Anyone who lives with more than one member of Felis catus knows that our beloved felines love to smell each other’s anal…
Hindsight is 2020, perhaps literally, when it comes to COVID-19. A compelling narrative predicting that a deadly virus – specifically, a coronavirus – would jump species, seeding the pandemic, runs through reports and opinions published in the major medical and scientific journals.
Hints From SARS
Exactly 17 years ago, Toronto physician Paul Caulford wrote in the last issue of The Lancet for 2003, in “SARS: aftermath of an outbreak,” that “SARS brought one of the finest publicly-funded health systems in the world to its knees in a matter of weeks.” His description of the daily devastation presaged the nightly news of much of 2020.
Dr. Caulford tried to warn us: “What will the world community learn from this initial round of SARS? Will it be seen as the revealing gift it was? I fear not!”
Where did the original SARS virus come from? Dr. Caulford acknowledged that “the way we treat our planet” had fueled its emergence and spread, imploring “every hospital, emergency room, and nursing home” everywhere to be ready for a return of SARS.
In 2007, a lengthy report from the World Health Organization that looked back on SARS offered telling observations that would prove prescient:
• nations must cooperate and be transparent in reporting disease statistics.
• 19th century practices are important (think masks, quarantine, contact tracing).
• animal husbandry and marketing practices seriously affect human health and enable the rise of viral plagues “from the animal world.”
Concluded the report, “it would be tragic if we did not learn from the experience of 2003 and make the most of it.”
A Time Machine to Glimpse Origin From a Bat Virus
After SARS faded, we grew complacent, although work on a vaccine left the beginnings of the shots now going into people’s arms.
Then, a more urgent warning surfaced in early 2019 from Yi Fan, Kai Zhao, Zheng-Li Shi, and Peng Zhou, investigators at the CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology in China. They would go on to contribute some of the earliest reports on COVID-19.
In “Bat Coronaviruses in China,” submitted to the journal viruses in January 2019 (published in March), the Wuhan group highlighted three coronaviruses of concern: those that caused SARS, MERS (in 2012), and Swine Acute Diarrhea Syndrome (in 2017). All three viruses are highly pathogenic, came from bats, and two originated in China. They concluded:
“Thus, it is highly likely that future SARS- or MERS-like coronavirus outbreaks will originate from bats, and there is an increased probability that this will occur in China. Therefore, the investigation of bat coronaviruses becomes an urgent issue for the detection of early warning signs, which in turn minimizes the impact of such future outbreaks in China.”
The bodies of bats are normally swimming with viruses, their immune responses dampened into an acceptance that keeps the flying mammals well while enabling transmission of viral disease. I reviewed the attributes of bats here.
By the end of 2019, the prediction from Wuhan earlier in the year had come true.
Three of the quartet of authors of the 2019 paper appeared, with colleagues, on another report that would attract far more attention, published February, 3, 2020 in Nature: “A pneumonia outbreak associated with a new coronavirus of probable bat origin” probed “a new coronavirus (2019-nCoV),” the enemy not yet christened SARS-CoV-2.
About 3,000 cases of the new infectious disease had been reported at the time, suspected then and known now to have been a gross underestimate. The paper detailed the results of whole genome sequencing of the viruses from five of those early patients, all of whom had sold at or delivered to the same seafood market in Wuhan.
The new virus’s genome sequence, just under 30,000 RNA building blocks, was 79.6% identical to that of the original SARS virus from 2003. But it was about 96% identical to the genome of a bat coronavirus, RaTG13. (The name reflects the bat species, location, and year of discovery.) Was it a precursor to SARS-CoV-2?
The team was able to go back in time to track a possible origin of the new virus because their research, for years, had compared the genomes of viruses found in the excrement of bats and other animal species to genome sequences of viruses in the preserved blood sera and lung fluid of patients suffering from severe, unknown respiratory infections. The connection? Human settlements encroaching on habitats of other animal species can foster a zoonotic event – a “jumping” of a pathogen from one type of host to another.
The bat virus RaTG13, discovered in 2013, was described in a 2016 paper, “Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft.” In 2020, when RaTG13 suddenly appeared to be related to the novel respiratory virus, the researchers had the idea to re-evaluate viral genome sequences in preserved sera from four patients who’d been sick in 2012. They’d all worked in an abandoned copper mine in Tongguan town, Mojiang County, Yunnan Province, China – a place festooned with bat dung.
In a November 1 addendum to the February 3, 2020 paper introducing COVID-19, the researchers presented their findings on the four patients from 2012, one of whom had died of the illness. The patients hadn’t been infected with Ebola or Nipah viruses, nor had they harbored the newcomer, SARS-CoV-2. What sort of virus had made them sick back then?
To find out, the researchers sequenced the genomes of viruses lurking in 1,322 excrement samples from musk shrews, rats, and bats, living in the mineshaft between 2012 and 2015. It was a glimpse into recent viral evolution.
Nine of the 293 coronaviruses identified were of the beta family, that of SARS-CoV-2. And the closest relative to the new coronavirus, with a 96.2% identical genome sequence, was RaTG13 – the same virus that was a very close match to the pathogen in the five early COVID-19 patients described in the February 3 paper.
So sometime during the latter half of the second decade of this century, did RaTG13 beget SARS-CoV-2? Further analysis of virus-laden samples from different times and species should fill in the gaps in the narrative. But of course we all know, have lived, the rest of the story.
My Most Important COVID Article
We may never know exactly when the critical species jump from bat to human transpired, whether it detoured through a bloody resident of a wet market, nor how long before clinicians noticed a new respiratory illness, or reported it. As clues accrue, the “start date” for the pandemic recedes into the autumn of 2019.
Clearly the new disease was already spreading by the time of the WHO’s first warning on January 5, four days after the seafood market implicated in the origin of the pandemic was closed “for environmental sanitation and disinfection.”
That market and similar settings all over the world are the problem: contact between humans and the raw flesh of other animal species, or with bat feces swimming with viruses, or crowded fowl or sneezing pigs or other scenarios and situations that juxtapose types of animals in ways that do not occur naturally.
We did it.
So of the 54 articles I’ve written about COVID-19, the most important is “How COVID-19 Arose and Amplified Along the Meat Supply Chain,” the DNA Science post from August 13.
Perhaps, by now, we’ve learned.
Our encroaching on the habitats of other animals spawned the current crisis. In tragic retrospect, we practically invited SARS-CoV-2 into our bodies, a tiny virus that will have killed millions of people by the time the pandemic winds down. But the past year has seen points of light, too: the invention (not “finding”) of vaccines in record time, the coming together of researchers and clinicians and the unprecedented communication of discoveries, and the new, and long overdue, respect for science and scientists among the public.
Now that vaccination is underway, it’s time to refocus on prevention. From personal choices to global policies, we can keep other novel viral pathogens from jumping animal species to us. Preserve natural habitats. Eat plants.
It’s been odd for me as a science writer during this strange year to have so suddenly pivoted from genetics, my area of expertise, to covering immunology, medical history, virology, vaccinology, epidemiology, and public health. For my fast adaptation I thank my mother for giving me the classic book Microbe Hunters when I was in fourth grade, a terrific course in virology in grad school, and writing and editing immunology chapters for my textbooks for many years. Most of my COVID articles were for this blog, the others published at Genetic Literacy Project, Medscape Medical News, The Niche, and MedPage Today.
It blows my mind that the year began with initial recognition of what would swiftly become the worst medical crisis of a century, a full-blown pandemic, yet end with deployment of the first vaccines. I cringe when politicians call it a “miracle.” Science isn’t about miracles.
Below is my chronology of the pandemic of 2020, with links, to the horror show that was 2020. I have a feeling ’21 is gonna be a good year.
The Wuhan Coronavirus Inspires a Look Back at the Discovery of Viruses
Will scientists ever get ahead of fast-mutating deadly health viruses? Exploring the coronavirus and the genetics of other plagues
COVID-19 Vaccine Will Close in on the-Spikes
Risk Factors for Death From COVID-19 Identified in Wuhan Patients
Early GI Symptoms in COVID-19 May Indicate Fecal Transmission
So You Have a COVID-19 Patient; How Do You Treat Them?
A Million COVID-19 Cases Already, Global Estimates Suggest
How the “F” word-flu-led to confusion as the coronavirus pandemic unfolded
Coronavirus Stays in Aerosols for Hours, on Surfaces for Days
Can Existing Drugs Treat COVID-19? From Viagra to Thalidomide to Cough Syrup
Digestive Symptoms Tied to Worse COVID-19 Outcomes
Comparing the coronavirus pandemic to past pathogenic threats: HIV, anthrax and Ebola
Drugs to Treat Novel Coronavirus Part 2: Rx for Restraints
Sophie’s Choice’ in the time of coronavirus: Deciding who gets the ventilators
‘Designed to be slow’: Why these coronavirus vaccines in the pipeline won’t be ready this year
A Brief History of Plagues and Pandemics: From the Black Death to COVID-19
Can genetics explain the degrees of misery inflicted by the coronavirus?
Normal Chest X-ray Doesn’t Rule Out COVID-19
Large Study of COVID-19 NYC Hospital Cases Shows High Mortality
‘At home’ coronavirus test? How CRISPR could change the way we search for COVID-19
Rare Disease Families Cope with COVID
May 5, 2020
Quest for coronavirus treatment inspires modern twist on antique technique using survivors’ plasma
May 12, 2020
The tricky path for using stem cells to treat coronavirus-ravaged lungs
May 14, 2020
Will the COVID-19 Pandemic End Like War of the Worlds or Logan’s Run?
May 19, 2020
Coronavirus immunity passports could create a world of ‘us and them’. But here’s why they make sense
May 28, 2020
The Fallacy of the “Make It So” Mentality to Rush a COVID-19 Vaccine
June 2, 2020
‘Humanized mice’: Chimeras fuel quest to treat chronic diseases, cancer and even COVID-19
June 4, 2020
Dr. Fauci Optimistic About COVID-19 Vaccine Progress
June 11, 2020
Protests and the Pandemic: Will COVID-19 Resurge?
June 18, 2020
How an Antibody Cocktail Against COVID-19 Channels the 3 Stooges – But is a Great Idea
July 6, 2020
Stem Cell Strategies Get Compassionate Use in COVID-19
July 16, 2020
A Tale of Two Clinical Trials: Gene Therapy for a Rare Disease and a Vaccine for COVID-19
July 23, 2020
Can Past Coronavirus Infection Protect Against COVID-19? Hints from Smallpox Vaccine
July 30, 2020
COVID Genomes Paint Portrait of an Evolving Pathogen
August 3, 2020
Vaccine ‘durability’: COVID-19 immunizations coming soon but will they last?
August 5, 2020
Sniffing Out Stem Cells Behind COVID-Skewed Olfaction
August 6, 2020
She Had Her Own Mutation, Sequencing Led to a Treatment and Major Genetic Discovery – Then She Died of COVID
August 13, 2020
How COVID-19 Arose and Amplified Along the Meat Supply Chain
September 10, 2020
How the Various COVID Vaccines Work
September 15, 2020
“Challenge studies”: Should we be testing COVID vaccines by intentionally infecting volunteers?
September 24, 2020
5 COVID-19 Updates: Cats, Kids, Seniors, Blood, and an Old Vaccine
October 14, 2020
Final weeks to approval: NIH’s Anthony Fauci and FDA’s Peter Marks on what’s ahead before we can expect a safe COVID vaccine
October 22, 2020
Can Some Antibodies Worsen COVID-19? The Odd Situation of Enhancement
October 26, 2020
Down Syndrome Tied to Tenfold Risk for Death From COVID-19
November 4, 2020
Waning COVID-19 Antibodies Expected, No Cause for Alarm
November 12, 2020
Genetic Clues in the Goop of a COVID Swab
November 18, 2020
T Cells May Tell Us More About COVID Immunity
November 19, 2020
Thinking About Thanksgiving? A Reminder of What COVID-19 Can Do To A Human Body
November 23, 2020
When it comes to COVID, nurture trumps nature – so far
November 26, 2020
Worse Than COVID? The Tasmanian Devil’s Contagious Cancer
December 3, 2020
Dr. Paul Offit Talks COVID Vaccines, With JAMA’S Howard Bauchner
December 9, 2020
Why Do Males Fare Worse With COVID-19? A Clue From Calico Cats
December 16, 2020
Are Old Vaccines Helpful Against COVID-19?
December 17, 2020
The First COVID-19 Vaccines: What’s mRNA Got To Do With It?