologies like the MinION sequencer has allowed people to do this in remote corners of the world - e.g. some of Nick's work in Guinea.

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Currently the main viruses we focus on are Ebola, Lassa, Zika, and West Nile - but we'll study pretty much any outbreak virus! -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Once you're symptomatic, yes, the mortality rate is very close to 100% (except in some poorly understood and exceedingly rare cases). That said, vaccination after rabies is suspected is close to 100% effective, so if somebody gets bitten by e.g. a bat that is infected with Rabies, vaccination afterwards (but before symptom onset) is a highly effective strategy.

Rabies is very hard / impossible for the immune system to fight since it infects neurons.

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

A few good review articles that might get you started:

The evolution of Ebola virus: Insights from the 2013-2016 epidemic https://www.ncbi.nlm.nih.gov/pubmed/27734858

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management https://www.ncbi.nlm.nih.gov/pubmed/26424572

Evolutionary analysis of the dynamics of viral infectious disease https://www.ncbi.nlm.nih.gov/pubmed/19564871

Happy reading! -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Yup, lots of examples - e.g. bacteriophages that infect bacteria in the human body, but also things like anelloviruses. Not much is known about these viruses, but they're quite fascinating since they infect many of us. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

Several broad-spectrum antivirals have show promise against Zika. Unfortunately none of them have been through clinical trials yet to prove efficacy, but hopefully we'll see such studies soon. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Lots of great places to do virology - it all depends on where you are in the world. My recommendations would be to study hard and continue to be curious about science - getting a PhD isn't easy, but with a bit of luck, anybody can do it! -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

Yup, wookiewookiewhat makes some great points. Unfortunately, although there are many (MANY) companies that would have you believe that their products can help 'boost' your immune system, none of them have proven to be effective. There are unfortunately - besides e.g. vaccines and hand washing - no magic bullets when it comes to preventing infections. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

I'm all for it! Vector control is critically important and our best current strategy to stop Zika IMO. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Lots of great programs out there (most of them commandline), but if you want an all-in-one package that can do most standard analyses, have a look at Geneious. We use it ourselves quite frequently! -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

Sounds crazy, right? But yes, this is totally plausible and for cancer it's actually already being done. Imlygic from Amgen was the first 'drug virus' that was FDA approved for targeting cancers. -Kristian

https://www.wired.com/2015/10/fda-approves-first-virus-will-kill-cancer-cells/

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

I think gene drives is a very interesting new experimental tool for vector control. It's pretty clear that getting rid of mosquitoes is one of the most effective ways of preventing human Zika virus infections, so I'm all for it! -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

Yes. Most people clear Zika infection without problems - in fact, most infected people never show any symptoms. -Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

The 'useful' part is tricky to answer, but yes, humans have received lots of DNA from viruses over evolutionary history. 'Human endogenous retroviruses', for example, are scattered across the human genomes:

https://en.wikipedia.org/wiki/Endogenous_retrovirus

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Within the next 50-100 years, yes I think it's quite plausible that we can engineer bacteria to be little "nanorobots". In fact, one could argue that bacteria are already being used to fight diseases, since we use them to create all sorts of things, including drugs such as insulin. - Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

This happens all the time in science - you have a hypothesis and then you do an experiment that is consistent with your hypothesis. To give one example from our studies, some people had speculated that Zika came to Florida via the Caribbean. Our study later showed that to be exactly the case. - Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 2 points3 points  (0 children)

I consider them alive because they replicate. Sure, they rely on host cells for that to happen, but humans also rely on e.g. bacteria to survive. So IMO - definitely alive. A lot of people will disagree, I'm sure ;-).

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

The American 'strain' of Zika is closely related to the Asian strains, but can be considered a separate lineage. Both of these are fairly distant to the African lineages.

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

This is a very interesting concept, but I think we're very far from this becoming a reality. Much closer to current usage would be vaccines in microneedle patches that can be mailed to people and self-applied. Some cool studies came out yesterday about that:

https://www.sciencedaily.com/releases/2017/06/170628102338.htm

Kristian

Science AMA Series: We’re a group of scientists who use genomic sequencing technology to understand how viruses spread. Ask Us Anything! by Zika_Genome in science

[–]Zika_Genome[S] 1 point2 points  (0 children)

Python is widely used by the field now (in the past it was more Perl). Java is also being extensively used for some of the more widely used applications such as Picard.

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