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Coronavirus Could Be a 'Chimera' of Two Different Viruses, Genome Analysis Suggests


Alexandre Hassanin, The Conversation

24 March 2020

In the space of a few weeks, we have all learned a lot about COVID-19 and the virus that causes it: SARS-CoV-2. But there have also been a lot of rumours.

And while the number of scientific articles on this virus is increasing, there are still many grey areas as to its origins.

In which animal species did it occur? A bat, a pangolin or another wild species? Where does it come from? From a cave or a forest in the Chinese province of Hubei, or elsewhere?

In December 2019, 27 of the first 41 people hospitalised (66 percent) passed through a market located in the heart of Wuhan city in Hubei province. But, according to a study conducted at Wuhan Hospital, the very first human case identified did not frequent this market.

Instead, a molecular dating estimate based on the SARS-CoV-2 genomic sequences indicates an origin in November. This raises questions about the link between this COVID-19 epidemic and wildlife.

Genomic data

The SARS-CoV-2 genome was rapidly sequenced by Chinese researchers. It is an RNA molecule of about 30,000 bases containing 15 genes, including the S gene which codes for a protein located on the surface of the viral envelope (for comparison, our genome is in the form of a double helix of DNA about 3 billion bases in size and contains about 30,000 genes).

Comparative genomic analyses have shown that SARS-CoV-2 belongs to the group of Betacoronaviruses and that it is very close to SARS-CoV, responsible for an epidemic of acute pneumonia which appeared in November 2002 in the Chinese province of Guangdong and then spread to 29 countries in 2003.

A total of 8,098 cases were recorded, including 774 deaths. It is known that bats of the genus Rhinolophus (potentially several cave species) were the reservoir of this virus and that a small carnivore, the palm civet (Paguma larvata), may have served as an intermediate host between bats and the first human cases.

Since then, many Betacoronaviruses have been discovered, mainly in bats, but also in humans. For example, RaTG13, isolated from a bat of the species Rhinolophus affinis collected in China's Yunan Province, has recently been described as very similar to SARS-CoV-2, with genome sequences identical to 96 percent.

These results indicate that bats, and in particular species of the genus Rhinolophus, constitute the reservoir of the SARS-CoV and SARS-CoV-2 viruses.

But how do you define a reservoir? A reservoir is one or several animal species that are not or not very sensitive to the virus, which will naturally host one or several viruses.

The absence of symptoms of the disease is explained by the effectiveness of their immune system, which allows them to fight against too much viral proliferation.

Recombination mechanism

On 7 February, 2020, we learned that a virus even closer to SARS-CoV-2 had been discovered in pangolin. With 99 percent of genomic concordance reported, this suggested a more likely reservoir than bats.

However, a recent study under review shows that the genome of the coronavirus isolated from the Malaysian pangolin (Manis javanica) is less similar to SARS-Cov-2, with only 90 percent of genomic concordance. This would indicate that the virus isolated in the pangolin is not responsible for the COVID-19 epidemic currently raging.

However, the coronavirus isolated from pangolin is similar at 99 percent in a specific region of the S protein, which corresponds to the 74 amino acids involved in the ACE (Angiotensin Converting Enzyme 2) receptor binding domain, the one that allows the virus to enter human cells to infect them.

By contrast, the virus RaTG13 isolated from bat R. affinis is highly divergent in this specific region (only 77 percent of similarity). This means that the coronavirus isolated from pangolin is capable of entering human cells whereas the one isolated from bat R. affinis is not.

In addition, these genomic comparisons suggest that the SARS-Cov-2 virus is the result of a recombination between two different viruses, one close to RaTG13 and the other closer to the pangolin virus. In other words, it is a chimera between two pre-existing viruses.

This recombination mechanism had already been described in coronaviruses, in particular to explain the origin of SARS-CoV. It is important to know that recombination results in a new virus potentially capable of infecting a new host species.

For recombination to occur, the two divergent viruses must have infected the same organism simultaneously.

Two questions remain unanswered: in which organism did this recombination occur? (a bat, a pangolin or another species?) And above all, under what conditions did this recombination take place?


Alexandre Hassanin, Maître de Conférences (HDR) à Sorbonne Université, ISYEB - Institut de Systématique, Evolution, Biodiversité (CNRS, MNHN, SU, EPHE, UA), Muséum national d'histoire naturelle



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The panic buyers at the local Makro is greatly reduced...many items are not to be found.

Zero eggs, which I have never seen before!

Milk, only the higher priced brands are available.

Parking lot was only 1/2 full...now will they get the store restocked? the chickens are still laying eggs...

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Strange ... I was in my local Tops grocery yesterday, shelves full and no shortage of anything. The small food stalls have all had to close (no more fried dishes, somtam, ice cream etc), but that is the only thing unusual.  A few days before that I was at The Mall in Ngamwongwan (Nonthaburi). No signs of any panic buying any many restaurants still open (take out only).





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You can protest, as long as you do so in groups of less than one.

Meanwhile ...

Under the state of emergency which went into effect around Thailand last night, the military has set up 357 checkpoints to monitor interprovincial travel in an additional measure to fight the spread of the Covid-19 coronavirus. A statement said the checkpoints are in response to the PM tasking the military command with supervising security measures.

The checkpoints are manned by soldiers, police and civil servants, checking travellers for symptoms of the virus and behaviour leading to the risk of transmission, according to the statement.

People at risk of infection or transmission will be kept at “appropriate locations.”

In Bangkok the checkpoints are on Chaeng Watthana Road near Klong Prapa canal, Suwinthawong Road, Kanchanaphisek 39 frontage road, Sukhumvit Road at the BTS Bearing station, Rachaphruek Road in Taling Chan district, Suksawat Road under Bhumibol Bridge and Rama II Soi 92 Road.



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Blaming America: China Weaponizes Misinformation About COVID-19

As of March 23, according to the John Hopkins Coronavirus Resource Center, there are 353,692 people infected with the novel coronavirus, officially known as SARS-CoV-2 or COVID-19, worldwide. A total of 15,430 have died, while 100,443 people have recovered.

In the United States, the number of cases has reached 35,345 with 459 deaths.

In addition to the human suffering, the pandemic has produced worldwide economic dislocations that have led to chaotic, and plunging, financial markets' dropping economic output; and burgeoning unemployment. World trade and associated global supply chains have been disrupted. The net result is a deepening sense of fear and anxiety around the world.

The crisis has also given rise to an enormous amount of deliberate misinformation about the crisis, its origins and its eventual consequences. Some of that misinformation is fueled by fear and ignorance -- some by crasser financial motives.

In the case of China, Russia and several other countries, however, misinformation is deliberately being spread by state media to deflect criticisms of their government actions, or lack thereof, and to push the blame onto someone else. Misinformation is also being weaponized as part of a broader foreign policy agenda that seeks to secure national advantage from the COVID-19 pandemic.

Weaponizing Misinformation

Every tragedy requires a culprit. Even so-called acts of God, like floods, earthquakes or disease outbreaks, invariably produce a culprit -- a badly designed building that collapsed; a dam that wasn't probably maintained; or civil administrators who were unprepared, failed to act or responded incompetently. It is a deeply rooted human tendency to find someone to blame when things go wrong, a fact long understood and exploited by tort lawyers.

It should not be a surprise, then, that the finger pointing has already begun in earnest.

The coronavirus' origins are still unknown. The fact that the outbreak occurred in Wuhan, the city that hosts China's only Level IV biomedical laboratory for dealing with infectious diseases, has fueled countless conspiracy theories that the virus is manmade and that somehow it "escaped" from the Wuhan Institute of Virology (WIV).

The available evidence suggests that the origin of COVID-19 is consistent with the origin of other coronaviruses, including those that led to the outbreak of severe acute respiratory syndrome ( SARS) in 2002-2004 and Middle East respiratory syndrome (MERS) in 2012-2014, and which every year lead to the development of several new strains of influenza. There is no evidence that the coronavirus is a man-made bio-weapon that somehow escaped from a research lab.

On the other hand, the evidence that East Asia has been at the center of successive epidemics of diseases linked to the coronavirus is clear and unmistakable.

Since 1957, there have been more than a dozen major coronavirus-linked infections that have emerged, almost all of them from East Asia. Several of them have reached pandemic proportions.

The 1957 Asian flu (H2N2) pandemic was responsible for the deaths of approximately 2 million people. Other pandemics were caused by the 1968 Hong Kong Flu, H3N2, (1 million deaths) and the 2009 Swine flu, H1N1, (500,000 deaths).

In addition, there have been three major outbreaks of acute respiratory distress syndrome (ARDS) that are linked to coronaviruses: severe acute respiratory syndrome (SARS) in 2002-2004, Middle East respiratory syndrome (MERS) in 2012-2014 and COVID-19. Only the COVID-19 outbreak rose to the level of a pandemic.

The good news is that these sort of outbreaks have happened before. The bad news is that these types of outbreaks will happen again.

China Blames America

Early on, Chinese state media suggested that the U.S. was responsible for the outbreak, and that it was an attempt by the U.S. to cripple the Chinese economy. Much the same thing happened during the SARS epidemic, leading to a deluge of conspiracy theories across Chinese social media sites that the virus was a CIA creation.

In late January, a Chinese military website, Xilu, which is owned and funded by China's Ministry of Defense, claimed that the coronavirus had been specifically engineered by the U.S. to target people of Han Chinese ancestry. The Han represent some 99% of China's population. Supposedly, according to Xilu, the virus was introduced into Wuhan by American servicemen participating in the Military World Games in October 2019. The report claimed that the "poor performance of the American athletes" was evidence that they were not in fact athletes but "biowarfare operatives."

Since late February, Chinese state media has shifted tack, arguing that "the virus may have first appeared in China but that did not mean that it had originated or been created there."

In the meantime, Chinese media have been emphasizing China's "heroic actions" in fighting the pandemic, describing its actions when the outbreak emerged as a "selfless sacrifice to buy the world more time." Beijing has also cracked down on the western media, limiting their ability to report on the coronavirus pandemic in China. Reporters from The Washington Post, The New York Times and The Wall Street Journal, among others, have been expelled. Additionally, Chinese natives who have been working for foreign news bureaus have been dismissed by the Chinese government.

The Chinese press has extensively covered the spread of the coronavirus around the world, pointing out other countries' failure to contain the virus, in particular Italy and Spain. They continue to stress the foreign origins of the virus. The consistent talking points across a broad number of media underscore that this is a widespread media campaign to shift blame away from the Chinese government.

Beijing has also continued to allow conspiracy theories that blame the U.S. to proliferate uncensored on Chinese social media. Beijing's censors are usually quick to delete comments that vary with the government's official position. The extent and continued presence of these conspiracy theories on Chinese social media represents a tacit endorsement by Beijing.

Likewise, Chinese media have been quick to label references to the "Chinese virus" or the "Wuhan flu" as racist and xenophobic -- a charge that has been echoed uncritically by certain elements of the American media.

The search for a cure, either in the form of a vaccine or a drug regime that will mitigate the worst effects of COVID-19, has become the latest geopolitical arena between China and the U.S. Both countries are rushing to find a cure so they can take credit for "saving" the rest of the world.

Europe has also emerged as the main arena where the Sino-American propaganda war is playing out. Beijing banned the export of most crucial medical supplies to the U.S., including face masks, testing swabs, hand sanitizer and surgical gowns. The ubiquitous N95 masks, for which China is the world's leading supplier, were reserved almost exclusively for Chinese customers.

In the meantime, however, both Chinese and European media outlets have been trumpeting Chinese aid in the form of the same badly needed medical supplies to European countries. In some cases, this aid is taking the form of "gifts" from leading Chinese companies like Huawei to their European business partners.

Russia is following suit. According to Reuters, following a Saturday telephone call between Italian Prime Minister Giuseppe Conte and Russian President Vladimir Putin, the Russian Defense Ministry announced "that military transport planes would deliver eight mobile brigades of military medics, special disinfection vehicles and other medical equipment to Italy from Sunday."

Russian state media has also been quick to take up and amplify the conspiracy theories from China. Multiple Russian media outlets have echoed the claim that the coronavirus is an American-designed bio-weapon intended to cripple the Chinese economy.

Zvevda, a news outlet controlled and funded by the Russian Ministry of Defense, for example, published an article, "Coronavirus: American Biological Warfare Against Russia and China," which claimed the virus was intended to weaken the Chinese economy in order to increase American leverage during the next round of trade talks. Numerous Russian politicians, most notably ultranationalist Vladimir Zhirinovsky, have echoed those claims, blaming the Pentagon as the source of the coronavirus.

The Russian misinformation campaign has also taken the form of widespread inflammatory comments on social media by thousands of accounts believed to be Russian controlled, designed to stoke public fear about the virus and its effects.

On Feb. 22, the U.S. State Department accused Russia of an "intent to sow discord and undermine U.S. institutions and alliances from within by spreading disinformation about coronavirus."

In many cases, Russian agents are, in a technique honed during the 2016 U.S. presidential election, simply amplifying and endorsing comments that are already circulating on social media and that often originated in the U.S. In this way, "fringe" comments that might otherwise have received little exposure get far broader circulation, building momentum and often become "trending" enough to attract the attention of the national media.

It should be noted, however, that Facebook, Twitter and other social media sites claim they cannot find evidence of a deliberate Russian disinformation campaign. The Kremlin has labeled the State Department charges "a deliberate false story."

Not surprisingly, Iranian state media has largely echoed Chinese and Russian stories blaming the U.S. for developing coronavirus and using it as a bioweapon. Tehran has claimed that the virus is part of the Trump administration's maximum pressure campaign against the Iranian government. The Iranian government has pushed for the elimination of American sanctions against Iran in response to the disease outbreak. Similar sentiments have cropped up in Venezuelan media and elsewhere.

The use of disinformation as a propaganda tool, and as an instrument of foreign policy, is nothing new. The Soviets were masters of it and employed it extensively during the Cold War to shape and create anti-American sentiments around the world. The advent of social media, however, has made this a far more potent weapon. Not only does it allow foreign countries to speak directly to Americans, but the freewheeling and uncensored nature of the Internet means that, in many cases, it can also serve to heighten and fan societal divisions and, in particular, fears and anxieties.

This is hardly the first time that America's adversaries have looked to blame it for their own shortcomings and problems, or have sought to capitalize on America's own problems and fears to their advantage. What the coronavirus does underscore is how prevalent such tactics have become and how even a global medical crisis can be used by an opponent to its advantage.

The Consequences of the COVID-19 Pandemic on China's Future

Beijing has good reason to try to deflect the blame for the outbreak. For now, governments around the world have their hands full dealing with the COVID-19 pandemic. There is no question however that the epidemic started in China, as have many of the coronavirus-linked influenza and ARDS disease outbreaks over the last half century.

It's equally clear that Chinese authorities suppressed information of the outbreak, initially denied the Centers for Disease Control and other national health authorities around the world access to samples, critical information about the disease pathogen and the pattern of disease transmission and were in general slow to advise the rest of the world on the outbreak.

The question of whether and, if so, how Beijing should be held responsible for the outbreak of the COVID-19 pandemic is not one that world leaders want to deal with currently. The question has come up at the daily White House briefings on several occasions and was deflected by President Donald Trump. Several members of Congress have already suggested that the U.S. Treasury should unilaterally cancel a trillion dollars of U.S. government debt held by China's central bank to offset the costs of dealing with the COVID-19 pandemic.

It's not clear whether the U.S. government could unilaterally cancel a portion of its debt held by foreign entities. Such a move would certainly roil financial markets and damage the standing of U.S. government debt.

On the other hand, there are clearly going to be consequences to China from how Beijing has dealt with the outbreak. Many companies have been reevaluating their dependence on China-centered global supply chains as a result of the trade war between Washington and Beijing. The realization that those supply chains are also vulnerable to disease outbreaks in East Asia is another strong reason to diversify global supply chains away from China.

Secondly, it is likely that at some point the Trump administration will intensify its efforts to get American companies to repatriate their manufacturing and cut their ties with foreign suppliers of critical items. Medical supplies and equipment, antibiotics and key components of essential drugs are all likely to be targeted with tax incentives, enabling legislation and/or grants to encourage or even force their manufacturing back to the U.S.

Ditto for many other products and industries where repatriation will be seen as a national security issue. It's likely that the Defense Department and defense contractors will be further mandated to seek out American suppliers for the hundreds of billions of dollars of goods they purchase. Other government departments won't be far behind.

Expect renewed pressure on China and other Asian countries to do away with so-called "wet markets" where live animals, both wild and domestic, are sold for human consumption. China banned wet markets during the 2002-2004 SARS crisis but allowed them to resume when the crisis ended. This may also lead to a broader reform of factory farming around the world and more stringent regulations on the use of antibiotics on farm animals.

It's also likely that some kind of medical screening will become standard for incoming passengers on overseas flights to the U.S., especially for those passengers arriving from countries that have wet markets. It may be nothing more than a temperature check initially, with a more rigorous regime as back up whenever major disease outbreaks occur elsewhere in the world.

In a broad sense, Beijing's handling of the COVID-19 pandemic is no different than how it has handled other disease outbreaks in the past. In fact, notwithstanding its initial reluctance to share information, Chinese authorities were probably more open in this instance then they have been in the past, even if they fell short of what was necessary.

The problem is that China plays a different role in the world today than it did 50 years ago. Given that role, its centrality to world manufacturing output and the significant presence of Chinese citizens around the world, the consequences of anything less than immediate and complete transparency when disease outbreaks occur are far graver on the rest of the world.

When China emerged from behind the "bamboo curtain," the presumption was that it would become more like the rest of the world -- that over time, Beijing's authoritarianism would give way to more open, freer markets and civil society. Instead, Beijing has been pushing the rest of the world to become more like China.

The rest of the world, beginning with the U.S., is going to be pushing back hard.


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