WIV Database of Viruses was altered on Dec. 30, the day before China
notified WHO
Newsletter published on May 8, 2020
(1) Several Labs in Wuhan could have been source of Covid-19
(2) Article by Chinese scientists, now removed, lists WIV & WHCDC as
likely sources
(3) WIV Database of Viruses was altered on Dec. 30, the day before China
notified WHO
(4) While Shi Zhengli was on a train from Shanghai to Wuhan, alterations
were made to her database
(5) Shi Zhengli speaks about SARS at TED-like talk in 2018
(6) Shi Zhengli article in Scientific American
(7) Virologist: WE INTRODUCED A FURIN-LIKE CLEAVAGE SEQUENCE in the S
protein
(8) US Patent for Chimeric Coronavirus Spike Proteins lists Ralph Baric
as Inventor
(9) Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function
Research
(1) Several Labs in Wuhan could have been source of Covid-19
by Peter Myers, May 8, 2020
Wuhan Institute of Virology (WIV), where Shi Zhengli runs the BSL-4 (P4)
lab, is regarded as the leading contender for the origin of Covid-19.
She has told how she could not sleep with worry that her lab might have
been the source, but found that her sample viruses did not match Covid-19.
She has had extensive involvement with US researchers including Raplh
Baric, and is presumably good friends with them. No doubt they have
vouched for her. However, she is not in control of WIV.
Her P4 lab would not be the only lab at WIV. What are the others? Did
any of them have access to her samples?
Where does China's military fit, in all of this? Does it have labs akin
to Fort Detrick? Given that Wuhan is China's research centre on viruses,
could the military have a lab at WIV or nearby?
There's also Wuhan University of Technology (WUT), which bribed Charles
Lieber of Harvard to transfer nanotechnology.
And Wuhan Center for Disease Control & Prevention (WHCDC), which has a
virology lab about 280 meters from the wet market which was thought to
be the source of Covid-19.
See item 2, and map of Wuhan showing WIV, WCDC, & Huanan Seafood Market:
(2) Article by Chinese scientists, now removed, lists WIV & WHCDC as
likely sources
ORIGINAL AT
Was at (but removed) https://www.researchgate.net/publication/339070128
The possible origins of 2019-nCoV coronavirus
Preprint - February 2020
DOI: 10.13140/RG.2.2.21799.29601
2 authors, including:
Botao Xiao
South China University of Technology
Some of the authors of this publication are also working on these
related projects: project National Natural Science Foundation of China
(11372116)
All content following this page was uploaded by Botao Xiao on 06
February 2020.
The user has requested enhancement of the downloaded file.
The possible origins of 2019-nCoV coronavirus
Botao Xiao12 and Lei Xiao3
1 Joint International Research Laboratory of Synthetic Biology and
Medicine, School of Biology and Biological Engineering, South China
University of Technology, Guangzhou 510006, China
2 School of Physics, Huazhong University of Science and Technology,
Wuhan 430074, China
3 Tian You Hospital, Wuhan University of Science and Technology, Wuhan
430064, China
The 2019-nCoV coronavirus has caused an epidemic of 28,060
laboratory-confirmed infections in human including 564 deaths in China
by February 6, 2020. Two descriptions of the virus published on Nature
this week indicated that the genome sequences from patients were 96% or
89% identical to the Bat CoV ZC45 coronavirus originally found in
Rhinolophus affinis 1,2. It was critical to study where the pathogen
came from and how it passed onto human.
An article published on The Lancet reported that 41 people in Wuhan were
found to have the acute respiratory syndrome and 27 of them had contact
with Huanan Seafood Market 3. The 2019-nCoV was found in 33 out of 585
samples collected in the market after the outbreak. The market was
suspicious to be the origin of the epidemic, and was shut down according
to the rule of quarantine the source during an epidemic.
The bats carrying CoV ZC45 were originally found in Yunnan or Zhejiang
province, both of which were more than 900 kilometers away from the
seafood market. Bats were normally found to live in caves and trees. But
the seafood market is in a densely-populated district of Wuhan, a
metropolitan of ~15 million people. The probability was very low for the
bats to fly to the market. According to municipal reports and the
testimonies of 31 residents and 28 visitors, the bat was never a food
source in the city, and no bat was traded in the market. There was
possible natural recombination or intermediate host of the coronavirus,
yet little proof has been reported.
Was there any other possible pathway? We screened the area around the
seafood market and identified two laboratories conducting research on
bat coronavirus. Within ~280 meters from the market, there was the Wuhan
Center for Disease Control & Prevention (WHCDC) (Figure 1, from Baidu
and Google maps). WHCDC hosted animals in laboratories for research
purpose, one of which was specialized in pathogens collection and
identification 4-6. In one of their studies, 155 bats including
Rhinolophus affinis were captured in Hubei province, and other 450 bats
were captured in Zhejiang province 4. The expert in collection was noted
in the Author Contributions (JHT). Moreover, he was broadcasted for
collecting viruses on nation-wide newspapers and websites in 2017 and
2019 7,8. He described that he was once by attacked by bats and the
blood of a bat shot on his skin. He knew the extreme danger of the
infection so he quarantined himself for 14 days 7. In another accident,
he quarantined himself again because bats peed on him. He was once
thrilled for capturing a bat carrying a live tick 8.
Surgery was performed on the caged animals and the tissue samples were
collected for DNA and RNA extraction and sequencing 4,5. The tissue
samples and contaminated trashes were source of pathogens. They were
only ~280 meters from the seafood market. The WHCDC was also adjacent to
the Union Hospital (Figure 1, bottom) where the first group of doctors
were infected during this epidemic. It is plausible that the virus
leaked around and some of them contaminated the initial patients in this
epidemic, though solid proofs are needed in future study.
The second laboratory was ~12 kilometers from the seafood market and
belonged to Wuhan Institute of Virology, Chinese Academy of Sciences
1,9,10. This laboratory reported that the Chinese horseshoe bats were
natural reservoirs for the severe acute respiratory syndrome coronavirus
(SARS-CoV) which caused the 2002-3 pandemic 9.
The principle investigator participated in a project which generated a
chimeric virus using the SARS-CoV reverse genetics system, and reported
the potential for human emergence 10. A direct speculation was that
SARS-CoV or its derivative might leak from the laboratory.
In summary, somebody was entangled with the evolution of 2019-nCoV
coronavirus. In addition to origins of natural recombination and
intermediate host, the killer coronavirus probably originated from a
laboratory in Wuhan. Safety level may need to be reinforced in high risk
biohazardous laboratories. Regulations may be taken to relocate these
laboratories far away from city center and other densely populated places.
Contributors
BX designed the comment and performed literature search. All authors
performed data acquisition and analysis, collected documents, draw the
figure, and wrote the papers.
Acknowledgements
This work is supported by the National Natural Science Foundation of
China (11772133, 11372116).
Declaration of interests
All authors declare no competing interests.
References
1. Zhou P, Yang X-L, Wang X-G, et al. A pneumonia outbreak associated
with a new coronavirus of probable bat origin. Nature 2020.
2. Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human
respiratory disease in China. Nature 2020.
3. Huang C, Wang Y, Li X, et al. Clinical features of patients infected
with 2019 novel coronavirus in Wuhan, China. The Lancet 2019.
ps:
4. Guo WP, Lin XD, Wang W, et al. Phylogeny and origins of hantaviruses
harbored by bats, insectivores, and rodents. PLoS pathogens 2013; 9(2):
e1003159.
5. Lu M, Tian JH, Yu B, Guo WP, Holmes EC, Zhang YZ. Extensive diversity
of rickettsiales bacteria in ticks from Wuhan, China. Ticks and
tick-borne diseases 2017; 8(4): 574-80.
6. Shi M, Lin XD, Chen X, et al. The evolutionary history of vertebrate
RNA viruses. Nature 2018; 556(7700): 197-202.
7. Tao P. Expert in Wuhan collected ten thousands animals: capture bats
in mountain at night. Changjiang Times 2017.
8. Li QX, Zhanyao. Playing with elephant dung, fishing for sea bottom
mud: the work that will change China's future, thepaper 2019.
9. Ge XY, Li JL, Yang XL, et al. Isolation and characterization of a bat
SARS-like coronavirus that uses the ACE2 receptor. Nature 2013;
503(7477): 535-8.
10. Menachery VD, Yount BL, Jr., Debbink K, et al. A SARS-like cluster
of circulating bat coronaviruses shows potential for human emergence.
Nature medicine 2015; 21(12): 1508-13.
map of Wuhan showing WIV, WCDC, & Huanan Seafood Market:
(3) WIV Database of Viruses was altered on Dec. 30, day before China
notified WHO
Database Of Wuhan's 'Batwoman' Altered 48 Hours Before COVID-19 Samples
Ordered Destroyed
by Tyler Durden
Thu, 05/07/2020 - 12:03
As Western intelligence continues to investigate China's handling of
COVID-19 as it spread throughout Hubei province in December, disturbing
evidence continues to emerge that the Chinese Communist Party (CCP)
engaged in a massive cover-up of what was going on.
Now, we've learned that the Wuhan Institute of Virology - which was
conducting controversial experiments into animal-to-human transmission
of bat coronaviruses, altered their database in an apparent attempt to
distance the lab from the outbreak.
"Days before the Wuhan wet market was bleached, whistleblowers were
punished and virus samples were destroyed, someone at the high-security
Wuhan Institute of Virology censored its virus database in an apparent
attempt to disassociate the laboratory from a novel-coronavirus outbreak
that would become a global pandemic," reports the New York Post's
Miranda Devine, citing a UK intelligence analyst who found the
alterations via open-source methods.
Notably, the alteration occurred two days before a gene sequencing lab
was reportedly ordered by the Health and Medical Commission of Hubei
Province to destroy samples of the new disease and withhold information.
According to the report, the alterations - conducted on the evening of
Dec. 30 - were substantial, and occurred the day before the CCP notified
the World Health Organization about the outbreak of a cluster of
pneumonia cases in Wuhan.
The primary database contact is none other than Shi Zhengli - now known
as "batwoman" for her controversial experiments, including the creation
of a 'chimeric' coronavirus that can infect humans. According to the
report, Zhengli was in Shanghai for a conference when she was summoned
back to Wuhan to deal with the outbreak which had been detected in two
pneumonia patients. While on the overnight train back to Wuhan, the
database was altered.
Most of the changes were to delete the keywords "wildlife" or "wild
animals." This is significant, because global health researchers say the
virus jumped from bats to humans via another wild animal — the crucial
"missing link" in the COVID-19 transmission chain.
Shi used to boast that her bat-virus database was unique because it
included data on virus variants in other wild animals.
Was her database censored to keep prying eyes away from references to
cross-species transmission of viruses in wild animals?
For instance, the title of the -database was changed that night from
"Wildlife-borne viral pathogen database" to "Bat and rodent-borne viral
pathogen database."
"Wild animal" was replaced with "bat and rodent" or "bat and rat" at
least 10 times in the database. Also, a reference to "arthropod vectors"
was removed.
Keywords that might facilitate searches potentially connecting the
database with the outbreak also were deleted. "Wild animal samples,"
"viral pathogen data," "emerging infectious diseases" and "cross-species
infection" were keywords associated with the original version.
On Dec. 30 they were replaced with "bat," "rodent" and "virus." -New
York Post
(4) While Shi Zhengli was on a train from Shanghai to Wuhan, alterations
were made to her database
What is China covering up about the coronavirus?: Devine
By Miranda Devine
May 6, 2020 | 10:17pm
Days before the Wuhan wet market was bleached, whistleblowers were
punished and virus samples were destroyed, someone at the high-security
Wuhan Institute of Virology censored its virus database in an apparent
attempt to disassociate the laboratory from a novel-coronavirus outbreak
that would become a global pandemic.
This is what open-source intelligence uncovered in the United Kingdom
reveals.
Substantial alterations to the WIV database on the evening of Dec. 30,
the day before the World Health Organization was alerted to the outbreak
of a cluster of pneumonia cases in Wuhan, are just another indication
that the Chinese Communist Party is hiding something when it comes to
the origins of COVID-19.
The question of whether the virus came from the Wuhan wet market, as
China insists, or leaked from the nearby WIV laboratory, where high-risk
research into animal-to-human transmission of bat coronaviruses was
being conducted, is at the center of allegations of a coverup and a
worldwide clamor for an independent investigation into the source of the
disease.
Shi Zhengli, the virologist known as China's "batwoman" for her work
with bat coronaviruses, directs the WIV's Center for Emerging Infectious
Diseases and is listed as the primary database contact.
On Dec. 30, she was in Shanghai for a conference when she was summoned
back to Wuhan with the news that a novel coronavirus had been detected
in two pneumonia patients.
On the overnight train from Shanghai, according to a March article in
Scientific American, she was stricken with worry about the coronaviruses.
"Could they have come from our lab?" she wondered. see also China's
‘Batwoman' still studies animal-borne coronavirus amid claims lab was in
on cover-up
After all, the closest known relative of this new coronavirus, a bat
virus named RaTG13, was in her lab.
Weeks later, she would post a message on WeChat saying, "I swear with my
life, [the virus] has nothing to do with the lab."
But at some point while she was on that train ride to Wuhan, alterations
were made to her database, which contained records of bat -viruses
transmitted to other wild animals.
Most of the changes were to delete the keywords "wildlife" or "wild
animals." This is significant, because global health researchers say the
virus jumped from bats to humans via another wild animal — the crucial
"missing link" in the COVID-19 transmission chain.
Shi used to boast that her bat-virus database was unique because it
included data on virus variants in other wild animals.
Was her database censored to keep prying eyes away from references to
cross-species transmission of viruses in wild animals?
For instance, the title of the -database was changed that night from
"Wildlife-borne viral pathogen database" to "Bat and rodent-borne viral
pathogen database."
"Wild animal" was replaced with "bat and rodent" or "bat and rat" at
least 10 times in the database. Also, a reference to "arthropod vectors"
was removed.
Keywords that might facilitate searches potentially connecting the
database with the outbreak also were deleted. "Wild animal samples,"
"viral pathogen data," "emerging infectious diseases" and "cross-species
infection" were keywords associated with the original version.
On Dec. 30 they were replaced with "bat," "rodent" and "virus."
"It looks like a rushed, inconsistent effort to disassociate the project
from the outbreak by -rebranding it," says the British open-source
intelligence analyst who found the alterations.
"It's a strange thing to do within hours of being informed of a
novel-coronavirus outbreak."
He surmises: "If the WIV had found the missing link between bat virus
RaTG13 and SARS-CoV-2 [the coronavirus that causes COVID-19] from an
animal vector, it would have been in Shi's database." see also
Ambassador's Orwellian op-ed asks US to stop blaming China for COVID-19
There's no conclusive evidence that any of the changes were made for
sinister reasons.
But China's lies and furtive -actions since the outbreak lead us to
believe the worst.
"This is an enormous crisis created by the fact that the Chinese
Communist Party reverted to form, reverted to the kinds of
disinformation, the kinds of concealment, that authoritarian regimes
do," Secretary of State Mike Pompeo said in an interview Sunday with ABC
News.
"There is enormous evidence that [the Wuhan lab] is where this began . . .
"These are not the first times that we've had a world exposed to viruses
as a result of failures in a Chinese lab."
On Wednesday, Pompeo walked back his comments slightly at a press
conference. "We don't have certainty," he said. "We're all trying to get
to clarity."
China's refusal to allow an investigation of the origins of the Wuhan
virus, or even to share original virus samples, impedes the search for
treatments and a vaccine. As if that weren't bad enough, now it is
threatening economic boycotts against countries like Australia that want
an investigation.
"The CCP organizational and governmental culture is to cover up and
ruthlessly control," says a retired senior Australian intelligence
officer who served in China.
"The arrest of frontline health professionals in January was standard
practice."
We don't know why the changes were made to the WIV database.
What we do know is they were made the same day a young ophthal-mologist,
Dr. Li Wenliang, warned colleagues in an online chat group about a
"SARS-like coronavirus" among patients in the emergency department of a
Wuhan Hospital.
Li was arrested two days later, along with seven other doctors, for
"spreading rumors" and forced to recant. He died a month later, of the
coronavirus, at age 33.
(5) Shi Zhengli speaks about SARS at TED-like talk in 2018
(6) Shi Zhengli article in Scientific American
How China's ‘Bat Woman' Hunted Down Viruses from SARS to the New
Coronavirus
Wuhan-based virologist Shi Zhengli has identified dozens of deadly
SARS-like viruses in bat caves, and she warns there are more out there
By Jane Qiu on April 27, 2020
Scientific American
Editor's Note (4/24/20): This article was originally published online on
March 11. It has been updated for inclusion in the June 2020 issue of
Scientific American and to address rumors that SARS-CoV-2 emerged from
Shi Zhengli's lab in China.
In 2004 Shi Zhengli found a natural reservoir of coronaviruses in bat
caves in southern China. Genetic analyses show they have leaped to
people several times, causing deadly diseases such as COVID-19.
Increasing contact between people and wild animals makes more outbreaks
likely.
The mysterious patient samples arrived at the Wuhan Institute of
Virology at 7 P.M. on December 30, 2019. Moments later Shi Zhengli's
cell phone rang. It was her boss, the institute's director. The Wuhan
Center for Disease Control and Prevention had detected a novel
coronavirus in two hospital patients with atypical pneumonia, and it
wanted Shi's renowned laboratory to investigate. If the finding was
confirmed, the new pathogen could pose a serious public health
threat—because it belonged to the same family of viruses as the one that
caused severe acute respiratory syndrome (SARS), a disease that plagued
8,100 people and killed nearly 800 of them between 2002 and 2003. "Drop
whatever you are doing and deal with it now," she recalls the director
saying.
Shi, a virologist who is often called China's "bat woman" by her
colleagues because of her virus-hunting expeditions in bat caves over
the past 16 years, walked out of the conference she was attending in
Shanghai and hopped on the next train back to Wuhan. "I wondered if [the
municipal health authority] got it wrong," she says. "I had never
expected this kind of thing to happen in Wuhan, in central China." Her
studies had shown that the southern, subtropical provinces of Guangdong,
Guangxi and Yunnan have the greatest risk of coronaviruses jumping to
humans from animals—particularly bats, a known reservoir. If
coronaviruses were the culprit, she remembers thinking, "Could they have
come from our lab?"
While Shi's team at the Wuhan institute, an affiliate of the Chinese
Academy of Sciences, raced to uncover the identity of the contagion—over
the following week they connected the illness to the novel coronavirus
that become known as SARS-CoV-2—the disease spread like wildfire. By
April 20 more than 84,000 people in China had been infected. About 80
percent of them lived in the province of Hubei, of which Wuhan is the
capital, and more than 4,600 had died. Outside of China, about 2.4
million people across 210 or so countries and territories had caught
the virus, and more than 169,000 had perished from the disease it
caused, COVID-19.
Scientists have long warned that the rate of emergence of new infectious
diseases is accelerating—especially in developing countries where high
densities of people and animals increasingly mingle and move about.
"It's incredibly important to pinpoint the source of infection and the
chain of cross-species transmission," says disease ecologist Peter
Daszak, president of EcoHealth Alliance, a New York City–based nonprofit
research organization that collaborates with researchers, such as Shi,
in 30 countries in Asia, Africa and the Middle East to discover new
viruses in wildlife. An equally important task, he adds, is to hunt down
other pathogens to "prevent similar incidents from happening again."
THE CAVES
To Shi, her first virus-discovery expedition felt like a vacation. On a
breezy, sunny spring day in 2004, she joined an international team of
researchers to collect samples from bat colonies in caves near Nanning,
the capital of Guangxi. Her inaugural cave was typical of the region:
large, rich in limestone columns and—as a popular tourist
destination—easily accessible. "It was spellbinding," Shi recalls.
Milky-white stalactites hung from the ceiling like icicles, glistening
with moisture.
But the holidaylike atmosphere soon dissipated. Many bats—including
several insect-eating species of horseshoe bats that are abundant in
southern Asia—roost in deep, narrow caves on steep terrain. Often guided
by tips from local villagers, Shi and her colleagues had to hike for
hours to potential sites and inch through tight rock crevasses on their
stomachs. And the flying mammals can be elusive. In one frustrating
week, the team explored more than 30 caves and saw only a dozen bats.
These expeditions were part of the effort to catch the culprit in the
SARS outbreak, the first major epidemic of the 21st century. A Hong Kong
team had reported that wildlife traders in Guangdong first caught the
SARS coronavirus from civets, mongooselike mammals that are native to
tropical and subtropical Asia and Africa.
Before SARS, the world had only an inkling of coronaviruses—so named
because their spiky surface resembles a crown when seen under a
microscope, says Linfa Wang, who directs the emerging infectious
diseases program at Singapore's Duke-NUS Medical School. Coronaviruses
were mostly known for causing common colds. "The SARS outbreak was a
game changer," Wang says. It was the first emergence of a deadly
coronavirus with pandemic potential. The incident helped to jump-start a
global search for animal viruses that could find their way into humans.
Shi was an early recruit of that effort, and both Daszak and Wang have
been her long-term collaborators.
ON THE SAME 2004 trip, a group of researchers prepare bat blood samples
that they will screen for viruses and other pathogens. Credit: Shuyi
Zhang With the SARS virus, just how the civets got it remained a
mystery. Two previous incidents were telling: Australia's 1994 Hendra
virus infections, in which the contagion jumped from horses to humans,
and Malaysia's 1998 Nipah virus outbreak, in which it moved from pigs to
people. Wang found that both diseases were caused by pathogens that
originated in fruit-eating bats. Horses and pigs were merely the
intermediate hosts. Bats in the Guangdong market also contained traces
of the SARS virus, but many scientists dismissed this as contamination.
Wang, however, thought bats might be the source.
In those first virus-hunting months in 2004, whenever Shi's team located
a bat cave, it would put a net at the opening before dusk and then wait
for the nocturnal creatures to venture out to feed for the night. Once
the bats were trapped, the researchers took blood and saliva samples, as
well as fecal swabs, often working into the small hours. After catching
up on some sleep, they would return to the cave in the morning to
collect urine and fecal pellets.
But sample after sample turned up no trace of genetic material from
coronaviruses. It was a heavy blow. "Eight months of hard work seemed to
have gone down the drain," Shi says. "We thought maybe bats had nothing
to do with SARS." The scientists were about to give up when a research
group in a neighboring lab handed them a diagnostic kit for testing
antibodies produced by people with SARS.
There was no guarantee that the test would work for bat antibodies, but
Shi gave it a go anyway. "What did we have to lose?" she says. The
results exceeded her expectations. Samples from three horseshoe bat
species contained antibodies to the SARS virus. "It was a turning point
for the project," Shi says. The researchers learned that the presence of
the coronavirus in bats was ephemeral and seasonal—but an antibody
reaction could last from weeks to years. The diagnostic kit, therefore,
offered a valuable pointer as to how to hunt down viral genomic sequences.
Shi's team used the antibody test to narrow down the list of locations
and bat species to pursue in the quest for genomic clues. After roaming
mountainous terrain in most of China's dozens of provinces, the
researchers turned their attention to one spot: Shitou Cave, on the
outskirts of Kunming, the capital of Yunnan, where they conducted
intense sampling during different seasons over five consecutive years.
The efforts paid off. The pathogen hunters discovered hundreds of
bat-borne coronaviruses with incredible genetic diversity. "The majority
of them are harmless," Shi says. But dozens belong to the same group as
SARS. They can infect human lung cells in a petri dish and cause
SARS-like diseases in mice.
In Shitou Cave—where painstaking scrutiny has yielded a natural genetic
library of bat-borne viruses—the team discovered a coronavirus strain
that came from horseshoe bats with a genomic sequence nearly 97 percent
identical to the one found in civets in Guangdong. The finding concluded
a decade-long search for the natural reservoir of the SARS coronavirus.
A DANGEROUS MIX In many bat dwellings Shi has sampled, including Shitou
Cave, "constant mixing of different viruses creates a great opportunity
for dangerous new pathogens to emerge," says Ralph Baric, a virologist
at the University of North Carolina at Chapel Hill. In the vicinity of
such viral melting pots, Shi says, "you don't need to be a wildlife
trader to be infected."
Near Shitou Cave, for example, many villages sprawl among the lush
hillsides in a region known for its roses, oranges, walnuts and hawthorn
berries. In October 2015 Shi's team collected blood samples from more
than 200 residents in four of those villages. It found that six people,
or nearly 3 percent, carried antibodies against SARS-like coronaviruses
from bats—even though none of them had handled wildlife or reported
SARS-like or other pneumonialike symptoms. Only one had traveled outside
of Yunnan prior to the sampling, and all said they had seen bats flying
in their village.
Three years earlier Shi's team had been called in to investigate the
virus profile of a mine shaft in Yunnan's mountainous Mojiang
County—famous for its fermented Pu'er tea—where six miners suffered from
pneumonialike diseases and two died. After sampling the cave for a year,
the researchers discovered a diverse group of coronaviruses in six bat
species. In many cases, multiple viral strains had infected a single
animal, turning it into a flying factory for new viruses.
"The mine shaft stunk like hell," says Shi, who, like her colleagues,
went in wearing a protective mask and clothing. "Bat guano, covered in
fungus, littered the cave." Although the fungus turned out to be the
pathogen that had sickened the miners, she says it would have been only
a matter of time before they caught the coronaviruses if the mine had
not been promptly shut.
With growing human populations increasingly encroaching on wildlife
habitats, with unprecedented changes in land use, with wildlife and
livestock transported across countries and their products around the
world, and with sharp increases in both domestic and international
travel, pandemics of new diseases are a mathematical near certainty.
This had been keeping Shi and many other researchers awake at night long
before the mysterious samples landed at the Wuhan Institute of Virology
on that ominous evening last December.
More than a year ago Shi's team published two comprehensive reviews
about coronaviruses in Viruses and Nature Reviews Microbiology. Drawing
evidence from her own studies—many of which were published in top
academic journals—and from others, Shi and her co-authors warned of the
risk of future outbreaks of bat-borne coronaviruses.
NIGHTMARE SCENARIO
On the train back to Wuhan on December 30 last year, Shi and her
colleagues discussed ways to immediately start testing the patients'
samples. In the following weeks—the most intense and the most stressful
time of her life—China's bat woman felt she was fighting a battle in her
worst nightmare, even though it was one she had been preparing for over
the past 16 years. Using a technique called polymerase chain reaction,
which can detect a virus by amplifying its genetic material, the team
found that samples from five of seven patients had genetic sequences
present in all coronaviruses.
Shi instructed her group to repeat the tests and, at the same time, sent
the samples to another facility to sequence the full viral genomes.
Meanwhile she frantically went through her own lab's records from the
past few years to check for any mishandling of experimental materials,
especially during disposal. Shi breathed a sigh of relief when the
results came back: none of the sequences matched those of the viruses
her team had sampled from bat caves. "That really took a load off my
mind," she says. "I had not slept a wink for days."
By January 7 the Wuhan team had determined that the new virus had indeed
caused the disease those patients suffered—a conclusion based on results
from analyses using polymerase chain reaction, full genome sequencing,
antibody tests of blood samples and the virus's ability to infect human
lung cells in a petri dish. The genomic sequence of the virus,
eventually named SARS-CoV-2, was 96 percent identical to that of a
coronavirus the researchers had identified in horseshoe bats in Yunnan.
Their results appeared in a paper published online on February 3 in
Nature. "It's crystal clear that bats, once again, are the natural
reservoir," says Daszak, who was not involved in the study.
Since then, researchers have published more than 4,500 genomic sequences
of the virus, showing that samples around the world appear to "share a
common ancestor," Baric says. The data also point to a single
introduction into humans followed by sustained human-to-human
transmission, researchers say.
Given that the virus seems fairly stable initially and that many
infected individuals appear to have mild symptoms, scientists suspect
that the pathogen might have been around for weeks or even months before
severe cases raised the alarm. "There might have been mini outbreaks,
but the viruses either burned out or maintained low-level transmission
before causing havoc," Baric says. Most animal-borne viruses reemerge
periodically, he adds, so "the Wuhan outbreak is by no means incidental."
MARKET FORCES To many, the region's burgeoning wildlife markets—which
sell a wide range of animals such as bats, civets, pangolins, badgers
and crocodiles—are perfect viral melting pots. Although humans could
have caught the deadly virus from bats directly (according to several
studies, including those by Shi and her colleagues), independent teams
have suggested that pangolins may have been an intermediate host. These
teams have reportedly uncovered SARS-CoV-2-like coronaviruses in
pangolins that were seized in antismuggling operations in southern China.
On February 24 China announced a permanent ban on wildlife consumption
and trade except for research, medicinal or display purposes—which will
stamp out an industry worth $76 billion and put approximately 14 million
people out of jobs, according to a 2017 report commissioned by the
Chinese Academy of Engineering. Some welcome the initiative, whereas
others, such as Daszak, worry that without efforts to change people's
traditional beliefs or to provide alternative livelihoods, a blanket ban
may simply push the business underground. This could make disease
detection even more challenging. "Eating wildlife has been part of the
cultural tradition" in China for thousands of years, Daszak says. "It
won't change overnight."
In any case, Shi says, "wildlife trade and consumption are only part of
problem." In late 2016 pigs across four farms in Qingyuan County in
Guangdong—60 miles from the site where the SARS outbreak
originated—suffered from acute vomiting and diarrhea, and nearly 25,000
of the animals died. Local veterinarians could not detect any known
pathogen and called Shi for help. The cause of the illness—swine acute
diarrhea syndrome (SADS)—turned out to be a virus whose genomic sequence
was 98 percent identical to that of a coronavirus found in horseshoe
bats in a nearby cave.
"This is a serious cause for concern," says Gregory Gray, an infectious
disease epidemiologist at Duke University. Pigs and humans have very
similar immune systems, making it easy for viruses to cross between the
two species. Moreover, a team at Zhejiang University in the Chinese city
of Hangzhou found that the SADS virus could infect cells from many
organisms in a petri dish, including rodents, chickens, nonhuman
primates and humans. Given the scale of swine farming in many countries,
such as China and the U.S., Gray says, looking for novel coronaviruses
in pigs should be a top priority.
The current outbreak follows several others during the past three
decades that have been caused by six different bat-borne viruses:
Hendra, Nipah, Marburg, SARS-CoV, MERS-CoV (Middle East respiratory
syndrome) and Ebola. But "the animals [themselves] are not the problem,"
Wang says. In fact, bats promote biodiversity and ecosystem health by
eating insects and pollinating plants. "The problem arises when we get
in contact with them," he says.
TOWARD PREVENTION When I spoke to Shi in late February—two months into
the epidemic and one month after the government imposed severe movement
restrictions in Wuhan, a megacity of 11 million—she said, laughing, that
life felt almost normal. "Maybe we are getting used to it. The worst
days are certainly over." The institute staffers had a special pass to
travel from home to their lab, but they could not go anywhere else. They
had to subsist on instant noodles during their long hours at work
because the institute's canteen was closed.
New revelations about the coronavirus kept coming to light. The
researchers discovered, for instance, that the pathogen enters human
lung cells by using a receptor called angiotensin-converting enzyme 2,
and they and other groups have since been screening for drugs that can
block it. Scientists are also rac-ing to develop vaccines. In the long
run, the Wuhan team plans to develop broad-spectrum vaccines and drugs
against coronaviruses deemed risky to humans. "The Wuhan outbreak is a
wake-up call," Shi says.
Many scientists say the world should move beyond merely responding to
deadly pathogens when they arise. "The best way forward is prevention,"
Daszak says. Because 70 percent of emerging infectious diseases of
animal origins come from wildlife, a top priority should be identifying
them and developing better diagnostic tests, he adds. Doing so would
essentially mean continuing on a much larger scale what researchers such
as Daszak and Shi had been doing before their funding ended this year.
Such efforts should focus on high-risk viral groups in mammals prone to
coronavirus infections, such as bats, rodents, badgers, civets,
pangolins and nonhuman primates, Daszak says. He adds that developing
countries in the tropics, where wildlife diversity is greatest, should
be the front line of this battle against viruses.
Daszak and his colleagues have analyzed approximately 500 human
infectious diseases from the past century. They found that the emergence
of new pathogens tends to happen in places where a dense population has
been changing the landscape—by building roads and mines, cutting down
forests and intensifying agriculture. "China is not the only hotspot,"
he says, noting that other major emerging economies, such as India,
Nigeria and Brazil, are also at great risk.
Once potential pathogens are mapped out, scientists and public health
officials can regularly check for possible infections by analyzing blood
and swab samples from livestock, from wild animals that are farmed and
traded, and from high-risk human populations such as farmers, miners,
villagers who live near bats, and people who hunt or handle wildlife,
Gray says. This approach, known as "One Health," aims to integrate the
health management of wildlife, livestock and people. "Only then can we
catch an outbreak before it turns into an epidemic," he says, adding
that the strategy could potentially save the hundreds of billions of
dollars such an epidemic can cost.
Back in Wuhan, where the lockdown was finally lifted on April 8, China's
bat woman is not in a celebratory mood. She is distressed because
stories from the Internet and major media have repeated a tenuous
suggestion that SARS-CoV-2 accidentally leaked from her lab—despite the
fact that its genetic sequence does not match any her lab had previously
studied. Other scientists are quick to dismiss the allegation. "Shi
leads a world-class lab of the highest standards," Daszak says.
Despite the disturbance, Shi is determined to continue her work. "The
mission must go on," she says. "What we have uncovered is just the tip
of an iceberg." She is planning to lead a national project to
systematically sample viruses in bat caves, with much wider scope and
intensity than previous attempts. Daszak's team has estimated that there
are more than 5,000 coronavirus strains waiting to be discovered in bats
globally.
"Bat-borne coronaviruses will cause more outbreaks," Shi says with a
tone of brooding certainty. "We must find them before they find us."
Jane Qiu is an award-winning science writer based in Beijing.
(7) Virologist: WE INTRODUCED A FURIN-LIKE CLEAVAGE SEQUENCE in the S
protein
From: javier.ortiza@ehu.eus
Following the discussion about coronavirus origin:
With respect to "PRRA" novel sequence. It is not really an "insert" or
frame mutation (this would require a no coincident broad sequence
between coincidents sequences.)
It is a point mutation where only few nucleotides are swapped or changed.
That means if it were an "insert" mutation hardly could be becuse of
natural evolution but, however, point mutation doesn't discard natural
evolution.
Now, following with the same discussion in the same youtube channel:
Two new arguments leading to man-made origin or at least to cast doubts
about natural origin.
Both concern mutations genoma.
The first one is when comparing a graphic of the named "cumulative
behavior codon by codon " of CoV-19 and the most alike RaTG13
coronaviruses sequence mutations, happens that the named "synonimous
mutations" (mutations without "relevant" outcome") are taken place along
the whole strain legnth in a "let's say" quite linear mode. However the
named "non synonymous mutations" (more important) suddenly from before
one half (codon 500 until 1250 final codon) of the total strain length
do not take place anymore. Comparing this behavior with the natural
evolution and mutations of other coronaviruses results very odd beacuse
usually both type of mutations have a parallel evolution.
The second one, is relative to the aminoacids sequence alignment of the
E structural protein of CoV-19. It happens that the early copies (Feb.
2020) of Wuhan coronavirus share 100% identity of this E protein with
the RaTG13 and relative known coronaviruses. But the recent copies
(April 2020) shows mutations in the aminoacids chain in four different
locations. From the time point of view it is not easy to understand how
this 100% identity has remained during long time (in nature?) without
any mutation and suddenly in few weeks when the virus is in humans
starts evolving rapidly. It sounds like this Wuhan CoV19 were a
"template" made from older coronaviruses and when coming to the natural
world has evolved.
More about scientific discussion:
The Virology Blog is a blog where participants have good knowledge of
the matter and make interesting comments.
In this blog, one participant comments, about possibility of virus
engineering theory:
"...By substitution of a single amino acid in the S protein WE CREATED A
RECOMBINANT PEDV (PEDV-S(FCS)) WITH AN ARTIFICIAL FURIN PROTEASE
CLEAVAGE SITE N-terminal of the putative fusion peptide. PEDV-S(FCS)
exhibited trypsin-independent cell-cell fusion and was able to replicate
in culture cells independent of trypsin... In capital letters
highlighting "the creation of an artificial furin protease cleavage
site" extracted from article published in:
(2015)
The same participant also comments about possibility of virus
enginneering theory: "...To explore this possibility, WE INTRODUCED A
FURIN-LIKE CLEAVAGE SEQUENCE in the S protein at amino acids 798 to 801
and found that the mutated S protein was cleaved and induced cell fusion
without trypsin treatment when expressed on the cell surface..."
Highlighting in capital letters the mutation of a S protein. (Extracted
from article Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583654/)
In this same blog another participant comments about the possibility of
engineering fragments of viruses: In this work a possible procedure to
generate chimeric viruses is described: Manipulation of the Coronavirus
Genome Using Targeted RNA Recombination with Interspecies Chimeric
Coronaviruses Cornelis A.M. de Haan, Bert Jan Haijema, Paul S. Masters,
and Peter J.M. Rottier
This participant later make some questions: I have now a question: why
the famous RaTG13 sequence, from a sample collected in 2013 was
submitted to NCBI only on 27-JAN-2020, after the outbreak of SARS-CoV-2?
and Sure that all the sequences obtained from bat or other animal
screening have been deposited? Why RaTG13, isolated in 2013, has been
made public only in 2020?
Those questions are very similar to one made by Dr Sean Lin in
https://www.youtube.com/watch?v=XO_kvtrfPWc He said that it sound
strange that one sample discovered in 2013 suddenly appears to be the
most similar to SARS_CoV-2 but during this years there has been not
paper mentioning works with these samples.
This question is more and more often asked about, because it is not
usual that after collecting important samples in 2013 no further work
has been published.
Finally again about the feasibility of making engineered viruses
Extracted from article:
"William McEwan: This afternoon I received in the post a slim FedEx
envelope containing four small vials of DNA. The DNA had been
synthesized according to my instructions in under three weeks, at a cost
of 39 U.S. cents per base pair (the rungs adenine-thymine or
guanine-cytosine in the DNA ladder). The 10 micrograms I ordered are
dried, flaky, and barely visible to the naked eye, yet once I have
restored them in water and made an RNA copy of this template, THEY WILL
ENCODE A VIRUS I HAVE DESIGNED. …
Willian McEwan is a postdoc researcher in Cambridge University (UK)
(8) US Patent for Chimeric Coronavirus Spike Proteins lists Ralph Baric
as Inventor
From: javier.ortiza@ehu.eus
Another interesting information:
Title: Methods and compositions for chimeric coronavirus spike proteins
United States Patent 9884895
Inventors: Baric, Ralph (Haw River, NC, US) Agnihothram, Sudhakar
(Ellicott City, MD, US) Yount, Boyd (Hillsborough, NC, US)
Publication Date: 02/06/2018
Assignee: The University of North Carolina at Chapel Hill (Chapel Hill,
NC, US)
(9) Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function
Research
Yuri Deigin
Apr 23
Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research
How I Learned to Start Worrying
Oh, come on. Lab-made? Nonsense! Back in January, that was my knee-jerk
reaction when ideas that Covid-19 is caused by a laboratory leak had
just surfaced. Bioweapon? Well, that is just Flat Earth crazies
territory. Thus, whenever I kept hearing anything about non-natural
origins of SARS-CoV-2, I brushed it aside under similar sentiments. So
what if there is a virology institute in Wuhan? Who knows how many of
those are sprinkled throughout China.
At some point, it became necessary to brush such theories aside in a
substantiated manner, as their proponents began to back up their theses
about the possible arti cial nature of the virus with arguments from
molecular biology, and when engaging them in debate, I wanted to smash
their conspiracy theories with cold, hard scienti c facts. Just like
that Nature paper (or so I thought).
So it was then, in pursuit of arguments against the virus’s
lab-madeness, that I got infected by the virus of doubt. What was the
source of my doubts? The fact that the deeper you dive into the research
activities of coronavirologists over the past 15–20 years, the more you
realize that creating chimeras like CoV2 was commonplace in their labs.
And CoV2 is an obvious chimera (though not nesessarily a lab-made one),
which is based on the ancestral bat strain RaTG13, in which the receptor
binding motif (RBM) in its spike protein is replaced by the RBM from a
pangolin strain, and in addition, a small but very special stretch of 4
amino acids is inserted, which creates a furin cleavage site that, as
virologists have previously established, signicantly expands the
"repertoire" of the virus in terms of whose cells it can penetrate. Most
likely, it was thanks to this new furin site that the new mutant managed
to jump species from its original host to humans.
Indeed, virologists, including the leader of coronavirus research at the
Wuhan Institute of Virology, Shi Zhengli, have done many similar things
in the past — both replacing the RBM in one type of virus by an RBM from
another, or adding a new furin site that can provide a species-specic
coronavirus with an ability to start using the same receptor (e.g. ACE2)
in other species. In fact, Shi Zhengli’s group was creating chimeric
constructs as far back as 2007 and as recently as 2017, when they
created a whole of 8 new chimeric coronaviruses with various RBMs. In
2019 such work was in full swing, as WIV was part of a $3.7 million NIH
grant titled Understanding the Risk of Bat Coronavirus Emergence. Under
its auspices, Shi Zhengli co-authored a 2019 paper that called for
continued research into synthetic viruses and testing them in vitro and
in vivo:
Currently, no clinical treatments or prevention strategies are available
for any human coronavirus. Given the conserved RBDs of SARS-CoV and bat
SARSr-CoVs, some anti-SARS-CoV strategies in development, such as
anti-RBD antibodies or RBD-based vaccines, should be tested against bat
SARSr-CoVs. Recent studies demonstrated that anti-SARS-CoV strategies
worked against only WIV1 and not SHC014. In addition, little information
is available on HKU3-related strains that have much wider geographical
distribution and bear truncations in their RBD. Similarly, anti-S
antibodies against MERS-CoV could not protect from infection with a
pseudovirus bearing the bat MERSr-CoV S. Furthermore, little is known
about the replication and pathogenesis of these bat viruses. Thus,
future work should be focused on the biological properties of these
viruses using virus isolation, reverse genetics and in vitro and in vivo
infection assays. The resulting data would help the prevention and
control of emerging SARS-like or MERS-like diseases in the future.
If the above quote might seem vague as to what exactly "using reverse
genetics" might mean, the NIH grant itself spells it out:
Aim 3. In vitro and in vivo characterization of SARSr-CoV spillover
risk, coupled with spatial and phylogenetic analyses to identify the
regions and viruses of public health concern. We will use S protein
sequence data, infectious clone technology, in vitro and in vivo
infection experiments and analysis of receptor binding to test the
hypothesis that % divergence thresholds in S protein sequences predict
spillover potential.
"Infectious clone technology" stands for creating live synthetic viral
clones. Considering the heights of user friendliness and automation that
genetic engineering tools have attained, creating a synthetic CoV2 via
the above methodology would be in reach of even a grad student. [...]
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