Science Counterpunch

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

Heavy breaths followed a claustrophobic chase around the hotel room. Peter Daszak was doing his workout run from the showers through the bedroom to the antechamber and back, again and again and again. The Chinese hosts in Wuhan had placed him in quarantine for two weeks, and the pressure, isolation, and restrictions were difficult to deal with at times. He was an outdoor person. Twice daily, a team in full hazmat gear would knock on his door to take his temperature. “It really makes you feel dirty. Contagious,” he remembered thinking. He was not the only one.

Marion Koopmans was two rooms away. “It was amazing; they were so strict. I really thought, ‘Okay, this is how plague victims must have felt.’ You really felt like contaminated waste, almost.” She showed me photos she’d taken at the time. “It’s dystopia; they have made a plastic corridor for us.” Plastic sheeting completely covered the hallway from top to bottom. They were sampled as per instructions: 5-second swabs and not a millisecond less. Everyone was suited up except them. Warning signs and restriction bands were everywhere. China had been COVID-free for months. She just hoped she would not get a fever from anything else because it was not clear what would happen if she did. And yet, they, along with eight other international experts, were finally there, where it all happened. “We had been asked before to be quiet about where we would go before,” she laughed, “then we landed in China and had an escort everywhere and a charade of media following us.”

Peter Daszak and Marion Koopmans were two obvious scientists to reach out to when the WHO was assembling a mission to Wuhan in January 2021. Peter, the British zoologist, and head of the non-profit EcoHealth Alliance, had worked for decades on understanding viral spillover from bats, identified the origin of SARS with Shi Zhengli from WIV, and worked together with various emergent disease collaborators all over the world. He would be on the WHO’s animal and environment working group, trying to make sense of what happened at the Huanan market.

I did not particularly want to serve. It irritated me. My big grant was canceled by Trump, and we went through months and months of misery. And I thought, “Why the hell should I help WHO? Doing the work that we should be doing for them?” That just seemed cruel, and then I am asked to volunteer for them?

On the phone, he told Peter Karim Ben Embarek, who had assembled the mission, that he didn’t want to do it. On top of that, his participation would invite terrible political attacks on the WHO. Embarek just replied, “What’s new?” The WHO has been under attack on a daily basis; he naively believed it wouldn’t matter. Then, the WHO mission chief reiterated the enormous significance this work would have for the world. After some back and forth, Peter said that he would be available to the group, but he did not want to do fieldwork. “Ben said okay, but he did not take this as an answer; he kind of treated me like I was on the team.” Peter shrugged at how he ended up on the mission. The WHO team knew what they were doing and why they wanted him. “They wanted access to Chinese scientists, not just [because of] the lab issue, but because George Gao and the Wuhan Institute of Virology were investigating the outbreak… so the WHO needed somebody close to them.” Reports suggested that Beijing had indicated he would be a good person to have on the team. As best I can tell from Embarek’s comments, the suggestion came from Shi Zhengli herself. “It’s obvious if you got a researcher who you’ve been working with for 20 years who has not ripped you off, who had been honest with them,” Peter explained the likely rationale. It is worth retelling how Peter came to be on the WHO team because many conspiracy theorists claim that he inserted himself purposefully to aid in a possible cover-up. His email records with Ben Embarek tell a much different story: one of hesitation and duty. Until October, he still did not want to go to Wuhan.

It was only on our first call when I saw the list that I had to begin to consider it. Fabian Leendertz was there, and a bunch of other people I had heard about. It was a very impressive team. Marion Koopmans was there too, and she is fantastic.

After that first video call, he decided to commit to the mission.

In the end, you just get carried over by the feeling of duty. This is what a scientist is supposed to do. If the outbreak of a global pandemic happens to be from a virus family you have been working on for years in the place you have been working, probably from the animals you have been working with, of course you should be sitting on that committee, trying to do everything you can.

The Dutch virologist Marion Koopmans, who was scanning me with a gazing look behind sharp spectacles and white, spiky hair as she listened in on our conversation, agreed with that sentiment. She has investigated countless outbreaks in her career. She had started with noroviruses, hepatitis A virus, bird flu, and arboviruses. During the Ebola outbreak in West Africa, she was responsible for the deployment of mobile laboratories in Liberia and Sierra Leone. One would be hard-pressed to find anyone more knowledgeable and experienced to study novel outbreaks. She was very quick and to the point. “Every virus, and with it every outbreak, is different,” she explained. However, “with every spillover, you have a couple of key questions.” Hospital records, patient samples, and molecular and sampling data tend to be spread out over multiple locations, times, and people. Her job was to make sense of it. For her, the WHO reaching out and wanting her on the team was “the honor of a lifetime.” She did not hesitate to say yes.

“I was leading the molecular epidemiology interaction. That collaboration actually was nice." She lauded her team and the Chinese collaborators. They basically had to figure out, from all the available data, which person, which genomic sequence, and what time. Putting that puzzle into place was challenging. The team made recommendations for analysis, and the Chinese side actually had scientists performing the work in real-time. “I think this group was maybe the least political because what you could do with genomics was not clear yet,” she laughed wholeheartedly. Indeed, the early epidemiologically linked sequences her team helped to establish and verify would hold incredibly important clues to the virus’s origin.

She was not a fan of the simple narrative that took hold that the Chinese were not sharing data with them. “Yes, there can be more transparency, but look at all that was shared.” She continued, “It was remarkable. There were no agreements in place. If somebody came to us and said, ‘Give us all your hospital and patient data,’ there is no way this would work.” Yet, as she says, the Chinese scientists tried hard to make much of it work.

That does not mean everything went smoothly, either. The WHO mission had two delegations: one of international scientists and one of Chinese scientists. The latter was constantly monitored and assisted by members of State Security, Foreign Affairs, and translators. “It was clear it is going to be this China-style process—you have these meetings where there is the director’s director, the director, the subdirector, and blah-blah—and everybody has to say something, and only then can you get to business.” Marion rolled her eyes. Working day and night analyzing data and being on group calls and meetings while in quarantine had been a strain, but their schedule afterward would not be much easier. The first two days out of quarantine, January 29th and 30th, they visited the Xinhua Hospital to interview doctors and staff and learn about patients.

There was the obligatory pol…

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

“They got a police escort to get us shoe shopping, and I basically wore a wedding dress… There are even photos in Pakistani newspapers… and I just thought, if I can give a talk wearing this, I can give a talk in anything.” Alice Hughes laughed wholeheartedly while I shook my head in giddy disbelief. It was a good day, which we both needed. She vividly recalled how she was culturally ambushed by her hosts on a day she was supposed to teach a course about spatial ecology in Pakistan in 2012. They needed her to put on a blue sari robe and traditional women’s shoes, which they could not find for her size anywhere in the city, despite chaperoning her through six shoe shops with a full police escort. This only came up because I had asked the renowned bat huntress about the most uncomfortable situation she had ever been in. She offered me this anecdote as an answer, which was telling in more ways than one.

Dressed in worn-out hiking shoes, a light jean shirt, and carrying a massive backpack, the 38-year-old professor sitting in front of me looked slightly out of place for a posh cafe in Zurich. She was a member of the university faculty in Hong Kong, and she has done her best to break any stereotypes one might have about ivory tower academics and women in academia. Her name appears in over 190 publications at the time of writing, and her resume is much closer to that of an accomplished male peer at the end of his career than someone her age. She is an adventurer, a world traveler, and a force to be reckoned with. At 17, she was the only one in her group to not get sick in the Peruvian rainforest. Drug traffickers had held her at gunpoint in Paraguay on the Brazilian border when she was 21. She had ventured too far while exploring; her colleagues had already filed an international missing person’s report. All alone, without knowing a word of Portuguese, she somehow talked her way out of it. At 23, her PhD was not spent behind a desk but was colored by visiting some of the remotest places in Southeast Asia. Climbing through picturesque mountain ridges plastered by checkered corn fields in Vietnam, traversing untouched lakes in Malaysia by rowboat, venturing deep into tiny caves in Thailand, or wading through rainforest creeks in southern China, her every day seemed like a nature documentary if it weren’t for dramatic motorcycle accidents, horrible falls in caves, and broken bones on remote islands while fending off angry snakes in her bed.

However, exploring hundreds of meters deep into low-oxygen caves, where some others never return, is her favorite way to spend her time. “Oh, remember the Thai cave where teenage football players got trapped by a flood that saw even a trained Navy Seal rescue diver die? Yeah, I was there too, kilometers deep.” She laughed again at my panicked expression. I would not be comfortable venturing into those narrow pits of darkness. Yet when I asked her about ever feeling some dread or panic on her trips, only the “Blue Sari Incident” came to her mind. Alice might not have worn a dress for the many years since (I quote: “I’m more comfortable in FieldKit even if it’s been soaked in cave water”), but she has explored hundreds of caves, captured thousands of bats, studied their ecosystems in more than a dozen countries, and continues to teach courses for students all over the world.

She lived for discovering new species of bats, fungi, lizards, or cave spiders, snakes, and scorpions; protocoling glow worms hanging from the walls and undescribed flying squirrels from the jungle; sometimes petting the occasional red panda; or investigating trafficked animals like pangolins, moonrats, muntjacs, raccoon dogs, and civets. Even mapping karst geography, local ecology and recording climate parameters were part of her routine. There was simply nothing about the natural world that didn’t fascinate her, and that made her incredibly knowledgeable. It is impossible to come away from a conversation with her without knowing some new and fascinating animal trivia that one must vow to read up on more. She delighted at the thought of being in places few humans have ever set foot in before. At times, her career seems much closer to an Indiana Jones-style adventure revamp than what one might picture as the dry academic research of an ecologist. “You know, my father wanted me to get married and be a homemaker since I was three,” Alice recalled, followed by some joshing around. “You might see me squeeze through a lot of narrow spots, but fitting in the narrow box of convention is the one tight spot I cannot accommodate.” It was a hilarious and carefree afternoon, a welcome distraction from her grim last few years.

After we sat down near the Zurich lakeside with ducks and swans gathering at our feet in hopes of a snack, I got her on a more serious note. Since she was eight, she wanted to be a conservationist. Listening to David Attenborough, Gerald Durrell, and other nature documentaries growing up in Great Britain, she remembered crying as a child about deforestation and habitat loss, about the unsustainable way we treated our planet. She lifted her hair behind her neck to pull up a modest necklace—a medallion with an extinct dodo on it, a sign of the Durrell Wildlife Conservation Trust—that she received as a child. She has been wearing it ever since, a reminder and talisman of her childhood pledge to save as much of the world as she could. We are all idealistic and naive when we are young, but as we grow older, most of us seem to forget or give up. Alice appeared to have found another way via science. “People see idealism as something to grow out of, rather than finding a pragmatic way forward where you can instrumentalize elements of it.” For her, saving the planet starts with truly observing it in all its detail, diversity, and vastness: the beautiful and the curious, the dangerous and the unconventional, the boring, the nerdy, and the slimy. She was in the business of understanding and saving ecosystems, not just token species that capture our attention. That’s what gets her up in the morning. That’s why she ventures into the wild, equipped with a geolocation device, a laptop, and whatever specialized gear she might need for the expedition or sampling, from basics like lights and ropes to diving gear, harp nets, field lab equipment, and what one of my friends would call a “bat Shazam”—a custom-made recording device that captures the echolocation sounds and frequencies from bats. Every bat species makes its own unique sounds. Usually, she has to listen with her bat shazam to what species are around before she can get research funding and a permit from the authorities to sample them.

Before the pandemic, she had finally found a place that would not get boring, even a second home, in Xishuangbanna—a large botanical garden and national park in the tropical Yunnan region of southern China. A biodiverse paradise nestled between green mountains with now-turquoise rivers cut out of the karst over the ages. A place of life and Chinese folk legends, and a hotbed for scientific collaborations. She was leading a team of 18 scientists, half of whom were bat researchers. She was a stable pillar of the small research community; her students loved her and came to her for advice. As one of the few female professors, she would also be a trailblazer and confidant for talented women in a male-dominated environment. Her publications often drew the jealousy of male peers, but her success and work ethic made her untouchable; many students from all over the world wanted to learn from her. And yet, one day, she had to leave it all behind.

By the end of 2021, she left as quietly as she could, crossing the border by foot to Hong Kong because it was less controlled than t…

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

I got interested in the lab origin controversy at an odd time in my life. After having spent a decade in biological labs for my research, I gradually developed an interest in systemic approaches to understanding biology. There are just too many moving pieces in a biological system to capture all, or even just the most relevant, causative molecular mechanisms of complex phenomena like cancer resistance. I always found analyzing genes one by one dissatisfying. I felt it would be more useful to find the right framework to explain what the larger rules, regularities, and limitations of their interactions might be. Towards the end of my PhD studies, I had done proteomics, metabolomics, and transcriptomics—the trifecta of despair when a project is not going well, some might joke—trying to understand my organoid model system. Imagine long, dry Excel lists with thousands of gene names, with some value and some statistical power behind them. But systems biology is about creating big data sets and analyzing them to discover informative, larger patterns. As biology transforms into information science, large quantitative methods have become more prominent. Data became destiny.

Accordingly, for my postdoc, I switched fields towards bioinformatics, learned how to code, and had the lucky opportunity to spend a few years in a machine learning lab to satisfy my curiosity. It was a personally enriching, albeit academically only semi-successful, period of my career. My experience, however, became handy later. When I decided to leave academia during the pandemic with vague ideas of writing about science for a living instead of, say, coding or pipetting, my dissatisfaction with not understanding the larger forces shaping the complex systems we are part of never really left me. Looking back, I must have sent over half a million of my words out on Twitter alone, the majority of them after being sucked into the man-made controversy. Originally in favor of lab leak speculations, I was getting all too familiar with the various contrarian scientists, conspiratorial actors, and conniving opportunists that thrived on this topic. Who had a point and who was making things up? Yet again, it seemed like there were just too many moving pieces to understand what was going on. Once more, I found myself curious about the larger forces—in this case, the complex dynamics within social media—that seemed to produce certain collective confusions in our public discourse. A different, more systemic approach was needed to bring them into the right frame. What caught my curiosity was the rise of the influencer economy.

“When I had the first thousand followers, I thought it was crazy that so many people wanted to hear from me,” Professor Angela Rasmussen (she prefers Angie) recalled the early days of her rise on Twitter. Today, the outspoken and sharp-tongued virologist is known for not taking b******t from anyone. Whether it is incompetent politicians, abusive contrarians, self-serving pundits, or out-of-touch institutions, if they make public declarations that go against what she knows the evidence to be, she is unwilling to let it slide. “The public deserves good information.” She is as sure of this today as she was in the early days of the pandemic. This simple conviction would lead her to become one of the most popular—and most harassed—virologists on Twitter, as well as a prominent figure in interviews, news reports, and articles. She admits she hasn’t always been confrontational, but it was a necessary skill she had to unfortunately learn to be listened to and to move up the ranks in a male-dominated academic environment.

Scientifically, the professor was occupying herself not so much with viruses per se as with their host's response to them. This dates back to her PhD, when she attempted to change a rhinovirus to infect mice with a mild flu. Researchers lacked any model systems to study these viruses plaguing the human upper respiratory tract. The project was mostly a struggle; it turned out that her rhinovirus was just not well suited for its new host and had a really hard time surmounting the animals’ basic immune responses to make them sick. After her seemingly endless uphill battle—speaking from experience, that is almost any PhD project—her curiosity about how much the host plays a role in infection and disease progression was ignited. Over the subsequent years, she has studied the host's varied responses to more and more dangerous viruses. Why do some patients with hepatitis C virus infection develop carcinomas rapidly, while for most others it is a slow process? Why was MERS, another zoonotic coronavirus, self-limiting and transient in Rhesus macaques but somehow causing deadly disease in humans? Why are some mice susceptible to a mouse-adapted Ebola virus, whereas others are resistant? What genetic factors decide which host gets to live or die?

While considered niche questions at the time, when the Ebola outbreak hit western Africa in 2013–2014, scientific interest in this topic suddenly spiked. Editors at the prestigious journal Science—who had first rejected her work identifying genetic factors responsible for Ebola susceptibility—came back and begged her to send them the manuscript again. An outbreak had suddenly made her findings highly relevant, putting Angie’s work on the map. “I still tell my students that getting published in the big journals is often luck; my Ebola paper would not have been any worse if published in PLOS Pathogens instead of Science magazine,” she explained. Unfortunately, these lucky events have become almost necessary to make it in the competitive world of science. It’s publish or perish. For Angie, the visibility of her Ebola work in a prestigious journal gave her enough wind in her sails to study a whole range of other virus-host interactions, from Lujo to Lassa to ultimately SARS-CoV-2. But with the latter, a whole different kind of exposure was soon to befall her.

In January 2020, she had less than a hundred followers on Twitter. She only started tweeting more frequently about the new virus (still called nCoV2019 at the time) when sensationalist headlines tended to run with a story before the evidence was in because it annoyed her. “I have been critical of journalists & armchair scientists who have been stoking #nCoV2019 panic,” she wrote at the end of January 2020 before highlighting some bad scientific takes that upset her. She bumped heads publicly with Pulitzer Prize-winning science writer Laurie Garrett and especially the mono-dramatic Harvard epidemiologist Dr. Eric-Feigl Ding, who painted a very stark picture of how bad this pandemic would turn out. Both cared more about getting the message out and jolting people into action than getting all the details straight. In contrast, Angie tended to be on the cautious side, not willing to step beyond the evidence—maybe even be too conservative about it. Science is a slow process, and even dramatic results usually require replication, contextualization, and further follow-ups. Angie was a cooler head, if you will, but one that had very little patience for dramatic announcements about inaccurate R0 numbers or freakouts about asymptomatic cases. Her smackdowns (strong-worded rebuttals) of Dr. Feigl-Ding’s sensationalist tweets, coupled with her “matter-of-fact” expert explainers, quickly found a receptive and thankful audience. She would gain over 1,000 followers in the second week of February 2020.

Her public spats soon increased as interest in the ins and outs of virology spiked, and the politicization of the pandemic gained momentum. The following week, she gained over 1,500 followers, mostly because of her response to US Senator Tom Cotton’s bioweapon fearmongering, which she followed up with…

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

The hollow sound of our footsteps echoed through the boundless darkness; a solemn silence had befallen us, like in a temple. Our cave guide held up a single old gas lamp, the only source of light. The flickering flame instilled the unmoving stone walls and pillars with life. Salt crystal veins grew over some walls, pure white, like frozen spiderwebs on a frosty graveyard. Ducking down and crawling through a narrow passage, we entered an underground dome. The constrained light did its best to fight back the darkness, with shadows seemingly chasing, encircling, and reaching for us. Bizarre shapes and figures carved from rock, resembling dogs and cat-like canines, chased us along our way. Some other formations evoked memories of lush forests, candle wax, and mossy grass, petrified here for immortality. Who or what could have created these shapes that played a trick on my eyes? For centuries, these rock formations were subject to interpretation by the locals. Like us, they would see in them animals and plants, contemporary objects, even spirits or stories. Elephants, lotuses, passion fruit, a candle, and a hermit shooting fire out of his eyes were among the objects they perceived. Clearly, what our guide stated as a matter of fact, or whatever elements others had perceived in the past, would not necessarily be intuitive to us. These figments were haunting yet oddly bewitching; the scars in the rocks were the perfect vehicle for the scars in our minds: tortured figures, painful convolutions, death, and decay.

A jovial mechanical skeleton that stood at the entrance to Chiang Dao Cave, shaking and waving hands at tourists, rushed back into my mind. “It’s a reminder that we should laugh at death,” Peter Daszak said, pointing out its purpose. He had seen similar things all over Thailand, especially at cave entries. There was, of course, a cultural history. Ajahn Mun, a monk credited with forming the Kammaṭṭhāna, or the Thai forest tradition of Buddhism that subsequently spread throughout Thailand, was known to seek out secluded places in the wilds to mediate. The reclusiveness of caves was meant to help eliminate the defilements in the mind, develop detachment from material things, and thus deepen Buddhist practice. He is said to have attained anāgāmi — the breakage of being reborn into the human world — after meditating for three years in the Sarika Cave in Ratchaburi, not too dissimilar from Chiang Dao. At first, the local villagers wouldn’t take Ajahn Mun to the cave because of a local legend. They believed a terrestrial deva (a spirit or deity) was occupying the cave and killing intruders. This was supported by serial accounts of monks stricken with fatal illnesses after residing in the cave. And indeed, on the fourth night of staying there, Ajahn Mun would fall sick to the point of passing blood. No herbal medication would help; only surrendering to the Buddhist path would save him, so the retelling goes. Many myths contain a kernel of truth, and the occurrence of a mysterious illness befalling humans in caves is certainly not unheard of. In fact, these stories are usually what motivate scientists like Peter Daszak and others to investigate caves in the first place. But not today. We were trying to understand a different enigma, one no less worthy of investigation.

¨What is the reason we tend to perceive patterns that are not real? It is a question that has fascinated me for a long time, because much of our behavior comes down to our quick inferences, not careful analysis.

§

In early February 2020, a WeChat message appeared:

The novel 2019 coronavirus is nature punishing the human race for keeping uncivilized living habits. I, Shi Zhengli, swear on my life that it has nothing to do with our laboratory. …I advise those who believe and spread rumors from harmful media sources, as well as those who believe the unreliable so-called academic analysis of Indian scholars, to shut their stinking mouths.

The Chinese bat researcher Shi Zhengli, who I will get to know as a very kind and polite person, finally had enough. She was at the end of her wit. Not only had she become known as the “Batwoman,” she had also become the target of conspiracy theorists, hate mobs, foreigners, and fellow countrymen alike just a week prior to posting this message. Her instinct was to fight rumors. Her mistake? She was too honest at the wrong time. Both now and a week earlier.

When the dramatic lockdown in Wuhan on January 23 drew worldwide attention to the outbreak, few outside of science realized another remarkable event on the same day. Zhengli and her team had uploaded a scientific publication to a preprint server. It was their own analysis of the new viral genome, compared to other SARS-related coronaviruses her lab had specialized in. Fifteen years of trying to figure out where SARS came from had yielded a sizable collection of bat samples for analysis. From thousands of samples, mostly bat saliva, urine, or poo, they would extract RNA — the less stable little brother of DNA — and send it to sequencing over the years. Their goal, like a DNA test we humans might do today, was to catalog the wider SARS-related viral family. With most samples, they could only look for a mere fingerprint of the degraded viral genomes, as most viral particles would be chewed up by enzymes, inactivated, or otherwise rendered dysfunctional in these samples. Naturally, they also wanted to have complete viruses. Shi Zhengli’s lab continuously attempted to isolate intact virus particles from some of these samples to grow and study them in the lab. But even after a decade of hard work, all they ever managed to isolate and grow were three bat viruses, all related to SARS. Virus isolation was incredibly challenging work. Other groups, in the US and elsewhere, had gone years without ever isolating bat viruses for cultivation. Cataloging these fingerprint sequences, even whole genomes, was much easier.

That is why Zhengli had hundreds of cataloged samples in the lab database by the time she went to look for family members of the novel coronavirus in Wuhan. She found a cousin. Formerly annotated as Sample 4991, collected from an old copper mine shaft seven years prior, the sequences would be re-christened and given the proper virus name of RaTG13: Ra for the bat species, Rhinolophus affinis; TG for Tongguan, the town where it was found in Southern China; and the number 13 for the year of its discovery. Collected from bats in 2013, this cousin exhibited up to 96% similarity to the new virus, making a compelling case that SARS-CoV-2 came from bats. She rushed to get the results published, and by January 23, she would upload the manuscript on a preprint server to give the world early access to her findings. A preprint server — an online repository without peer review — provides an early view of new analyses before they are submitted to scientific journals for thorough quality control checks. This mostly ensures that trivial and basic mistakes, sloppy science, or unsound and unscientific ideas are challenged before final publication.

During the pandemic, many researchers used preprint servers to quickly share new analyses with the wider community, but it also led to many half-baked ideas getting undue publicity. For example, on January 17th, a preprint implied that SARS-CoV-2 might have come from snakes, animals not really associated with CoVs in the first place. Zhengli’s paper, outlining a likely bat origin, was much more credible, and it was immediately taken up for peer review and published in the journal Nature on February 3rd. However, by the time it was published, Zhengli was already under fire.

We mentioned last chapter that on January 30th, a group of Indian researchers used the RaTG13 sequence from Zh…

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

“Without a harmonious and stable environment, how can there be a home where people can live and work happily?” Xi Jinping's words on New Year’s Eve in 2019 were intended to reign in pro-democracy protests in Hong Kong. For months, the city has been in a renewed battle for its soul against the oppressive and subversive influence of the Chinese Communist Party (CCP). Tens of thousands, if not hundreds of thousands, were expected to march again on January 1, 2020. The goal was to maintain political pressure after a landslide victory of pro-democracy candidates in district court elections weeks prior. Six thousand police officers were deployed to deal with potential unrest—the wrong signal to send, given previous escalations and excessive police brutality. “Safety concerns” led to the cancellation of the midnight fireworks despite months of planning. The next day, a peaceful protest with families, kids, and the elderly, often dressed up in costumes, quickly escalated into violence, tear gas, and mass arrests. The police blamed some radical student agitators who had hijacked the march. Maybe it was inevitable; tensions had been high for months. ​​Universities and their students were front and center of the recent civil rights movement, and the police claimed these institutions had become “weapon factories.” As a result, sieges and raids on universities have become part of campus life over the last few months.

The last thing the exasperated Jasnah Kholin (pseudonym) needed at the time was “one more f*****g thing to worry” about. The unfiltered coronavirus researcher (who swore like a sailor) now uses a pseudonym to hide her real identity for safety reasons (I promised her that I would omit any details that she felt would compromise her safety). She, like many others, had been at these protests for civil rights and experienced firsthand how they were squashed by the police, often with force. Once, the young academic had a pepper ball barely miss her face that would certainly have knocked her out. Another time, the police came to pick her up, and she was in prison for weeks before they let her go. Wrongfully suspected or not, she was among the lucky few who got out uncharged because there was no evidence to place her at the scene. It’s not surprising she had an innate distrust of the Chinese authorities, who were more and more entrenched in Hong Kong, her only home.

When she heard about the pneumonia outbreak in Wuhan around New Year's on ProMED-mail, an internet service supported by volunteers that tracks unusual health events, she immediately started screenshotting and saving every bit of information that was coming out of Wuhan: every pdf, every Weibo message, every picture, all kinds of vital info. Because of Chinese censorship, information can sometimes be lost within minutes of appearing online. What foresight! “Oh, I am very familiar with how information works in China,” she would later explain to me. In any crisis, Chinese authorities shut down the information flow to try to control the narrative. This is not unusual; it happens for things big and small, important or insignificant. This approach might even help to contain false and harmful rumors during a crisis. However, it also creates a layer of obfuscation and political spin that can make it challenging to assert pertinent facts with any confidence. For example, consider how dangerous the virus was and how it spread. In the very beginning, the Chinese authorities claimed that the virus ​​was barely, or not at all, transmissible human-to-human in an attempt to not cause panic, a claim that was still being repeated by the World Health Organization (WHO) on January 14th.

Jasnah Kholin and her academic colleagues in Hong Kong did not believe any of it. They had been burned before. On January 4th, Jasnah caught wind of a concerning story on Weibo (Chinese Twitter) about an infected father who had not gone to the Huanan market. Chinese censors deleted it within the hour. Yet for her, already gathering as much from rumors, the specifics of this story were the final indication of human-to-human transmission, vehemently denied by Chinese authorities until weeks later. Many other coronavirus experts were just as suspicious as her, including SARS-veterans Yuen Kwok-Yung, a giant among Hong Kong's infectious disease experts, and Leo Poon, who developed the first PCR diagnostic for SARS in 2003. They all independently read the signs on the wall and raised the alarm in Hong Kong about the human spread. “SARS was a generational trauma for Hong Kong; this was not our first f*****g rodeo,” Jasnah kept cursing. According to her, SARS-1 had also been much closer to a pandemic than people commonly realize. However, all of them knew this and did everything they could to make the rest of Hong Kong take this seriously.

Most likely, their actions at the time helped the city avoid the worst. By any measure, Hong Kong's early and harsh response has been a success story. With the high uncertainty and unclear messaging from mainland China, it fell mostly to outbreak professionals and coronavirus academics like Jasnah to exert caution and inform society. Speed is everything in emerging outbreaks; the longer it takes to mount collective action, the worse it usually gets. Because of their warnings, both the population and Hong Kong’s chief executive would take the threat seriously and implement strict pandemic prevention protocols. From the first to the fourth wave, Hong Kongers succeeded where most of the world would fail; they suppressed community transmission of the virus.

Yet not everybody was happy. Pro-democracy protests saw their momentum decline under new restrictions. They were especially concerned about the ubiquitous use of contact tracing and digital surveillance, which they feared would be a new and powerful tool in the hands of the police. In the following months, civil rights protests were canceled, and the CCP exerted even more political pressure on Hong Kong. Stuck between a rock and a hard place, Jasnah, like many in the wider Chinese diaspora, wished that somebody would blow the lid off this thing in those early days. Why did the CCP initially deny the obvious human-to-human spread? Why the silencing of doctors? Did the communist party really think they could hush up the severity of the outbreak? When will the world wake up about the Chinese government? Somewhat ironically, the tumultuous cultural and political moment, along with this appropriately placed mistrust, made the Chinese diaspora, especially Hong Kong, very susceptible to a different type of viral spread.

Since December 30, when the outbreak of pneumonia of unknown etiology became official, sporadic voices both on Chinese and Western social media have put the connection of WIV’s biosafety level 4 (BSL-4) laboratory into public spaces, albeit in the context that they had the capacity and expertise there to handle the outbreak. The positive connotation did not last long. Within five days, this information would be presented by a pro-civil rights protester in Hong Kong to suggest quite a different connection. A tweet from the time, still visible today, reads:

My guess is China has ordered an attack on Hong Kong with bio-weapons to stop the continuous protests. Like in 2003, the CCP assisted the outbreak of SARS in HK to pave the way for #CEPA. You can't underestimate how evil this regime is. #Bioweapon

Others echoed the idea, highlighting the particular timing right after the New Year’s protests that ended in violence. While none of these rumors gained any wide-reaching traction, they symbolized both fear and suspicion about the CCP and what they would or would not do. Suspicion was warranted. Independent information from Wuhan was hard to come …

Note: This is a freely accessible serialized version of Lab Leak Fever. Audio voiceover was AI generated for accessibility. Find an overview of all chapters here or consult the book website for further information.

A disturbingly dry cough broke the silence of the Malaysian night; the pigs resting under the mango trees had been uneasy that day. Loud, whooping breaths filled the backyards of small farmhouses. Pig farming had been a family business in the villages of Bukit Pelandok and Sikamat, and for the Foochow Chinese, it was a source of pride and good income. While most Malay are Muslim and not permitted to touch pigs, for Mr. Yap, handling these animals would feed his family of five, the youngest just three years old. The pork supply chain had recently exploded into a huge industry in Malaysia, employing thousands and lifting many more out of poverty. Within the lush and dense green vegetation, small streets connected scattered farmhouses, and the many small pig operations that originally started in backyards kept expanding, requiring more space and cultivation of the land.

Mr. Yap’s days were humid and hot, but the nights were pleasant, and he would often sit outside until the tropical sunset. A brighter and more hopeful future lay ahead for the immigrant family. He had felt a bit tired the last few days, and then he developed a fever on that fateful Monday in March 1999. A week later, he fell into a mysterious coma, never to wake up again. He would not be the only one.

“My father died of Nipah virus,” Wee Chee revealed timidly. “So did my uncle.”

Mr. Yap’s then-three-year-old daughter was sitting in front of me 23 years later. She was tall with straight hair, and her large round glasses amplified her intelligent mocha eyes, exuding curiosity. She was a young researcher on her journey to earn a PhD in virology at one of the best labs in Singapore. “I don’t remember him; I was too young.” Her soft voice and casual tone were in stark contrast to the severity of the revelation about her father. I felt a bit uneasy interrogating her about the painful past, but I needed to understand what drove her to be out here with the other virus hunters.

“The authorities first thought it was Japanese encephalitis,” she explained, a virus transmitted by mosquitoes. The year before, after the first unusual encephalitis casualties in 1998, the pig farmers in Malaysia received vaccinations. Despite taking mosquito protection measures, the outbreak continued unabated, and the death toll skyrocketed. Something did not add up. Although some of the initial patients demonstrated cross-reactivity with Japanese encephalitis antibodies in serological assays, indicating their recent exposure to the virus, not all patients tested positive. Some would even get sick after being vaccinated against the Japanese encephalitis virus. These cases were attributed to an ineffective vaccine — something almost unheard of. Confused, the department heads were more concerned with confirming Japanese encephalitis through PCR tests rather than challenging their assumptions. In the meantime, the authorities would continue with their prevention measures, even telling the pig farmers it was safe to keep working. Wee Chee’s father trusted them despite knowing his pigs had died too.

However, Dr. Kaw Bing Chua, a tenacious local scientist had developed a hunch that it was a new virus that caused the disease, jumping over from pigs to farmers. With a subtle tone of admiration in her voice, Wee Chee briefly recounted his history. He would isolate the virus from the cerebrospinal fluid of patients and attempt to cultivate it not only in insect cell lines, as is indicated for the Japanese encephalitis virus, but also in human, canine, pig, and monkey cell lines available at the University Malaya Medical Center. He discovered that the isolated virus would not only grow in various cell lines but also show a cytopathic effect — the infected cells looked rugged and sick under a microscope, quite similar to syncytial virus infection, a respiratory pathogen. Excited, he raised the alarm, but his supervisor initially attributed his findings to contamination. He had to keep pushing. Time was working against them, as a new wave was killing more farmers. With the help of the CDC in the US, he eventually figured out that the suspected new virus was of the paramyxoviridae family.

“Paramyxoviridae,” a word that rolled off Wee Chee’s tongue easily. Even today, I mess up sometimes. It meant that the new virus, later named Nipah, was part of the same larger family as measles, mumps, and many parainfluenza cold viruses causing bronchitis or pneumonia. This insight had dramatic significance. The control measures against a paramyxovirus are completely different from the mosquito-transmitted Japanese encephalitis virus. The authorities had to switch tactics, which they did after a short review process.

Unfortunately, the necessary policy change would come too late for Mr. Yap, who was infected just two days prior to that recognition. Two freaking days. A sinking feeling entered my gut. “If actions would have followed immediately…” Wee Chee ended her thought mid-sentence. I understood. Nothing was to be gained from what-ifs anymore. The history of emergent diseases is often one of cruel timing and unlucky circumstances. Mr. Yap was among the last of the farmers to become infected before the pigs were finally identified as the intermediate culprits spreading the disease to humans. Pig farms were shut down, over a million pigs were culled, and a half-billion-dollar industry crashed overnight. While “what happened” was eventually figured out and the outbreak stopped, the victims and impacted families were often left with no answer as to “why did it happen?”. Why did Nipah appear in Malaysian pigs, and when and where did it appear? Why did nobody see it coming? And, perhaps most crucially, could it happen again?

Disease outbreaks are almost always shrouded in mysteries and uncertainties. The true origin story and transmission route of the Nipah virus, a pathogen that can lurk in fruit for days, was only worked out conclusively years later. Leading the effort were the talented scientific teams of Dr. Linfa Wang from Duke-NUS Medical School in Singapore and non-profit organization EcoHealth Alliance, headed by the zoologist Peter Daszak. This was a whole decade before their research into pandemic outbreaks would become controversial. It was long before the global spotlight fell on them and their close collaborator Shi Zhengli from the Wuhan Institute of Virology (WIV). Back then, they had found that pig farms had not only extended into local fruit bat territory, but also the plantation of fruit carrying trees like Mango trees around the farms had attracted bats. While feasting, some of the bats ended up contaminating the tree fruits with their saliva full of Nipah virus. Their leftovers or half-eaten pieces would fall to the ground, where they would remain infectious for days. Some of these contaminated fruits were snuffed up and eaten by the pigs.

Given the factory farming environment, the unlucky farm animals would become infected, even intermediate reservoirs of Nipah. Usually, such an outbreak in animals would burn itself out. Adult pigs would be culled, die off, or gradually develop immunity. Yet Peter Daszak’s team could show through epidemiological modeling that it was the young piglets, coupled with the rapid breeding and selling practices of farmers, that provided fresh immune-naive hosts to sustain the outbreak. Protected by Nipah antibodies from their immune mother sows while being raised, the moment these piglets got weaned off to be sold to other farms, they could become infected by Nipah. The Foochow farmers, who bought those piglets to raise them for their backyard businesses, would gradually spread the outbreak to other provinces. Like Mr. Yap, most of them would eventually contract the infection, and four out of ten wo…

With the GOP ramping up voter manipulation efforts for the general election, the “gain-of-function lab leak” myth is back in full swing

Yesterday, the GOP-led House Select Subcommittee on the Coronavirus Pandemic announced in a grandstanding letter the public interrogation of Dr. Peter Daszak, President of the non-profit organization EcoHealth Alliance.

This announcement is the second one this week, following an earlier such proclamation addressing the editors-in-chief of the flagship scientific journals Nature, Science, and TheLancet.

The announcements were coordinated with multiple right-leaning news outlets such as Fox News and the Washington Times, who had long articles lined up the moment the announcement went public. Further such announcements of public interrogations are expected, ultimately leading to the GOP-led public haranguing of Dr. Anthony Fauci, who will likely be required to testify in early summer.

The origin controversy is political and polarizing. The “gain-of-function lab leak” myth is emotionally powerful; it stokes fears about reckless, unaccountable, and mad scientists who performed arcane experiments that led to a deadly chimeric pathogen causing the pandemic. A flask monster. The myth is also hopeful; it offers the illusion that if only somebody can stop them, we will be spared another tragedy like COVID-19.

And who would not want to vote for the politicians who promise to hold these mad scientists accountable? Right?

These efforts from the GOP are part of a larger media manipulation and voter mobilization strategy for the upcoming general election.

Yet these upcoming battles over the origin controversy are not just about a handful of scientists and public health officials, they are a sign that science and an evidence-based worldview as a whole have come under pressure this election season.

While Trump is consolidating power and acquiring old allies in the media, disinformation researchers and journalists who track manipulation campaigns have similarly been harassed, discredited, and smeared by elected representatives and their client propagandists.

As the NYT apt headline writers put it: Trump’s allies are winning the war over disinformation.

“... Half of politics is "image-making", the other half is the art of making people believe the image” ― Hannah Arendt, Crises of the Republic: Lying in Politics, Civil Disobedience, On Violence, and Thoughts on Politics and Revolution

In the presence of so much manipulation and power, standing up for an evidence-based worldview is as much a duty as an act of courage.

Science is an important guardrail of democracy because of its unique ability and role to solve informational conflicts and dispel false myths. That puts it in confrontation with usurping politics that aim to rewrite reality to fit ideology.

I am not an important person, I have no insights to give into what best to do in politics, nor do I command the attention of large audiences. But the small thing I can do is to address the “gain-of-function lab leak” myth the best I know how. With science, curiosity, and an appreciation for the vastness of our complex world.

This is where you will find me putting my effort in the near future.

See you next week with the release of my big article titled:

Treacherous Ancestry, a phylogeographic hunt for the ghosts of SARS-COV-2

Cheers,

Philipp

Update April 12: Here is the full article now

The lab leak hypothesis is dead, but the lab leak myth will never die.

A new paper makes the rounds in the media by claiming a risk assessment score sheet can determine the "unnatural" nature of the COVID-19 outbreak in Wuhan. A stark contrast to the scientific consensus on zoonotic spillover.

Over the years, we have seen many such probabilistic, Bayesian, or “common sense” analyses from various sources and all of them were of dubious quality and distributed by dubious actors with a very limited grasp of scientific evidence. However, this does not mean that alternative methods for looking at a problem can not add valuable insights.

Will a risk assessment questionnaire finally offer something new? A hard look at the facts? A real conceptual contribution to the scientific literature? Or is it going to be what I tend to call a “meme paper”, abusing the format of a scientific article to launder unsubstantiated opinions and influence public perception?

To answer this question, I invited two fantastic guests for a scientific discussion:

Prof. Alice Hughes, a conservation biologist, bat huntress, and directly involved in the scientific search for the origins of SARS-CoV-2. She has published multiple papers of critical importance on the topic and continues to research with her team at the University of Hong Kong.

Dr. Sam Gregson is a former CERN physicist, scicomm YouTuber, and bad statistics debunker. He has monitored bad actors and sensationalist claims on the origin topic while giving renowned experts room to lay out the scientific case for a zoonotic origin of the pandemic.

If you see somebody reference this new paper as strong evidence for a lab leak, please share our video discussion to correct the record. Thank you!

PS: If you have not gotten enough about this topic, I also was interviewed this week by the journalist Walker Bragman asking about the status of the origin controversy.

I think this was a very nice conversation and some meta-discussion about the forces driving the lab leak myth, despite it having no evidence behind it.

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