I'm a virologist and Chief of Science at the California Academy of Sciences, where I spend a lot of time looking into where viruses that infect humans come from (we call these zoonotics). I use clues in the genomes of viruses about how they mutate and evolve to read their origin stories as well as find their fitness "pressure points," which for humans translates into how they spread and how virulent they are. I've been tracking the emergence and spread of the virus SARS-CoV-2, agent of the disease COVID-19, based on its unique biological features. I really became fascinated with pathogens when I was a college student volunteering in west Africa—in the span of a few weeks I contracted malaria, amoebic dysentery, a staph infection, and was hospitalized in a leper colony. It taught me a new level of respect for my parasite foes, all of whom evolve rapidly, have natural reservoirs, and can cause significant disease. Sound familiar? Here's more about me on this website, and my twitter handle is @MicrobeExplorer.

Proof: https://i.redd.it/378x45vsghn41.jpg

UPDATE: I have to head out now, but will try to come back later and address some more. Thanks for all the great exchange! Meanwhile, stay healthy and help flatten the curve!

Comments: 541 • Responses: 27  • Date: 

1000thusername151 karma

I know a LOT of people who around mid Jan to mid Feb had “flu” but with exceptional levels of pneumonia way beyond what flu is “supposed to” bring.

How likely is it that many people have already had this and don’t know it and that there is likely a portion of the population walking around who can’t be reinfected? I feel like if this possibility exists, it needs to be looked at.

Thank you.

MicrobeExplorer101 karma

There are lots of causative agents of viral pneumonia and the disease syndrome can also vary, especially with co-infections that could occur.

Here's one source of evidence, and that is that the genetic information from all the COVID-19 viruses sequenced so far (713 worldwide https://nextstrain.org/ncov?p=grid) point to a single origin in late November or early December 2019 (https://nextstrain.org/narratives/ncov/sit-rep/2020-03-13).

-13-88 karma

Like most people, my anxiety surrounding this virus has been steadily ramping up over the last few months.

  • I read that it is airborne but I don't quite understand what that means. Does that mean "Don't leave the house because it's in the air" or does that mean "if someone breathes/sneezes/coughs near you, you'll be infected"

  • Is infection guaranteed? Is it like a game of tag...basically if you're in contact with it, you're 100% going to get it or is it possible that it will not be transmitted to you?

MicrobeExplorer163 karma

Sorry! I'm reposting this at the beginning of the conversation!

It is not airborne, like measles, which can float in the air up to 100 feet. This coronavirus is transmitted by airborne droplets, so it doesn't float, and drops off as the droplets fall, in about 6 feet. It can also be transmitted on surfaces, which are called fomites. Wipe of your cell phone, or "phonite!"

Infection rate is a really good question but hard to answer, because all the data confounds both exposure rate and susceptibility. It would probably depend on dose and a person's innate immunity - we would probably need to do an experiment in a controlled environment to know for sure.

the_goose_says14 karma

Not OP but my understanding is it’s Airborne as in if someone coughs it will slowly fall to the ground over several minutes. It’s not blowing in the wind all around us like in The Happening.

MicrobeExplorer39 karma

It is not airborne, like measles, which can float in the air up to 100 feet. This coronavirus is transmitted by airborne droplets, so it doesn't float, and drops off as the droplets fall, in about 6 feet. It can also be transmitted on surfaces, which are called fomites. Wipe of your cell phone, or "phonite!"

Infection rate is a really good question but hard to answer, because all the data confounds both exposure rate and susceptibility. It would probably depend on dose and a person's innate immunity - we would probably need to do an experiment in a controled enivronment to know for sure.

ChowRunn3G081 karma

Do you think that we will eventually develop an immunity to the virus or is this going to continue to spread until we create a vaccine?

MicrobeExplorer120 karma

No one really knows, but a vaccine program is most successful if it leverages some natural immunity we develop. With viruses, in some cases we develop strong immunity that is long lasting (like with measles) but with other viruses immunity wanes (like influenza). Here's hoping!

Finalrose2night81 karma

Is it possible that the virus is suffering mutation as it “passes through” the population?

MicrobeExplorer140 karma

The virus is definitely mutating, at a rate of about 1-3 mutations in the genome per month, which is its normal rate in any population (human or otherwise). If it was adapting to humans we would see an accelerated rate of evolution, and would have to follow up any of those mutations with lab work to see if it really has an effect. Check out this site for a summary: https://nextstrain.org/narratives/ncov/sit-rep/2020-03-13

the_goose_says68 karma

What metrics should we look at to know when to relax isolation measures. Should we relax these measures as soon as we are far enough post peak for the healthcare system to not overload? Or is the goal to as fully as possible reduce infections before relaxing measures?

MicrobeExplorer154 karma

The key metric is the number of new cases each day. When that number starts to grow MORE SLOWLY then we know we are approaching the peak of the epidemic wave. From the peak, number of new cases per day will start to drop increasingly and isolation measures can be relaxed when we approach the end of the wave with very few new cases per day. This is where China is at now.

FullSpectrumSurvival39 karma

Why did the 1918 pandemic stop infecting the population? Did it lessen in severity or immunity and it didn't mutate?

MicrobeExplorer86 karma

The 1918 pandemic essentially ran out of susceptible people to infect. There is an epidemiological model called the SIR model (for Susceptible, Infected, Recovered) that models how viruses (or other pathogens) move through a population. Susceptibles are those exposed (in the line of fire, could depend a lot on behavior) in which the virus can get a foot hold (depends on biological properties including immune status), at which point the Susceptible becomes Infected, stays in this bucket for a while, then moves into Recovered (hopefully) and potentially immune (TBD with this virus). In the case of the 1918 Spanish flu, people that recovered did develop protective immunity.

However, genetic elements of the 1918 Spanish flu did assemble into new combinations with other flu strains (we call this reassortment) and showed up in the H1N1 swine flu virus and pandemic of 2009.

I-braveheart36 karma

What do you tell people that say this isn't any different than the flu?

MicrobeExplorer88 karma

Firstly, it is a completely different virus in terms of its genetic makeup, way it evolves, host distribution, etc. So, different biology.

Second, it is different epidemiologically and in terms of the disease progression, for example, it doesn't seem to cause as much disease in children (but it definitely infects them at the same rate). The R0 or reproductive rate of the virus (related to how fast it spreads) and case fatality rate have both had preliminary estimates that range higher than seasonal flu. In terms of disease, both flu and coronavirus cause immune disregulation (and ultimately possible death by cytokine storm), but the pathways in our cells seem to be different ... all of this is still emerging knowledge - we don't know enough!

Lastly, flu has become a regular infectious agent for humans, cycling in the temperate zone seasonally and at low levels year-round in the tropics. We have no idea if this coronavirus will follow the same route, and importantly, we don't know if vaccines will be able to control it, the way they can with flu.

irrelevant_ranting34 karma

At what temperature is this virus destroyed? If I bought a take n bake pizza, and coronavirus was on the pizza, would it survive in the oven at 400° for 10 minutes?

MicrobeExplorer91 karma

Most certainly pizza is a safe bet - those temperatures will kill any virus! Now I'm getting hungry...

Actually, fever is our own body's protective reaction to killing off pathogens with heat - many don't survive or get knocked back when our body temperatures go above 100 F. Viruses that live outside the host cell, say on surfaces, are even more susceptible to extreme temperatures, and enveloped viruses like the coronavirus are among the most delicate. I "heard" that outside on surfaces, 26-27 Celsius might be an upward bound, but this is unverified and needs to be validated in a lab setting.

zach_link51231 karma

How worried should we actually be and if we do become infected, what are our best options?

MicrobeExplorer39 karma

"Worried" about your own risk of infection will depend on how much you think you can control your exposure (wash hands, social distance, etc), and your underlying factors such as whether you have certain co-morbidities. If you become infected, check with your health care professional, but at this time there are no confirmed antivirals so it would be supportive care, but this is developing/changing fast.

We can also "worry" about the community and our role in propagating this infection, even if we aren't too worried about ourselves. Older people as a population are experiencing high case fatality rates - this article tells you more: https://jamanetwork.com/journals/jama/fullarticle/2762130

Because the cases in the US are climbing exponentially, the risk of spreading is substantial, but social distancing will help! Check out this report modeling the dynamics of the outbreak: https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf?fbclid=IwAR14FfG8zV17eoJ3aFl8JNe-IvjZEcmP3g_iMYgrAs2xb3TV-SOs7CEvLOs

ComandanteDiego30 karma

A fair amount of the population of my country (Chile) is under voluntary isolation, under recommendation of the government and the media. With that voluntary isolation we were told that it's the way of flattening the spread curve (or something like that).

My question is: if we have about 14 days of isolation, washing hands and following all the health instructions, do we have less risk of being infected at the end of these 14 days of voluntary quarantine, when we go out again?

MicrobeExplorer52 karma

Yes, if you voluntarily isolate as a community, there will be a lower risk of infection in general over time (fewer other people sick, fewer viruses on surfaces or being distributed in droplets, by coughs/sneezes). 14 days might not be enough if everyone doesn't do it though.

Flattening the curve means essentially this, that the number of new infections grows more slowly, and that the peak of new infections per day will be lower.

MicrobeExplorer25 karma

Hi folks, thanks for all your great questions! I have to go, now, but I will try to tackle some more later - be safe and healthy and help flatten the curve!

Toru_Stones21 karma

Maybe a dumb question. But why can't we swab our own mouths and test ourselves? What's in the test kits? Can we not look at our own culture samples through a microscope at home to see if we have the virus?

MicrobeExplorer72 karma

No dumb questions!

Yes, in theory you could collect your own mouth swabs but you would need to send them in, because the current test is based on detecting the genetics of the virus by a polymerase chain reaction that uses coronavirus-matching molecules and other reagents to amplify fragments of the virus genome (accelerate its replication) for detection through a series of cycles (e.g. 30) that typically alternate between 95 celsius to 55-65 celsius to 75 celsius. In summary, this is a real-time reverse-transcriptase polymerase chain reaction [aka real-time RT-PCR] that includes short sequences of DNA (primers and probes) that bind exclusively to SARS-CoV-2 matching sequence and give off, once bound, a detectable fluorescent signal whose brightness matches the number of binding events aka virus fragments. Although the test parameters are now open access you would need this fancy real-time PCR machine plus a centrifuge plus a biosafety cabinet...

The good news is that many folks are working on different kinds of tests, maybe even a protein-based test that could be bundled into a system like a pregnancy test kit, and you could use this RAPID test kit at home...

Normal microscopes won't help because viruses are too small to reflect light (this coronavirus, if it is like others in the family Coronaviridae, is probably on the order of 120 nanometers [a nanometer is a billionth of a meter in diameter) - you need to use an electron microscope that fires electrons at the virus and reads their reflections.

Retireegeorge18 karma

It was fascinating to read about your student experiences in Africa. What is it like to be in a hospital in a leper colony? What virus fascinates you the most?

MicrobeExplorer38 karma

Actually the leper colony wasn't a real hospital, just a low compound with some nursing staff. But it was wonderful to see how self-contained and reliant the colony was, with very efficient mixed farming methods and a self-contained economy.

My favorite viruses are in the genus Flavivirus, which includes dengue, Zika, and West Nile. All mosquito-borne viruses are particularly fascinating to me!

matthewspillstea14 karma

Does the virus attach itself to healthier people and infect others before they show symptoms? Also, does the virus reinfect with stronger symptoms than the previous infection?

MicrobeExplorer35 karma

I think your question is, can asymptomatic people transmit the virus? The answer is yes, both in the case of asymptomatic people that never develop symptoms, as well as people that are incubating the virus and are asymptomatic because they have YET to develop symptoms - this incubation period can be from 2 to 14 days with an average of 5-7 days.

We actually don't know if the virus can reinfect people.

laadedaaaaa12 karma

What is your opinion on gain of function research?

MicrobeExplorer17 karma

One of the hypotheses for why this virus emerged into the human population is that it "gained" the function, or ability, to more efficiently infect human cells. This post discusses that further: http://www.virology.ws/2020/02/13/furin-cleavage-site-in-the-sars-cov-2-coronavirus-glycoprotein/

This would absolutely need to be studied and verified in a laboratory setting. This research could be important in identifying a mechanism for virus infection that could be interrupted with antivirals, for example.

AeliaTKC12 karma

When do you think we'll know if the Bay Area's shelter in place orders have been effective or not, based on what we know about COVID-19 right now?

Edit: I personally feel like this is the right response so far, and I'm interested to see if/when we see this roll out in other metropolitan areas soon. But I'm also curious if you feel like this is the right response, if you feel like addressing that, too.

MicrobeExplorer17 karma

We will know if it was effective when the number of new cases per day stops growing exponentially. In a plot of cumulative cases, that would look like the inflection point in the S, after which the cumulative curve should level off. The leveling off reflects ever-shrinking numbers of new cases per day. I like to tract this site, but it only reports data at the state level: https://www.worldometers.info/coronavirus/country/us/

Yes, I strongly believe shelter in place was the right thing to do. Any means of social distancing helps, and has had a huge positive impact in China and South Korea.

Right now, different urban areas in the US are at different points on the epidemic wave, and virus activity seems to be staggered in seeding outbreaks in other cities - its almost as though we are a metapopulation.

MicrobeExplorer8 karma

See my first post but also here is an article about tracking coronavirus in California: https://www.latimes.com/projects/california-coronavirus-cases-tracking-outbreak/

TheBumblez11 karma

In more mild cases, can it cause upper respiratory infection symptoms?

MicrobeExplorer41 karma

A study reports that "Symptoms of COVID-19 are non-specific and the disease presentation can range from no symptoms (asymptomatic) to severe pneumonia and death. As of 20 February 2020 and 12 based on 55924 laboratory confirmed cases, typical signs and symptoms include: fever (87.9%), dry cough (67.7%), fatigue (38.1%), sputum production (33.4%), shortness of breath (18.6%), sore throat (13.9%), headache (13.6%), myalgia or arthralgia (14.8%), chills (11.4%), nausea or vomiting (5.0%), nasal congestion (4.8%), diarrhea (3.7%), and hemoptysis (0.9%), and conjunctival congestion (0.8%)." This is the report: https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf

Durian88110 karma

Would weather conditions have any effect on mutation of coronavirus?

MicrobeExplorer24 karma

Not directly. Mutations are actually occurring all the time to DNA and RNA, no matter what the organism, based on error rates at the chemical level when the genetic strand is being copied for replication, or due to a mutagen, like UV radiation or a carcinogenic chemical. Most mutations are lethal and kill the cell or virus (viruses aren't cellular). When a mutation persists in the progeny, we call that evolution. Sometimes these evolutionary changes are neutral and don't confer any particular fitness benefit, sometimes they can be even bad for the organism under certain conditions, and sometime they can confer a fitness benefit. The larger the population size, the more variants.

So, with many viruses that are seasonal in the temperate zone, they are seasonal because humans cluster together in warm dry rooms with recirculated air, increasing their own susceptible population size artificially, as well as by extension the virus population size. Larger population size of the viruses, larger amount of standing genetic variation, more opportunity for a potential beneficial mutation to occur that could eventually become fixed in the virus population - more fit virus, usually not so good for us.

redbellpeppers187 karma

Are people with heart arrhythmias at a higher risk?

Do disinfectant sprays and wipes kill the virus on surfaces? If you’re being forced to work, could wearing a reusable mask protect you from the virus? I feel like if nothing else it keeps you from touching your face until you have a chance to wash your hands.

Is it a guarantee everyone who gets this virus will get pneumonia?

Can you catch the virus through food if you order takeout? Does microwaving kill the virus?

MicrobeExplorer18 karma

If you have any health problems, you should definitely check with your doctor. People that are particularly vulnerable to developing sever disease are listed here, and this list does include heart disease: https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/high-risk-complications.html

Wipes with 60-90% alcohol are believed to kill this virus on surfaces - here are cleaning tips based on your specific situation: https://www.cdc.gov/coronavirus/2019-ncov/community/organizations/cleaning-disinfection.html

Masks are actually not that helpful unless you are working with/around people that are spraying droplets (coughing, sneezing) as in a healthcare setting. See here:https://www.cdc.gov/coronavirus/2019-ncov/hcp/respirator-use-faq.html. In terms of transmission of virus particles on surfaces, that is, through fomites, it is definitely important not to touch your face, but one could also argue that wearing a mask might cause you to adjust it more often, depositing fomites on the mask itself or your face...

It is definitely not guaranteed that every infection will lead to pneumonia. In a study from the China situation, 27% developed severe pneumonia aka Acute Respiratory Distress Syndrome - see this paper: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext30183-5/fulltext)

kyledukes7 karma

How worried are you about this virus mutating so quick the vaccines are nearly impossible?

MicrobeExplorer20 karma

The virus doesn't seem to be mutating extra fast, see here: https://nextstrain.org/ncov?p=grid, but that doesn't mean that if we add a vaccine into the mix as a selection pressure, it might not evolve in response, basically immune escape. This is one feature of influenza A and one of the reasons we have to be re-immunized with a different vaccine each year.

AdmiralAkbar16 karma

What is the possibility of a second wave that is just as (if not more) virulent or deadly, like what happened with the Spanish Flu in 1918?

MicrobeExplorer9 karma

This will depend on the impact of the current wave on the population: will it run out of susceptibles (like Spanish flu did), how quickly will susceptibles re-enter the population (depends on what is driving susceptibility) and do we develop protective immunity (as we did with Spanish flu). See my other post on track susceptibles with an SIR model.

Ottomatik806 karma

Do you know if COVID-19 reacts to Ozone similarly to the way SARS did?

Can we utilize ozone generators to disinfect areas, and kill COVID-19?

HappyNachoLibre4 karma

What is the actual process for testing? Like what are they actually physically doing? And what do they need to do to mass produce those tests?

MicrobeExplorer10 karma

Here is some information on testing: The test kit is intended to amplify only SARS-CoV-2 viruses in the sample and produce a positive signal when present (the test is a real-time reverse-transcriptase polymerase chain reaction [aka real-time RT-PCR] that includes short sequences of DNA (primers and probes) that bind exclusively to SARS-CoV-2 matching sequence and give off, once bound, a detectable fluorescent signal whose brightness matches the number of binding events). Although typically only certain CLIA certified labs can run these, the good news is that all the test parameters are now open access and the FDA is allowing labs emergency authorization to develop their own tests based on these parameters: see https://www.sciencemag.org/news/2020/02/bid-rapidly-expand-coronavirus-testing-us-agency-abruptly-changes-rules.

Homeskillets11 karma

Are the mutations severe or just average? Is there any way that we haven't heard on the news to prevent the spread? Have we had any step backs with the vaccine?

MicrobeExplorer2 karma

Mutations are so far accruing with time at a standard rate, and any tests of the impacts of any particular mutations would have to be studied in the lab. See this website to examine those mutations: https://nextstrain.org/ncov?p=grid

I don't know of any other ways to prevent spread than what is currently talked about: protect yourself from being a host by washing your hands, not touching your face, and maintaining a social distance of at least 6 feet except from people you live with; protect people from you as a transmitter by self-isolating (and calling your doctor) if you're experiencing flu-like symptoms plus all of the above.

Happily, because the data on this virus, especially the genetics, has been open-source, many labs are using the information to explore vaccine candidates. The barrier is actually in terms of regulation and completing the necessary steps of human testing to make sure that the vaccine is safe and effective in humans. This will take time (12-18 months?).