Tuesday, March 31, 2020

To Mask or Not To Mask

There's a stark difference between Asian and American cultures regarding the wearing face masks in public - embraced in Asia and shunned in America. And that difference seems to be having an effect on the control of the novel coronavirus outbreak. But before we jump into why that might be the case, I'd like to share something I witnessed on a flight to Florida in early February. 
Source: Jeremy P. Howard, Twitter
Our family was headed to Orlando to celebrate my father in law's birthday. On the flight down from Newark, we were seated behind a young Asian couple and a middle aged white man with Mickey Mouse ears on his head (we'll call him Mickey for the story). I say Asian because I don't know what ethnicity they were because their faces were largely obscured by face masks. The white man (seated directly in front of me) was traveling with a cheer squad but was seated away from the team and the rest of the chaperones. And he was very clearly unnerved by the couple seated next to him because this is what transpired.

coughing while asian is not a crime girl with sign gif
NOTE: The couple in our story never actually coughed the whole flight.
I'm distracted by my baby when a woman across the aisle from Mickey says loudly, "Did you just take a picture of them without asking their permission?" Everyone around becomes silent. Mickey sputters something unintelligible and tenses up.

The young man turns to Mickey and pulls down his mask. "Did you just take a picture of us? Why did you just take a picture?" His English is clear and his voice is measured. Lady across the aisle says, "That is really rude. You should delete that picture." Mickey continues to try to ignore both of the people talking to him.

The young man turns to his partner and says something in another language. Then he turns to Mickey and says "I would like you to delete that picture. Why did you take a picture of us without asking?"

Mickey finally responds. "Because I'm uncomfortable. Why are you wearing those masks?"

The young man says "We are wearing these masks to protect ourselves. I'm going to ask again. Please delete that picture off your phone."

But Mickey doesn't do it. He starts playing a game on his phone and acts like the interaction never happened. The couple speak to each other in their native language for a bit and the tension dissipates some. But let's just say it was a very long and uncomfortable flight to Florida for more than just Mickey and the young couple.

1918 flu pandemic mask ad
1918 Newspaper Ad: Helpful Hints for Making Your Own PPE
Interestingly, the history of many East Asian cultures (like China and Japan) embracing facial coverings dates back to the 1918 flu pandemic, a time when everyone was wearing face masks.

two women flu masks 1918
Why didn't this fashion trend stick?
The mask wearing habit has been reinforced in Asia over time as a way to grapple with both poor air quality and pollution as well as infectious diseases like SARS and bird flu. It can also be a bit of a fashion statement. But this tradition is looked at warily (or conversely fetishized) by many in the West - leading to outbursts of xenophobia like what we witnessed on our flight to Orlando.

Currently, both the WHO and CDC do not recommend wearing masks unless: 1) you know you are sick OR 2) you are caring for someone who is sick. But some folks are beginning to question whether or not those recommendations were put in place as a way to try to discourage the rush for N95 masks that has lead to shortages for healthcare workers. The personal protective equipment (PPE) shortages are so severe that many organizations have taken to encouraging people to make homemade cotton masks to provide to employees. It's like 1918 all over again.

trajectory covid19 spread financial times figure
Source: John Burn-Murdoch, Twitter
A few days ago a lot of people started to take note of the data compiled by John Burn-Murdoch about how efforts to control COVID19 are going. There is an obvious difference in the doubling speed of the virus in countries that use masks versus those that don't - of course there are a lot of other factors at play, like differences in quarantine policies and testing programs. The fact that more general mask usage didn't stop China from experiencing rapid exponential growth of the virus is a cautionary tale - correlation is not causation, folks. Just because two things occur simultaneously, it is not definitive proof that one thing made the other happen. We need more careful analysis to separate out the truth. Only time will tell exactly how strong of an impact the routine wearing of masks has on flattening the curve of COVID19 spread. 

In the meantime, when interviewed by Science magazine (March 27), George Gao, the head of the Chinese Center for Disease Control and Prevention, said the following:

"The big mistake in the U.S. and Europe, in my opinion, is that people aren’t wearing masks. This virus is transmitted by droplets and close contact. Droplets play a very important role—you’ve got to wear a mask, because when you speak, there are always droplets coming out of your mouth. Many people have asymptomatic or presymptomatic infections. If they are wearing face masks, it can prevent droplets that carry the virus from escaping and infecting others."

Sui Huang, MD, PhD of the Institute of Systems Biology in Seattle recently wrote a piece on Medium to explain this line of thinking further. Here's one of the figures from the article. It suggest that a 2007 study showed that homemade masks reduced the number of aerosol particles inhaled by two-thirds, although they weren't very effective at preventing particles from escaping into the environment. 

mask figure medium article

On Monday, Dr. Fauci (the infectious disease physician in charge of NIAID and the coronavirus task force) was interviewed on Good Morning America about the mask question. Here's a summary of what he said.
Source: Good Morning America
Sounds like a definite maybe to me. There are several well written pieces in the Washington Post, the NY Times, Wired Magazine and Politico about this topic if you would like to learn more about the push for more mask usage in the US. If you want to learn more about how to make masks to donate to our health care heroes or make for your own family, check out the Joann Fabrics website. Until next time...

Let's be careful out there.

Monday, March 30, 2020

Who Can You Trust?

I've taken a step back from writing about COVID-19 for the past couple of days. Not that I've stopped reading voraciously, but trying to sum up everything is overwhelming. But now I feel a little selfish about that decision. I may not be an epidemiologist or a virologist, but I have the benefit and privilege of having an education that makes it easy for me to interpret scientific and medical reports.

Quote: Maria V. Snyder, author
In undergrad, I earned a Bachelors of Science in Biology, while volunteering in a cytogenetics lab and being paid to deliver specimens (blood, sputum, feces etc) and setup cultures for microbiology in a general hospital lab. Then I spent 5 years earning a PhD in biomedical science with a concentration in genetics and developmental biology, followed by further post doctoral training in genetics. My research ranged from in vitro biochemistry (engineering and purifying proteins to test their affect on the cellular process of RNA splicing) to mouse husbandry. Then I spent a year creating continuing medical education programs for doctors and nurses on topics related to dermatology, allergy and diabetes. And I've spent the past nearly 13 years as an educator.

But most people don't have that luxury. Maybe they've taken one biology class once in high school. Maybe they've never taken biology. Should everyone be trying to make sense of the rapid fire barrage of COVID19 info?

I think Hobbes gets it.
Ideally, yes. The more educated folks are about what's going on, the better off we will be as a society. No one expects you to be an expert or to easily understand all the lingo. That's what professional science communicators are for.

But let me start with a few words of caution. Understand that not everyone who claims they have a doctorate of some kind is actually qualified to speak on what's going on.

Sometimes those people have made up their degree or purchased it from an online degree mill or earned it in something completely unrelated to public health. Other times people who legitimately went through rigorous training to become an MD or PhD will spout dangerous and misleading information. All of these folks tend to be motivated by a few things - desire for recognition / power and desire for monetary gain. I'll concede that some may even think they are helping people - after all the Dunning Kruger effect is a very real thing.

https://www.thedailystar.net/shout/health/news/judging-yourself-the-dunning-kruger-effect-1730974
DKE-19 is seriously making it hard to keep up with COVID-19
That being said - why should you trust me? I have nothing to gain by talking about science - other than relieving some of the busyness of my mind. My main motivation for writing is that I want as many people to be safe as possible. Since I can't wish this nightmare away, writing about what I do know is the next best thing.

So I think I need to make baby steps. Rather than covering every report that comes out, I'm going to start by compiling a list of reputable resources for folks to follow. There are a lot of great science writers out there - people with actual backgrounds in research and medicine - who can be trusted. If you don't already use Twitter, I would strongly recommend using it to get information directly from the folks on the front lines of research and hospitals. Here goes...

World Health Organization aka WHO - an organization of physicians and clinical researchers and epidemiologists based in Geneva Switzerland who track all kinds of diseases and compile best practices from data collected around the globe (also follow them on Twitter)

Centers for Disease Control aka CDC - the US government agency responsible for tracking diseases (Twitter)

Johns Hopkins School of Public Health - There's a ton of experts working at JHU and several of them (lead by Lauren Gardner) built a very cool COVID19 tracker. (Twitter)

Anthony Fauci, MD - Dr. Fauci is the head of the National Institutes of Health's National Institute of Allergy and Infectious Disease (NIAID) and President Trump's COVID19 task force. While he doesn't have his own social media accounts, he's all over social media these days.

Trevor Bradford, PhD - He's a molecular epidemiologist, meaning he tracks how viruses mutate and helps link specific patient samples to determine how infections spread. (Twitter)

David Gorski, MD, PhD - He's a surgeon and the creator of the blog Science Based Medicine. He has championed clinical practice based on actual evidence, rather than anecdote or historical precedence for years. He does a really good job of explaining why certain claims are crap. (Twitter)

Ed Yong, MPhil - He's a British science journalist with a masters degree in biochemistry. He started out writing for Nat Geo on a blog called Not Exactly Rocket Science, but is currently working for The Atlantic. He follows a lot of great physicians and scientists on his Twitter so you could get additional ideas of who to follow there.

This by no means is an exhaustive list, but it's a place to start. I'm going to sign off here with a quote from my high school choir teacher, Mr. Eckstein.

Let's be careful out there.

Wednesday, March 25, 2020

A Slippery Slope

In the past few days, some politicians have come out urging the public to consider returning to "normal" in a very short amount of time - counter to what health experts are telling us is necessary.
Tweet Tiffany Trump return to work
Get back to work by April 1st?
The idea is this: tanking our economy is worse than some people dying. Buoyed by President Trump's calls to get back to business as usual by Easter, the lieutenant governor of Texas basically said that older folks ought to take one for the team to save the economy for the children.
tweet Dan Patrick coronavirus
Bad economy worse than death?
There's quite a few problems with this interpretation, not the least of which is that it's encouraging a game of Russian roulette with your health. I mean you probably won't die if you contract the disease, right? Ignore the fact that folks who recover appear to have permanent lung damage, which would make them more susceptible to other illnesses in the future. Or the fact that we don't always know who has underlying conditions putting them at a higher risk of a fatal outcome. (Did you hear about the 21 year old Spanish soccer coach, the 36 year old Brooklyn school principal, the first person under 18 years old who died in LA and on and on?)

If we simply consider the healthcare system, you can see the fatal flaw (yes, pun intended) with the calls to live like we're not in the midst of a pandemic. There are only so many hospitals with so many health care professionals with so many supplies available at any given time. If we do not stop the exponential spread of the virus, these precious resources will be overwhelmed and consumed.

cartoon exponential growth flatten the curve
Source: Dr. Siouxsie Wiles
The healthcare system will fail and the death rate will climb. This is not just a thought experiment - we have evidence of this happening in Italy. We have evidence of it happening in the US too - if we look back at history to understand the 1918 flu pandemic.

So hopefully we can all agree - rushing to end social distancing prematurely will not get things back to "normal" like waving a magic wand. Believing it's a viable option is wishful thinking - highly dangerous wishful thinking. And with it the specter of eugenics begins to rear its ugly head once again. Let's not accept defeat already - we can minimize the loss of human life by listening to the folks on the frontline of this war. Stay home and be well everyone.

thank you workers

EDIT: A new interview with Dr. Bruce Ayland of the WHO just came to my attention - please read it.

Sunday, March 22, 2020

Social Distancing Outdoors

On Friday, my husband and I decided to take a walk through the Dismal Swamp - one of the last remaining wetlands in urban New Jersey - with our infant son. My husband had driven past the signs for the preserve many times on grocery store runs since we moved to the area in the fall, but had never stopped. With the weather cooperating and us feeling a little stir crazy, we set out on the Songbird Trail with high hopes.

man baby dog hiking
My loves on the trail
We made it easily through the clearing - the mud wasn't too bad and it was too early in the season for mosquitoes - but we didn't see any wildlife. We could definitely hear insects and birds, but they were apparently camera shy. It surprised us to find ourselves on another road (New York Blvd) so soon so we decided to cross to continue on. We saw a couple of houses ahead on a small road and decided to swing right along an abandoned railroad track. Here's when the swamp really started living up to its name.

All sorts of trash littered either side of the path - some in garbage bags, some strewn loose about the landscape. Discarded alcohol containers and other food waste, tires, even furniture! We remarked to each other that it was good that the baby was in a carrier and not able to roam around on his own. And how it was unlikely that we would come back...

A short distance along the trail - still near the shotgun style house on a cinder block foundation - our dog started rolling on the ground. The way that she does to signal she's found something particularly foul. Sure enough she was rolling in tuffs of black and white fur. I looked ahead just a bit and found the source.

Mystery Carcass
Much to my husband's amusement, I took the time to carefully document the critter - which I assumed was a skunk based on the fur coloration and the size of the body.

decomposing foot opossum
Decomposing Toes Can Still be Cute?

opossum skull beetles
Death Doesn't Stop Life or Beetle Sex on the Skull
We continued along our way, following the railroad tracks, trying to avoid the trash and remarking on the signs warning the area on our left was contaminated (with what?!?). When we got within sight of the end of the path, we stumbled across another skull.

groundhog skull
Mystery Skull #2
groundhog skull
Definitely a rodent

I'll be honest - even though I knew it was a rodent looking at the front teeth - I assumed it was a possum based on the size of the skull. I'm a geneticist after all and not a mammalogist or ecologist. I knew that #ScienceTwitter would set things right once I got home and uploaded my finds. I was not disappointed.

tweet
Skull 1 = Opossum & Skull 2 = Groundhog (aka marmot)
You'd think the story ends there, but upon the urging of some friends and a student, we decided to make the trip back to the trail yesterday to pick up the bones. I do teach forensic science after all. Husband and baby waited patiently while I ran back to grab the skulls in plastic ShopRite bags with nitrile gloves on (yes, we always have these around the house for cleaning, not just because of COVID-19). When I came upon the groundhog skull, I noticed that not too far off from it were several other bones we hadn't noticed the day before, though I am sure they were there considering the weathering they display. I'm pretty sure they are deer bones, though I could certainly be wrong again (#ScienceTwitter do your thing please).

Femur

Broken scapula?

Vertebrae
Of course as I was photographing these new finds with my bright blue gloves (plastic bags burgeoning with skulls), a jogger came down the path. He raised his eyebrows at me. To which I very gracefully blurted, "I'm a forensic science teacher. I'm grabbing these bones for my students." He gave a surprised "Oh", then went a little ways down the trail, turned around and ran back the other direction. So yeah. Hopefully I didn't get reported to the police for suspicious behavior. And I hope this post finds everyone well enough to enjoy the outdoors separately too.

Want to learn more about bones? This is an amazing blog by a teenage self taught naturalist Jake McGowan-Lowe.

Friday, March 20, 2020

Quarantine Reading

Are you looking for something to read while you are stuck inside? I have a few suggestions for science non-fiction that I definitely think you should check out.

BOOK 1: SPILLOVER
Spillover book cover
Amazon: Spillover
Spillover came out in 2012 and became a NY Times' best seller. Author David Quammen explains how infectious diseases (with a heavy emphasis on viruses) can hop from other species into human populations in very accessible prose. He explains how epidemiologists do their job and how we can learn from the history of other diseases (there's a fascinating bit about the development of HIV for example) to better cope with emerging ones. I read this book about 6 or 7 years ago and I could not put it down. In light of the emergence of SARS-coV2 (COVID-19), it's content is particularly timely.

spillover sample text
Sample Text: Spillover
If you are interested in the topic, but don't have time for the book consider watching this TED talk from virologist Nathan Wolfe: The Jungle Search for Viruses.

BOOK 2: BAD SCIENCE
Amazon: Bad Science
We've already begun to see a lot of questionable claims related to COVID-19, but misleading sciency sounding claims and "cures" are nothing new. Ben Goldacre is a physician epidemiologist from the UK. His book Bad Science is the result of the following he gained on his blog with the same title. (Not every blog post made it into the book so you might want to check it out too.) Dr. Goldacre's basic premise is that there is a lot of junk science out there - either because of unintentional mistakes or outright skulduggery. He covers the gambit of shifty folks pushing pseudoscience to the media misreporting real data. The beauty of this book's format is that each chapter is really standalone so it's easy to pick up and put down if you are the kind who likes to be able to switch between multiple books.

bad science sample text
Sample Text: Bad Science
If you are interested in "seeing" Dr. Goldacre speak, he has two TED talks available: Battling Bad Science and What Doctors Don't Know About the Drugs They Prescribe.

If you can't get a physical copy of these books through your library, local bookseller or Amazon, you can listen to them through Audible or download it to your Kindle or Nook.

Thursday, March 19, 2020

The Problem With(out) Peer Review

Both the mass media and scientific journals have relaxed their rules about access to information regarding SARS-coV2. Paywalls are down on sites like NY Times and the Washington Post, as well as on scientific journals. Peer review and common sense seems to be waived too.

On March 16, 2020, a pre-print of an article found on MedRxiv tried to make the claim that "people with blood group A have a significantly higher risk for acquiring COVID-19 compared with non-A blood groups, whereas blood group O has a significantly lower risk for the infection compared with non-O blood groups."

This was subsequently reported on MSN, Newsweek, Fox News and more. No doubt people who are type A are starting to freak out even more than they already were. But they really shouldn't be. Here's why...

medRxiv


MedRxiv is a server that allows authors to submit manuscripts that have not been peer reviewed or published for the research community to view. By submitting to the server, the manuscripts will be evaluated by dozens of actual scientific journals which actually have a peer review process. They have a bolded disclaimer on their home page and About Us page that states:

"Preprints are preliminary reports of work that have not been peer-reviewed. They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information."

So other scientists haven't verified the claims made by the authors. And despite clear guidance from the organizers of MedRxiv not to extrapolate clinical significance from reports submitted to their server, some journalists (likely without any science background at all) began to spread these unverified claims.
ABO blood groups
Source: BioNinja
Before we dive into an analysis of the paper, it would be good to review ABO blood types. The ABO blood group was discovered by Karl Landsteiner in the early 1900s. The 4 types - A, B, AB, and O - refer to the configuration of specific carbohydrates on the surface of red blood cells. These blood types are genetically determined and do not change over the course of your life.

Now let's look at the actual claims.

"The proportion of blood group A and O in COVID-19 patients were significantly higher and lower, respectively, than that in normal people (both p < 0.001)."

previous study of 3.8 million Chinese people found the following distribution of the ABO types: A 30.5%, B 29.4%, AB 9.7%, and O 30.4%. Keep that in mind when we look at their data. Here's what they reported:
data table
The authors claim that they did a Chi square test to check for statistically significant differences between the 4 blood groups. The p-value represents the probability of something occurring. We can interpret small p-values as certainty that our hypothesis is correct - that there is a real difference between categories not due to random chance. A p-value < 0.05 is like saying we are 95% certain it's not random chance at play.

Right away, I smelled a rat. The sample size of those infected with the virus was quite small compared to the control group. Ideally, you want as many data points as possible (bigger sample size is better) and you want your experimental and control groups to be similar in size. And eyeballing the data (I've done enough Chi square tests to have a sense for when something isn't going to be significant), it didn't appear to have enough of a difference to warrant a p-value of <0.001 (equivalent to 99.99% certainty). 

So I decided to run a Chi square test of my own (see the chart below). Whether I looked at Wuhan and Shenzhen separately or as aggregated data, there was no significant difference between folks with the virus and the controls for any of the blood groups. Not at a p-value of 0.01 (99% certainty) or a p-value of 0.05 (95% certainty) - and definitely not for the strict p-value they reported.
Chi square chart
Wuhan Data from Paper
What are the takeaways here? Should you be freaked out if you have type A blood? No. There's nothing to suggest from this report that you are anymore likely to be infected than anyone else. Should you be angry that people are reporting on preliminary data that hasn't been reviewed by other experts? Yes. I'm all for more transparency in research, for making raw data available to more people more quickly. BUT it's hugely irresponsible for researchers to rush to publish something without actually having data to support the claim they are making AND for journalists without a solid grasp of the content to be raising alarm bells. My final analysis of this research and the lay press reporting on it?

bullshit meter


Wednesday, March 18, 2020

A Rose By Any Other Name...

is still a rose. So let's be honest: there are a lot of people who are using SARS-coV2 to share racist thoughts. If we aren't careful, racism and xenophobia will spread as rapidly as the virus.*

twitter screenshot

twitter screenshot
* That's not to say racism and xenophobia aren't endemic to the USA - they are.

There's been an uptick in incidents (both verbal and physical) against folks of Asian descent in the US. [More evidence of this here, here and here.]

So let's be real for a minute. Yes, SARS-coV2 originated in China. But calling it the Chinese virus or the Kung Flu or anything of the like is problematic. We don't call Ebola the "Congo virus", Zika the "Uganda virus", or Hantavirus the "New Mexico virus". We call them by the virus family name or the specific strain. Because that's being scientifically accurate and not xenophobic.

And guess what? It doesn't matter where a virus emerged - new viruses are being discovered every year in locations all over the world - because if a virus is virulent enough, it will spread well beyond the first place it was identified. While it was first discovered in Uganda in 1947, the major outbreak of the Zika virus in 2015-2016 that caused complications like microcephaly in newborns was centered in the Americas. Viruses don't recognize nationality. And neither should our politicians or citizens when discussing the current pandemic. Do better, people.

Glutton for Punishment? A Primer on Coronavirus

It's impossible to avoid reading, hearing, or talking about coronavirus or COVID-19 right now. There's a lot of conflicting information out there that can make your head spin. So I thought I'd do a quick summary of what this #coronapocalypse is and how you can help #flattenthecurve.

What is coronavirus/COVID-19?
People are using these terms pretty interchangeably, but they don't mean exactly the same thing. Coronaviruses are a family of RNA viruses (first identified in the 1960s) that cause upper respiratory infections. Typically that looks like a cold (up to 30% of common colds are thought to be caused by coronaviruses) - though sometimes they can cause fatal reactions. Coronaviruses get their name from the glycoprotein spikes that stick out past the main enveloped viral particle - because the spikes look sort of like a crown.
SARS-coV

Credit: Dr Linda Stannard/UCT/Science Photo Library

There are quite a few that only infect other animals (like pigs, cows, chickens, dogs, cats, etc.), but there are 7 known to be able to affect humans. The virus that is currently causing a pandemic is called SARS-coV-2 (for severe acute respiratory syndrome-coronavirus-2). The term COVID-19 refers to the disease caused by SARS-coV-2 - AKA coronavirus disease 2019.

So why is this coronavirus such a big deal?
On December 31, 2019, the Chinese government alerted the World Heath Organization (WHO) that an outbreak of a novel SARS-like pneumonia was going on in Wuhan. It is believed that the SARS-coV2 virus originated in either a bat or a pangolin population, mutated and hopped into our species. Unlike the most commonly circulating coronaviruses, this strain has a death rate anywhere from 2-15% (it's hard to say because of variability in testing around the globe). Some studies even suggest the real death toll will be more like 1.4% of infected individuals. Thankfully, it's no where near as deadly as MERS (about 34% of those patients died), but it is more virulent - meaning it is able to spread from host to host more efficiently.

Virulence is usually described using the term R0 (r-naught) - where R represents the reproductive rate of the virus. The R0 value tells us how many people one sick person might go onto infect - the higher the number, the quicker the spread of the disease. The H1N1 virus of 2009 had an R0 about 1.4 to 1.6. The virus that caused the 1918 flu pandemic is estimated to have had an R0 of 1.4 to 2.8. As many as 50 million people died in a single year as a result of the 1918 flu pandemic. Early data suggests that SARS-coV2 has a R0 between 2-3. This means that for every one person who is infected, we can expected them to go on and infect another 2 to 3 people.

Vox R0 r-naught zika measles ebola hiv chart
Source: Vox
A lot of people keep saying "The seasonal flu kills as many as 50,000 Americans a year. Why the overreaction to a few thousand people dead from in the whole world?" This is very dangerous thinking.

Seasonal influenza viruses - there are many strains circulating which is why sometimes you can get sick even after getting vaccinated - typically kill 0.1% of those infected. If we assume that 50,000 people represent 0.1% of infections - that gives us 50 million influenza infections in a single season in the United States alone. Let's imagine, for argument's sake, 50 million Americans become infected by SARS-coV2. Considering that it has an R0 higher than seasonal flu that's not a huge stretch of the imagination, how many people would die? Approximately 1.5 million people. 

Let that sink in.

COVID-19 can be a mild infection for those who are young and otherwise healthy. Some people don't even show symptoms while they are infectious. But we know that the elderly, the immuncompromised or others with underlying health conditions are extremely vulnerable to this disease taking a fatal turn.

So how is COVID-19 spread? And how can we stop it?
Like other respiratory infections, COVID-19 spreads when viral particles are shed by an infected person through coughing, sneezing, or even talking AND then are inhaled by an unwitting bystander. There's also some research to suggest that SARS-coV2 can "live" up to 3 days on surfaces - raising the possibility of transmission by touching a contaminated object and introducing the particles into our respiratory system. The worst part is that the incubation period can be as long as 14 days - meaning you could be infectious and not know it, all the while shedding virus as you go about your business.

So to stop the spread we need to be proactive. We need to act like we've been infected in order to protect ourselves and our communities.
Cleveland Clinic coronavirus poster
Cleveland Clinic: Recommendations based on CDC Guidelines
That means the following:
  1. Do NOT travel anywhere unless you absolutely need to! (Yes, this means don't go to stores or hang out with friends. Just #staythefhome.)
  2. Wash your hands FREQUENTLY with soap and water. (The soap helps destroy the membranous envelope around the virus so it can't get inside your cells. Alcohol based hand sanitizer is good to have if you are out and about for some reason, but washing is best.)
  3. Do NOT touch your face - your eyes, nose, and mouth are exactly what the virus is hoping to come into contact with. (I know it's hard not to - we do it unconsciously - so focus.)
  4. Cover your mouth and nose if you cough or sneeze. (Ideally - do the dab. Try not to cough or sneeze directly into your hands.)
  5. Avoid contact with people who are sick AND stay home if you suspect your are sick. (See #1.)
  6. CLEAN EVERYTHING! 

But understand that even following all this advice, it's too late for containment. COVID-19 is in 154 countries and all 50 states. There's a very good chance that a lot of us will become infected - thankfully a vaccine trial is already under way. How many people are affected and die depends on the actions we take now though. Check out this Washington Post article about exponential growth and how social distancing can impact how many people are impacted.

And then... Stay the F home.

Tuesday, March 17, 2020

Dancing DNA

I belong to several Facebook groups dedicated to genetic genealogy. I've seen quite a few posts asking about the variability of DNA centimorgans (cMs) shared between posters with their distant cousins versus their siblings and those same cousins or why family history claims a particular ethnicity but the DNA results don't support those claims. I thought it might be helpful to explain how chromosomes behave when someone makes sex cells (eggs or sperm) to clear some of this up.

We all have 23 pairs of chromosomes - 22 pairs of non-sex chromosomes called autosomes and one pair of sex chromosomes (XX = female, XY = male). We inherit one copy of each autosome from our mother and one copy from our father - likewise each parent contributes one sex chromosome as well. So half of your DNA came from your mother and half from your father*. Typically most people assume that you inherit exactly half of your maternal DNA from her father and half from her mother - or 25% from each grandparent - and the same for your father's family. But that isn't necessarily true.


The reason why this isn't true is that during sex cell formation, chromosomes of the same type find each other, get tangled up and can swap segments. This is called recombination. It creates chromosomes that contain DNA from both grandparents. It's a random process so the relative amount of DNA from each grandparent in a single chromosome can vary a lot. As the sex cell continues to mature, the chromosomes need to separate so that the cell ends up with half the number of normal chromosomes. This process is also random. It is possible for more genetic material from one grandparent to end up in the mature sex cell that is used for fertilization than the other grandparent. In fact, it's been calculated that there is a 1 in4 million chance of all 50% of a parent's DNA contribution coming from only one of their parents!


Since each sex cell has experienced both chromosome recombination and random assortment independently, even full siblings can inherit markedly different quantities of DNA from their grandparents. Saying you have 25% of DNA in common with each grandparent is just an average estimate. Great grandparents you might expect 12.5% of DNA in common, great great grandparents only 6.25% and so on and so forth. But the reality is that it's possible to be quite a bit less (or sometimes more) than that, depending on how recombination and assortment occurred.


This is why it's possible to share no DNA in common with a significant chunk of 3rd cousins and beyond - even with a verified paper trail of ancestry. Your siblings might match with a distant cousin and you do not - not necessarily because of a non-parental event (NPE), but simply due to normal cellular processes. To help with visualizing how chromosomes might pass from generation to generation, I've drawn a pedigree with one pair of chromosomes. For simplicity's sake, I started with non-recombinant chromosomes in the first generation of ancestors. In the 4th generation, the second cousins do not happen to share DNA from the same great grandparent, although they are descendant from the same couple. 



pedigree chromosomes

Hopefully this clears up some confusion and convinces you that you need more relatives to spit in tubes to really get at the migration of your family. 🤣


(*Turns out there is a really rare chance that you can inherit more DNA from one parent than the other - check out uniparental disomy.)