Why It's So Hard To Know The Origins Of The COVID-19 Outbreak

The Novel Coronavirus SARS-CoV-2
The Novel Coronavirus SARS-CoV-2
Marilyn J. Roossinck*

Every time there is a major disease outbreak, one of the first questions scientists and the public ask is: "Where did this come from?"

In order to predict and prevent future pandemics like COVID-19, researchers need to find the origin of the viruses that cause them. This is not a trivial task. The origin of HIV was not clear until 20 years after it spread around the world. Scientists still don't know the origin of Ebola, even though it has caused periodic epidemics since the 1970s.

As an expert in viral ecology, I am often asked how scientists trace the origins of a virus. In my work, I have found many new viruses and some well-known pathogens that infect wild plants without causing any disease. Plant, animal or human, the methods are largely the same. Tracking down the origins of a virus involves a combination of extensive fieldwork, thorough lab testing and quite a bit of luck.

Viruses jump from wild animal hosts to humans

Many viruses and other disease agents that infect people originate in animals. These diseases are zoonotic, meaning they are caused by animal viruses that jumped to people and adapted to spread through the human population.

It might be tempting to start the viral origin search by testing sick animals at the site of the first known human infection, but wild hosts often don't show any symptoms. Viruses and their hosts adapt to each other over time, so viruses often don't cause obvious disease symptoms until they've jumped to a new host species. Researchers can't just look for sick animals.

Another problem is that people and their food animals aren't stationary. The place where researchers find the first infected person is not necessarily close to the place where the virus first emerged.

In the case of COVID-19, bats were an obvious first place to look. They're known hosts for many coronaviruses and are the probable source of other zoonotic diseases like SARS and MERS.

For SARS-CoV-2, the virus that causes COVID-19, the nearest relative scientists have found so far is BatCoV RaTG13. This virus is part of a collection of bat coronaviruses discovered in 2011 and 2012 by virologists from the Wuhan Virology Institute. The virologists were looking for SARS-related coronaviruses in bats after the SARS-CoV-1 pandemic in 2003. They collected fecal samples and throat swabs from bats at a site in Yunnan Province about 932 miles (1,500 kilometers) from the institute's lab in Wuhan, where they brought samples back for further study.

Researchers catch bats in a Thai cave —​ Photo: Andre Malerba/ZUMA

To test whether the bat coronaviruses could spread into people, researchers infected monkey kidney cells and human tumor-derived cells with the Yunnan samples. They found that a number of the viruses from this collection could replicate in the human cells, meaning they could potentially be transmitted directly from bats to humans without an intermediate host. Bats and people don't come into direct contact very often, however, so an intermediate host is still quite likely.

Finding the nearest relatives

The next step is to determine how closely related a suspected wildlife virus is to the one infecting humans. Scientists do this by figuring out the genetic sequence of the virus, which involves determining the order of the basic building blocks, or nucleotides, that make up the genome. The more nucleotides two genetic sequences share, the more closely related they are.

Genetic sequencing of bat coronavirus RaTG13 showed it to be over 96% identical to SARS-CoV-2. This level of similarity means that RaTG13 is a pretty close relative to SARS-CoV-2, confirming that SARS-CoV-2 probably originated in bats, but is still too distant to be a direct ancestor. There likely was another host that caught the virus from bats and passed it on to humans.

Because some of the earliest cases of COVID-19 were found in people associated with the wildlife market in Wuhan, there was speculation that a wild animal from this market was the intermediate host between bats and humans. However, researchers never found the coronavirus in animals from the market.

Likewise, when a related coronavirus was identified in pangolins confiscated in an anti-smuggling operation in southern China, many leaped to the conclusion that SARS-CoV-2 had jumped from bats to pangolins to humans. The pangolin virus was found to be only 91% identical to SARS-CoV-2, though, making it unlikely to be a direct ancestor of the human virus.

To pinpoint the origin of SARS-CoV-2, a lot more wild samples need to be collected. This is a difficult task – sampling bats is time-consuming and requires strict precautions against accidental infection. Since SARS-related coronaviruses are found in bats across Asia, including Thailand and Japan, it's a very big haystack to search for a very small needle.

Creating a family tree for SARS-CoV-2

In order to sort out the puzzle of viral origins and movement, scientists not only have to find the missing pieces, but also figure out how they all fit together. This requires collecting viral samples from human infections and comparing those genetic sequences both to each other and to other animal-derived viruses.

To determine how these viral samples are related to each other, researchers use computer tools to construct the virus's family tree, or phylogeny. Researchers compare the genetic sequences of each viral sample and construct relationships by aligning and ranking genetic similarities and differences.

The direct ancestor to the virus, sharing the greatest genetic similarity, could be thought of as its parent. Variants sharing that same parent sequence but with enough changes to make them distinct from each other are like siblings. In the case of SARS-CoV-2, the South African variant, B.1.351, and the U.K. variant, B.1.1.7, are siblings.

Building a family tree is complicated by the fact that different analysis parameters can give different results: The same set of genetic sequences can produce two very different family trees.

For SARS-CoV-2, phylogenetic analysis proves particularly difficult. Though tens of thousands of SARS-CoV-2 sequences are now available, they don't differ from one another enough to form a clear picture of how they're related to each other.

The current debate: Wild host or lab spillover?

Could SARS-CoV-2 have been released from a research lab? Although current evidence implies that this is not the case, 18 prominent virologists recently suggested that this question should be further investigated.

Although there has been speculation about SARS-CoV-2 being engineered in a lab, this possibility seems highly unlikely. When comparing the genetic sequence of wild RaTG13 with SARS-CoV-2, differences are randomly spread across the genome. In an engineered virus, there would be clear blocks of changes that represent introduced sequences from a different viral source.

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There is one unique sequence in the SARS-CoV-2 genome that codes for a part of the spike protein that seems to play an important role in infecting people. Interestingly, a similar sequence is found in the MERS coronavirus that causes a disease similar to COVID-19.

Though it is not clear how SARS-CoV-2 acquired these sequences, viral evolution suggests they arose from natural processes. Viruses accumulate changes either by genetic exchange with other viruses and their hosts, or by random mistakes during replication. Viruses that gain a genetic change that gives them a reproductive advantage would typically continue to pass it on through replication. That MERS and SARS-CoV-2 share a similar sequence in this part of the genome suggests that it naturally evolved in both and spread because it helps them infect human cells.

Where to go from here?

Figuring out the origin of SARS-CoV-2 could give us clues to understand and predict future pandemics, but we may never know exactly where it came from. Regardless of how the SARS-CoV-2 jumped into humans, it's here now, and it's probably here to stay. Going forward, researchers need to continue monitoring its spread, and get as many people vaccinated as possible.The Conversation

*Marilyn J. Roossinck, Professor of Plant Pathology and Environmental Microbiology, Penn State

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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7 Ways The Pandemic May Change The Airline Industry For Good

Will flying be greener? More comfortable? Less frequent? As the world eyes a post-COVID reality, we look at ways the airline industry has been changing through a pandemic that has devastated air travel.

Ready for (a different kind of) takeoff?

Carl-Johan Karlsson

It's hard to overstate the damage the pandemic has had on the airline industry, with global revenues dropping by 40% in 2020 and dozens of airlines around the world filing for bankruptcy. One moment last year when the gravity became particularly apparent was when Asian carriers (in countries with low COVID-19 rates) began offering "flights to nowhere" — starting and ending at the same airport as a way to earn some cash from would-be travelers who missed the in-flight experience.

More than a year later today, experts believe that air traffic won't return to normal levels until 2024.

But beyond the financial woes, the unprecedented slowdown in air travel may bring some silver linings as key aspects of the industry are bound to change once back in full spin, with some longer-term effects on aviation already emerging. Here are some major transformations to expect in the coming years:

Cleaner aviation fuel

The U.S. administration of President Joe Biden and the airline industry recently agreed to the ambitious goal of replacing all jet fuel with sustainable alternatives by 2050. Already in a decade, the U.S. aims to produce three billion gallons of sustainable fuel — about one-tenth of current total use — from waste, plants and other organic matter.

While greening the world's road transport has long been at the top of the climate agenda, aviation is not even included under the Paris Agreement. But with air travel responsible for roughly 12% of all CO2 emissions from transport, and stricter international regulation on the horizon, the industry is increasingly seeking sustainable alternatives to petroleum-based fuel.

Fees imposed on the airline industry should be funneled into a climate fund.

In Germany, state broadcaster Deutsche Welle reports that the world's first factory producing CO2-neutral kerosene recently started operations in the town of Wertle, in Lower Saxony. The plant, for which Lufthansa is set to become the pilot customer, will produce CO2-neutral kerosene through a circular production cycle incorporating sustainable and green energy sources and raw materials. Energy is supplied through wind turbines from the surrounding area, while the fuel's main ingredients are water and waste-generated CO2 coming from a nearby biogas plant.

Farther north, Norwegian Air Shuttle has recently submitted a recommendation to the government that fees imposed on the airline industry should be funneled into a climate fund aimed at developing cleaner aviation fuel, according to Norwegian news site E24. The airline also suggested that the government significantly reduce the tax burden on the industry over a longer period to allow airlines to recover from the pandemic.

Black-and-white photo of an ariplane shot from below flying across the sky and leaving condensation trails

High-flying ambitions for the sector

Joel & Jasmin Førestbird

Hydrogen and electrification

Some airline manufacturers are betting on hydrogen, with research suggesting that the abundant resource has the potential to match the flight distances and payload of a current fossil-fuel aircraft. If derived from renewable resources like sun and wind power, hydrogen — with an energy-density almost three times that of gasoline or diesel — could work as a fully sustainable aviation fuel that emits only water.

One example comes out of California, where fuel-cell specialist HyPoint has entered a partnership with Pennsylvania-based Piasecki Aircraft Corporation to manufacture 650-kilowatt hydrogen fuel cell systems for aircrafts. According to HyPoint, the system — scheduled for commercial availability product by 2025 — will have four times the energy density of existing lithium-ion batteries and double the specific power of existing hydrogen fuel-cell systems.

Meanwhile, Rolls-Royce is looking to smash the speed record of electrical flights with a newly designed 23-foot-long model. Christened the Spirit of Innovation, the small plane took off for the first time earlier this month and successfully managed a 15-minute long test flight. However, the company has announced plans to fly the machine faster than 300 mph (480 km/h) before the year is out, and also to sell similar propulsion systems to companies developing electrical air taxis or small commuter planes.

New aircraft designs

Airlines are also upgrading aircraft design to become more eco-friendly. Air France just received its first upgrade of a single-aisle, medium-haul aircraft in 33 years. Fleet director Nicolas Bertrand told French daily Les Echos that the new A220 — that will replace the old A320 model — will reduce operating costs by 10%, fuel consumption and CO2 emissions by 20% and noise footprint by 34%.

International first class will be very nearly a thing of the past.

The pandemic has also ushered in a new era of consumer demand where privacy and personal space is put above luxury. The retirement of older aircraft caused by COVID-19 means that international first class — already in steady decline over the last decades — will be very nearly a thing of the past. Instead, airplane manufacturers around the world (including Delta, China Eastern, JetBlue, British Airways and Shanghai Airlines) are betting on a new generation of super-business minisuites where passengers have a privacy door. The idea, which was introduced by Qatar Airways in 2017, is to offer more personal space than in regular business class but without the lavishness of first class.

Aerial view of Rome's Fiumicino airport

Aerial view of Rome's Fiumicino airport

Hygiene rankings  

Rome's Fiumicino Airport has become the first in the world to earn "the COVID-19 5-Star Airport Rating" from Skytrax, an international airline and airport review and ranking site, Italian daily La Repubblica reports. Skytrax, which publishes a yearly annual ranking of the world's best airports and issues the World Airport Awards, this year created a second list to specifically call out airports with the best health and hygiene standards.

Smoother check-in

​The pandemic has also accelerated the shift towards contactless traveling, with more airports harnessing the power of biometrics — such as facial recognition or fever screening — to reduce touchpoints and human contact. Similar technology can also be used to more efficiently scan physical objects, such as explosive detection. Ultimately, passengers will be able to "check-in" and go through a security screening anywhere at the airports, removing queues and bottlenecks.

Data privacy issues

​However, as pointed out in Canadian publication The Lawyer's Daily, increased use of AI and biometrics also means increased privacy concerns. For example, health and hygiene measures like digital vaccine passports also mean that airports can collect data on who has been vaccinated and the type of vaccine used.

Photo of planes at Auckland airport, New Zealand

Auckland Airport, New Zealand

Douglas Bagg

The billion-dollar question: Will we fly less?

At the end of the day, even with all these (mostly positive) changes that we've seen take shape over the past 18 months, the industry faces major uncertainty about whether air travel will ever return to the pre-COVID levels. Not only are people wary about being in crowded and closed airplanes, but the worth of long-distance business travel in particular is being questioned as many have seen that meetings can function remotely, via Zoom and other online apps.

Trying to forecast the future, experts point to the years following the 9/11 terrorist attacks as at least a partial blueprint for what a recovery might look like in the years ahead. Twenty years ago, as passenger enthusiasm for flying waned amid security fears following the attacks, airlines were forced to cancel flights and put planes into storage.

40% of Swedes intend to travel less

According to McKinsey, leisure trips and visits to family and friends rebounded faster than business flights, which took four years to return to pre-crisis levels in the UK. This time too, business travel is expected to lag, with the consulting firm estimating only 80% recovery of pre-pandemic levels by 2024.

But the COVID-19 crisis also came at a time when passengers were already rethinking their travel habits due to climate concerns, while worldwide lockdowns have ushered in a new era of remote working. In Sweden, a survey by the country's largest research company shows that 40% of the population intend to travel less even after the pandemic ends. Similarly in the UK, nearly 60% of adults said during the spring they intended to fly less after being vaccinated against COVID-19 — with climate change cited as a top reason for people wanting to reduce their number of flights, according to research by the University of Bristol.

At the same time, major companies are increasingly forced to face the music of the environmental movement, with several corporations rolling out climate targets over the last few years. Today, five of the 10 biggest buyers of corporate air travel in the US are technology companies: Amazon, IBM, Google, Apple and Microsoft, according to Taipei Times, all of which have set individual targets for environmental stewardship. As such, the era of flying across the Atlantic for a two-hour executive meeting is likely in its dying days.

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