Skip to content
Branch: master
Find file Copy path
Find file Copy path
4 contributors

Users who have contributed to this file

@marialma @reedtaylor @jwilk @duckysherwood
281 lines (159 sloc) 27.4 KB

Hi. I'm Maria Ma. I have an MPH in Infectious Diseases from UC Berkeley. My undergrad degree is in Microbiology, and I spent several years working as a biotech professional before transitioning to public health. I tell you my qualifications to let you decide whether or not you can trust the information I sifted through.

Some key points I want to emphasize:

  • Please, stay home for now. For the next two weeks if you can. Here's a good explainer for why!
  • Wash your hands!!!!!!! Also, moisturize them!
  • We are still learning about this. It's a brand new virus. We're learning about this faster than we ever have before. Truly bold new technologies are being applied by the scientists trying to figure this stuff out. You might feel like we don't have enough information, but actually having this much information at this stage of an outbreak of a new virus is completely unprecedented.
  • It's going to take some time. Vaccine development will take a while. Finding and testing cases will take a while. Recovery even takes a while.
  • Responders are human too. They will get tired. Try not to harass them too much or spread too many wild theories that make their job harder.

COVID-19/ SARS-CoV-2 Information

Honestly, check out this Twitter thread. It's pretty much everything you should know.

A lot of the latest information these days is actually off of Twitter, as many top researchers are using it to quickly share information with large groups of people.

Here's a list of good people to follow. They are all either journalists or researchers:

Maia Majumder

Julia Belluz

Trevor Bedford

Ellie Murray

Mark Lipsitch

Kai Kupferschmidt

EpiEllie's Coronavirus Experts List

So uh, what's it actually called?

COVID-19 is the name of the disease.

SARS-CoV-2 is the name of the virus.

SARS-CoV-2 causes COVID-19, the same way that the influenza virus causes the flu. Sorry, I know it's confusing.

Before it was formally named, people were generally using the terms novel coronavirus, nCoV, and "Wuhan pneumonia" to refer to the disease/ virus.

Where did this come from?

We believe this virus crossed over from bats to humans at some point in early November 2019. This type of species-jumping is called a 'spillover event', and happens, honestly, with some degree of regularity. Spillover events have a probability of happening every time humans come into contact with wild animals, and bats can get around a lot.

I heard the R0 was really high!

Eeeugh. This is tough.

The R0 is a value that represents the average number of new infections that will stem from a single infection. An R0 of 1 means that for every new infection, one other person will be infected. This number is NOT an immutable characteristic of a disease, but rather an estimate that changes based on the social dynamics of the outbreak as well. Implementing control measures changes the R0. This might seem pedantic, but citing an R0 tends to be a little misleading without understanding this context.

Mathematically, R0 is a function of an infected person's infectious contact rate (β) * the average infectious period (γ). The infectious contact rate is the number of contacts you have made * your likelihood of having infected them. Each part of this is affected by different things - your likelihood of having infected a contact would be a biological property, but the number of contacts you have would be a property of the social dynamics.

The goal of every outbreak epidemiologist is to reduce the R0 to below one, so that the outbreak will die out.

What are the symptoms?

Symptoms have generally been described as nonspecific, involving fever, cough, and shortness of breath (CDC). The real distinguisher from your garden-variety cold or flu is the shortness of breath. If you feel like you are having trouble breathing (other than just because your nose is blocked up or because you ran up six flights of stairs), that's worth paying attention to.

However, other symptoms have also been recorded, including fatigue and body pains.

What is the incubation period?

The incubation period is a bit tough to pin down exactly, but appears to be, on average, about 5.1 days, with 97.5% of patients developing symptoms by 11.5 days. This study was done with secondhand data, but the results are consistent with other studies. As we see more cases in the US, unfortunately, we will be able to confirm this number.

In general, people have been using 14 days/ 2 weeks as the benchmark.

What is attack rate? What percentage of cases are asymptomatic?

It's hard to say what number of exposed people go on to actually develop the disease. Because of the way different countries are testing, we aren't necessarily able to say what number of truly exposed people have developed disease.

According to the WHO & WHO Director General Dr. Tedros, very few confirmed cases were asymptomatic. However, we can't actually get a true answer until we can do serological testing... which China has just developed a test for. This will let us figure out the actual number of people who had been infected and fought off the infection.

However, this seems to conflict with this not-peer-reviewed preprint looking at the Princess Diamond data, which implied an 18% asymptomatic rate.

Note that the Report of the WHO-China Joint Mission on Coronavirus Disease 2019 points out that many of the patients who were asymptomatic on the date of identification/report went on to develop disease.

There are very many biologically plausible explanations for this discrepancy, and we will know more about asymptomatics and the attack rate as time goes on.

What percentage are mild? What does "mild" mean?

80% of cases are considered mild (which includes asymptomatic cases) according to the WHO Situation report, but the WHO mission report says that 80% are "mild to moderate".

However, it's not super clear to me what "mild cases" means. The WHO mission report includes pneumonia cases where the patient was hospitalized but who did not need to be intubated in "mild to moderate", which most people would not think of as "mild to moderate". We will find out more from South Korea and Seattle.

So, when people say "it's just a mild disease for most people", keep in mind that "mild" could still mean "spent days in the hospital".

How bad is it if you have a worse than "mild to moderate" case?

20% have severe disease, which means they were put on respiratory support machines & experienced pretty scary complications. WHO Situation report

When people are sick, they seem to be sick for a long period of time (>20 days). This has worrying implications for the US hospital system, which is not terribly well equipped to handle the sudden need to take care of a lot of patients at once.

Who's going to get it? Who's gonna die?

As time goes on, we'll learn more about the virus and its patterns as we just deal with it. South Korea, China, and Singapore are offering pretty good information.

Per the report from China CDC : In China, 86.6% of diagnosed patients were between the ages of 30-79. About 70% of the patients were between the ages of 40-79. Curiously, young children appear to be almost unaffected, though they can still get the disease and potentially transmit it. However, because of how China was doing the diagnosing at the time this report came out, we don't really know if younger patients are truly unaffected, or if their symptoms were just mild enough. Testing data from other countries should firm up some of this knowledge.

Per the same report, the highest mortality rate is in the >80 crowd, with almost 15% mortality.

Can you get it more than once?

There have been some reports that say that you can get infected twice. However, even if this were truly the case for this patient, this appears that it would be a rare event.

How long does it survive on surfaces?

This preprint from Doremalen et al contains the best we know so far. However, we know that temperature and humidity both have significant effects on a virus' ability to persist in the environment. Under the specific conditions used in the paper (65% relative humidity, ~70F/22C), a piece of plastic or stainless steel that was contaminated might still have viable virus up to 2-3 days later. On other surfaces: copper had viable virus up to 4 hours later, and cardboard had virus up to 24 hours later. This tells us that transmission through touching objects is definitely possible. It's important to note though that these numbers are only valid for the lab condition, under specific humidity/ temperature. Viral viability changes as a function of heat and temperature, too.

But, the only way this virus gets into your lungs from that surface is if you bring it there! The best way to manage this is to treat all surfaces as if they might be contaminated. If you touch a table at a cafe, don't touch your face right after. Don't lick your finger after touching a doorknob. Definitely don't lick the doorknob itself. But also, don't rub your nose after opening the door. Don't try to chew off a hangnail before washing your hands. Don't bite your nails.

Caveat: This sounds like it's really easy to not do. After all, who would lick a dirty hand? But, it really is a pretty difficult thing to not do through an entire day. Every time you take your glasses off, scratch an itch, rub your nose... if your hands are contaminated, then you just put yourself at risk of infecting yourself. Washing your hands often will reduce this chance.

Can asymptomatic people transmit the disease?

To the best of our knowledge, the answer is yes, asymptomatic people can transmit it, however, it requires close contact. By close contact, I mean sharing-utensils-and-cups, spending lots of time together kind of close contact.

Early on in the epidemic, there appeared to be a case where one person had asymptomatically transmitted the disease to coworkers abroad. However, it turns out that the original authors of the paper had not interviewed the first case about what symptoms she had. She was symptomatic, with a light fever.

However, there was at least one case in China of an a/presymptomatic patient transmitting disease to their family. The a/presymptomatic patient later went on develop the disease as well.

Basically, getting on public transit with an asymptomatically/presymptomatically infected patient most probably isn't going to give you the disease unless you make out with them or lick their face or something

How do you get it? How easily transmissible is it?

So far, we believe that it is very probably droplet transmission. This is partly because so far, most of the evidence does not point to airborne transmission being common (one kind of shaky study was published and almost immediately retracted by the authors). Also, our understanding of general respiratory diseases right now is that, people don't usually generate those types of aerosols easily.

However, aerosols with infectious particles can be generated through medical procedures such as airway suctions and intubations. This is why N95 masks (designed to protect against aerosols) are especially important for medical professionals, but maybe a little overkill for most people. The preprint discussed earlier from Doremalen et al does talk about aerosols persisting in the air, but the main context is for healthcare workers to know to protect themselves.

A bit of a roundabout here: the reason why we generally say that asymptomatics don't transmit disease is because even if you are producing virus in your throat, if that virus doesn't infect other people, it still wasn't transmitted. Coughing and sneezing is a symptom that really helps disperse the virus farther. Think about a spray bottle. If the nozzle is jammed and the liquid just dribbles out, you get a much smaller surface area than if you were able to really disperse a fine mist. So, this is also why covering your mouth when you cough is important. But, it's also possible to transmit the disease by talking, as you know if you've encountered any especially... spitty.

We don't know much yet about how long the virus can stay airborne for, and how infectious it is while airborne. Droplets are usually heavier and fall to the ground quickly, and have a shorter range that they can travel (because they're heavier). If you want to be extra paranoid, keeping a distance of like 3-6 feet between you and the person you're with is a generally safe rule.

Emphasizing again, if you touch a surface that has the virus on it, and then touch your face, you might have just given yourself the virus. Wash your hands!! Don't touch your face!!

Can recovered people transmit the disease?

We know that people can test positive for some time after they've fully recovered. However, we don't actually know if this means that they are infectious. Because the current test is a PCR test, it only tells us if that person has virus fragments in them. We don't know if those virus fragments can infect anyone else or not.

What is going on with testing?

Currently, due to a series of bungled missteps from the federal government, the US has not actually tested very many people. This involved the CDC inexplicably trying to develop its own test (which did not work), which meant that useful test kits were not given to health departments for a while.

Additionally, the lack of CDC guidance on when was appropriate for the test to be used (leaving it kind of up to local decisionmaking) has caused a lot of confusion and made it very hard to actually obtain a test.

What's with the US' case counts? We don't have that many!

The thing about diagnosing diseases is that you're going to have to first go look for them. If you don't look for them, you'll never find them. We know there's community transmission going on; we just don't know how much.

However, you should not take this to mean that everyone around you is infected. Consider: using even the most generous estimates of asymptomatic individuals, most people have symptoms. If you're not surrounded by people coughing, you're probably not surrounded by people with the virus.

Do I have to pay for the test? Will I have to pay for treatment?

In Washington State and in California, the governors have stated that all costs associated with testing will be covered. However, for other costs, such as for ERs, I cannot give you any definitive answer. You will have to call your insurance company for guidance.

Where do I / How can I get a test?

Talk to your physician. The CDC/ Coronavirus task force has made it up to the local level to decide what testing guidances are. In some places, despite demonstrated local transmission, they may still require you to be a close contact of a case, or have recent travel.

Labcorp and Quest are two diagnostic companies that have just finished developing an LDT (laboratory developed test, which is a specific FDA designation) that can be ordered by your physician. Otherwise, testing is done in hospital clinical labs or at the state public health lab.

When are we going to get a vaccine?

Anthony Fauci suggests the fastest we could get a vaccine is a year to a year and a half. This is an extremely responsible estimate, given the amount of time it'll take to figure out if the vaccine is safe & works, and time to actually produce and deliver the vaccine.

So, given clinical trials, you might be able to get the vaccine earlier, but there's no guarantee that it will work.

Basically, don't hold your breath.

What's social distancing? What's flattening the curve?

Flattening the curve has been going around social media a bit. Basically, since this is poised to overwhelm a lot of our hospital resources, and we don't have a vaccine at all, we want to slow down the spread of the disease as much as possible. Social distancing is when you stay home and avoid others even when you're healthy, so you reduce the spread of the disease.

Also, check out this explainer, which illustrates it way better than I can.

Here is another post that is a great read on this subject!

I heard that hydroxychloroquinine is the cure!

Despite what certain political leaders and certain electric car makers say, we do not know if hydroxychloroquinine (HCQ) is a 'cure'. The paper for the clinical trial is shoddy at best and has a number of unanswered questions. Several Twitter threads [1, 2] detail many of them, but the biggest problems are these:

  • The outcome looked at was viral load, not clinical outcomes.
  • Several patients who received HCQ were deemed ineligible for analysis because they weren't able to give a sample at the end timepoint, but probably would have been considered failures (as in, 3 got worse and had to go to the ICU (and so they couldn't give samples), 1 died, 1 couldn't take the side effects)
  • Viral load was not properly measured in most samples. Basically, this study really doesn't provide any convincing evidence that HCQ or HCQ+ azithromycin really is a 'cure'. To be clear, what I mean is this: we do not know if HCQ is a treatment or not. There are many other studies looking at HCQ now. But this study does not provide any evidence for that at all.

I have heard anecdotal stories of people getting sham prescriptions for HCQ and self medicating. Do not self medicate on this stuff. The side effects are very much not trivial, and it's not clear at all that it can be used proactively. HCQ can also cause heart problems, and if you have certain underlying conditions, it can kill you. Please, only take this with a doctor's guidance! Other common side effects include nausea, headache, loss of appetite, rash, and nightmares + hallucinations. This last point I kind of want to emphasize: think about how bad the nightmares have to be that they end up as side effect on here. Also, please don't hoard it; it's a drug that some people legitimately need to take and we should not cause shortages for them!

SF Specific

What's happening in San Francisco?

San Francisco declared a state of emergency. This sounds scary, but is mostly a way to access resources that they need to fight the outbreak. Gatherings of more than 250 people have also been banned.

How many beds do hospitals in San Francisco have?

The City of San Francisco has three hospitals, with 1,400 beds between them. I do not know how many isolation rooms there are.

What do I do if I think I might be infected?

Try to not panic! Don't just go to your doctor's office or the emergency room unless you are like, imminently about to die. Call your doctor or your local health department first and let them know what's going on, so that they can direct you properly, or prepare for your visit. Some doctors' offices have been adopting telemedicine visits as well, and Kaiser has a mobile swabbing unit for high risk patients. Because of this, and to reduce risk to other patients, you should call and see what they're doing first.

Calling your doctor is probably the best, but here are some local numbers for health departments:

  • Alameda County Communicable Disease Unit: (510) 267-3250
  • City of Berkeley: (510) 981-5300 (Yes, this is somehow separate from Alameda County)
  • San Francisco Disease Prevention and Control: (415) 554-2500
  • San Mateo County Communicable Disease Control: (650) 573-2346
  • Santa Clara County: (408) 885-4214
  • Contra Costa County Communicable Disease: (925) 313-6740

I'm afraid this is all we can do right now. I'm sorry. Hang in there. We got this.

How many cases have been in the Bay Area?

As of: 2020-03-09:

  • 13 in San Francisco
  • 43 in Santa Clara County
  • 9 in San Mateo County
  • 3 in Alameda County
  • 12 in Contra Costa County
  • 2 in Marin County

Frequently asked questions

I want to note here that this is how I have been answering the questions that people have asked me specifically. You should pay attention to what your local health department says. Check their website!

Should I work from home?

Yes, if you can. Try to reduce the burden on those who can't.

Should I try to stay at home as much as possible?

Please do! Try to reduce your social contact as much as you can right now. Don't forget to use the internet and phone calls to stay in touch with your friends and family!

Should I travel?

Would really, really, really not recommend it, especially if you have older family that you're in contact with a lot. But, if you really insist on it because no one can stop you, absolutely do not go while sick and immediately quarantine yourself if you develop symptoms.

Also recognize, depending on where you're going, a ton of shit's probably closed anyway, and there is a non-zero chance of getting officially quarantined on your way back. Do you really want to go?

Should I stock up on masks? What measures can I take?

The typical refrain: wash your hands, don't touch your face, avoid large crowds, make sure you have your emergency kit. Wear a mask only if you're sick

Masks will provide some marginal level of protection, but most people also use masks incorrectly which might lead to them actually putting themselves at greater risk. The value a mask provides is kind of dependent on how many sick people are actually around you.

Additionally, there will definitely be a mask shortage for our healthcare workers, who are in constant contact with infectious particles. You should not hoard masks when health workers need them the most. It is in your best, selfish interest for those people to not get sick. If too many health workers get sick, it'll cripple a hospital, resulting in worse outcomes for sick people, and even less ability to control the outbreak. But, you should still wear a mask if you're sick, to prevent infecting anyone else.

Many respiratory infections are actually from people with dirty hands touching their faces and inoculating themselves with pathogen. So, wash your hands and don't touch your face.

Generally speaking, make sure you've got at least 2 weeks of food. You should have this anyway if you're in SF. It's earthquake country after all, and you should make sure you have an emergency kit.

Exercise ...?

One of the other guides going around tells you to do aerobic exercise to "strengthen your lungs". I deeply resent this wording - your lungs aren't like a muscle. You can improve your lung capacity, but you can't just 'strengthen your lungs'

BUT exercise can help your immune system (less strengthening it and more just not weakening it). So does eating healthy foods, especially getting enough sleep, not drinking excessively, and not stressing out. Hahhvahd

So, really, one of the best things you can do for yourself is to just go to bed and not try to obsessively follow the latest scraps of news.

But what can I do to help??

  • Convince your friends and family to practice social distancing. Try not to scare them too much (sometimes people react the opposite of what you want if you do that), but do emphasize that this is just all of us doing our part to stop this disease that can kill people. It can only happen if we all work together, so please pitch in!
  • Reach out to your friends and do things together online so you can help them not get cabin fever and go outside! Maybe now is a good time to watch a movie together over video chat

Unrelated to coronavirus, but I think a whole lot of you probably suddenly are working from home. A reminder: get up and walk around every now and then. Don't put yourself at risk for blood clots in your legs that can lead to life threatening pulmonary embolism. Just walk around a little bit.

I have skills, how can I help?

There's lots of groups that have set up ad hoc coronavirus response stuff. They are all over the place, but I haven't had time to vet them all. You can find them fairly easily online!

Though, I wanted to give a particular shout out to this group I trust because of the backgrounds of the people running the show - namely that most of them understand what it takes to integrate into existing government systems : US Digital Response

Other resources (SF -centric)

PLEASE PLEASE PLEASE check your local ordinances for recommendations.

Concluding remarks

Anyway, I urge you to take care, but be mindful of others. The only way we beat epidemics is to beat them together. Selfishness will harm others and make it harder for things to go "back to normal". Try not to scare others on purpose and offer help (while taking precautions) if your friends and neighbors need it. Every man for himself is not the way to do things here.

You can’t perform that action at this time.