Excerpt: Investigating the origin of pandemics

In November, doctors in southeastern China began to see the first cases of what would later be a global pandemic. Doctors had never seen the viral illness before, and at first, thought the cases they were seeing might be atypical pneumonia. Even after doctors began to realize that there was something new about the illnesses they were seeing, “it was kept locally for a while, which was one of the problems.” The disease jumped from mainland China to Hong Kong when a medical professor who was infected, checked into a hotel. The professor soon became sick from the illness and went to the hospital, where he died within two weeks. But during his short stay at the hotel, he unwittingly infected several other guests. Those people then took the disease with them to Singapore, Toronto and Hanoi. It soon spread to neighboring areas and then around the world via air travel. Some infected people spread illness more than others do in the same situation, but these superspreaders were a major factor in the spread of this disease. Patients 40 and older who have chronic ailments like those affecting the heart, liver, lungs, and bowel seem to be those who have become sickest. China was criticized and later apologized, for failing to alert world health authorities of the initial outbreak and taking proper precautions to contain it. The mortality rate of this disease was 10%.

The weird and surprising fact I is that I was talking about the 2004 SARS pandemic and not the current COVID 19 pandemic. Even the timelines of the COVID and SARS outbreak, starting in November are eerily similar, whether 2004 or 2020. In 2004, a possible source of SARS was identified as a cave full of wild horseshoe bats carrying hundreds of SARS-related viruses. This work, published in a draft paper in 2005, unearthed the link between SARS (severe acute respiratory syndrome) and bats for the first time. The SARS virus seemed to have been adapted to live in bats and not in humans.

The researchers investigating SARS drew heavily upon lessons from two earlier outbreaks.

Hendra virus: In September 1994, a horse trainer in Hendra, Brisbane contracted a virus from his horses. 21 horses were involved and of those, 14 died. Two people caught the disease – a stable hand had a self-curing influenza-like illness, and Vic Rail, a 49-year-old trainer. Both men had very close exposure to the sick horses including nursing and hand feeding them during their illness. The disease, infecting horses and humans, was new to both medicine and veterinary science. Within 7 days of hospitalization, Vic Rail needed ventilation. His condition continued to deteriorate, and he died six days later.
As it happened, one month before the case of Vic Rail, in August 1994, a 36-year-old cane farmer fell ill with an aseptic meningitis-like disease after nursing two of his horses. His horses died, but he recovered. In September 1995 (13 months later) he was readmitted to hospital suffering irritable mood and low back pain with seizures. Over the next week, he developed a fever and more generalized seizures, and despite treatment with anti-bacterials, antivirals, corticosteroids, and anti-convulsants his fever continued, whereupon he lost consciousness and died 25 days after admission.
Somebody noted that the most likely periods for contracting the virus coincides with the birthing season of Australian fruit bat species. By 1996 it had been determined that bats were the most likely natural vector and means of infecting horses. Bats harbored the virus without showing infection, and the virus could be found in a number of tissues in a bat. From the 1990’s onward, it has been suspected that habitat disturbance amplifies the production of Hendra virus by bats. As their habitat disappears, bats are forced to live closer to humans, perhaps the ultimate bad neighbors, and so the opportunity for horses and humans to be exposed to the virus has risen.

Nipah virus: This Malaysian virus was named Nipah after a river in the town where the first victim lived. One afternoon during March 1999 in Singapore, an emergency room doctor had just seen two consecutive patients with fever and confusion and was admitting a third, all of whom were abattoir workers. One of them needed to be intubated. The same afternoon saw another two workers from the same abattoir with similar symptoms. Later it was learned that a further six abattoir workers had presented to other hospitals the same week, one of whom died after a rapid neurological deterioration. A team of microbiologists at the University of Malaya in the Malaysian capital Kuala Lumpur isolated a paramyxovirus 5 days after obtaining the first patient samples. Researchers studied a large bat colony on Tioman island, off the eastern coast of West Malaysia. After collecting over 1,000 bat urine samples, the virus was detected in the urine of a species of flying fox. The virus was also found in a piece of fruit that had been partially eaten by a bat. This implied the presence of the virus in the animal’s saliva. Because many Malaysian pig farms have fruit trees, it is easy enough to imagine how the virus can be transmitted from bats. Pigs probably serve as amplifying hosts after ingesting infected bat urine, saliva, or discarded food items.

The COVID 19 scare: Reporter Jane Qiu has a nice writeup on the Scientific American:

“In November 2019, mysterious patient samples arrived at 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 bat-borne viruses like 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. If coronaviruses were the culprit, she remembers thinking, “could they have come from our lab?” She walked out of the conference she was attending in Shanghai and hopped on the next train back to Wuhan.

To Wuhan based virologist, Shi Zhengli, life came full circle. Her first virus-discovery expedition was on a breezy, sunny spring day in 2004, when she joined an international team of researchers to collect samples from bat colonies in caves near Nanning, the capital of Guangxi. These expeditions were part of the effort to catch the culprit in the SARS outbreak. Shi’s team used the antibody test to narrow down locations and bat species to pursue in the quest for these genomic clues. After roaming mountainous terrain in the majority 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 throughout 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. In Shitou Cave—where painstaking scrutiny has yielded a natural genetic library of bat viruses—the team discovered a coronavirus strain in 2013 that came from horseshoe bats and had a genomic sequence that was 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.

And by January 7, 2020 the Wuhan team determined that the new virus had indeed caused the disease those patients suffered—a conclusion based on results from polymerase chain reaction analysis, 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—now officially called SARS-CoV-2 because it is related to the SARS pathogen—was 96 percent identical to that of a coronavirus the researchers had identified in horseshoe bats in Yunnan, they reported in a paper published last month in Nature. “It’s crystal clear that bats, once again, are the natural reservoir,” says Daszak, who was not involved in the study.

Source: shorturl.at/rKPS8

COVID 19 could be another virus programmed to live in bats and not in humans. It was initially called the SARS COV 2 virus (SARS family of viruses) before being called as COVID 19. There are reports that patient zero in the COVID pandemic was a shrimp seller from the Huanan seafood market who contracted it on November 17, 2019. While paradoxically this place is just a couple of miles away from the Wuhan center of disease control and the Wuhan Institute of Virology, scientists have declared that COVID 19 has natural origins. In addition to bats, there is also research that indicates the source could have been wild pangolins, with a match of 88-92% (the most trafficked wild animal in the world). It is very important to stamp out wildlife consumption by humans to prevent similar outbreaks in the future. On February 24, 2020, China took bold steps to shut down the wildlife market industry worth $76 billion, even though it put approximately 14 million people out of a job. These are unconfirmed reports that the wet markets are up and running again. As of 29 March, this has infected 722435 people and caused 33996 deaths, with a mortality rate of 4.7%.

A natural question to ask is why bats are implicated in COVID, SARS and other outbreaks in the past. It turns out that Bats are the natural reservoir all types of dangerous viruses, namely the Ebola, Marburg, Nipah and Hendra viruses. Except for the rabies virus, bats can host all these viruses without becoming sick. So, the question is why do viruses co-exist and tolerate all these dangerous viruses. In a paper published in the journal Cell Host & Microbe in February 2018, scientists at the Wuhan Institute of Virology in China found that the energy demands of bat flight are so great that cells in the body break down and release bits of DNA that are then floating around the body. In most mammals, this would cause serious inflammation as the body would treat DNA particles like viruses. Bats have lost some genes involved in that response, which makes sense because the inflammation itself can be very damaging to the body. They have a weakened response but it is still there. Thus, the virologists write, this weakened response may allow them to maintain a “balanced state of ‘effective response’ but not ‘over response’ against viruses.” The DNA damage repair genes in bats also work more efficiently.

Bats could also harbor a large number of viruses (more than 60 which are harmful to humans alone) because they live in close proximity to each other, and viruses spread quickly in these groups. Since humans also tend to live in groups, viruses primed to live in bats can easily spread to humans. They also have adopted peculiar human traits allowing viruses which live in bats to spread among humans. For example, bats exhibit altruistic behavior, which can serve as transmission routes for viruses. When a bat that has not fed in the night begs for food, other bats, especially females, have no qualms about regurgitating the blood and allowing that unfed bat to feed. Even nursing bats are known to share their milk with males that are hungry. In addition, when a baby bat is orphaned, it is normally adopted by an older female in the colony.

Other researchers have suggested that bats’ super-tolerance might have something to do with their ability to generate large repertoires of antibodies or the fact that when bats fly, their internal temperatures are increased to around 40 deg C, which is not ideal for many viruses. Only the viruses that have evolved tolerance mechanisms survive in bats. These hardy viruses can therefore more tolerate human fever and thrive in humans much better than they would inside bats.


Photo: DR_MICROBE/ISTOCK/GETTY IMAGES PLUS https://www.sciencenewsforstudents.org/article/who-calls-covid-19-a-global-pandemic

Published by Vinod Aravindakshan

Engineer, Economist and Manager

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