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COVID-19: A human adapted virus

Written By: - Date published: 9:30 am, July 24th, 2020 - 23 comments
Categories: China, covid-19, Environment, International, science - Tags: ,

One of the things that has been obvious about COVID-19 from the start has been that it is very well adapted to humans. It has evolved a good entry system to the human airways, is often has mild symptoms, has a long pre-symptomatic infectious period, and doesn’t kill many of its hosts.

These are very good characteristics for a virus evolved to get hosts to make more copies of it’s genetic code. It gets to spread before people are aware that they have it. It didn’t cause too much alarm during its initial spread because most of its hosts got something that was like a mild flu.

By contrast, its close cousin the SARS virus wasn’t well adapted to humans. At the time it becomes infectious in a human host, the human host is aware of it. They’re running a temperature, have chills, muscle aches, headache sneezing, coughing and feeling quite sick. Those are the very things that induce people to go to doctors and hospitals. Which in turn cause our social systems to report and start to contain the disease.

Consequently SARS got identified early before it spread widely through urban populations. With its early fever aspect it was easy to test for. Elevated temperatures provided a efficient way for human societies to isolate hosts and to prevent the replication and spread of the SARS genetic code. Consequently it is effectively extinct in urban human populations

But that same subtlety of its operation has always implied that COVID-19 has been circulating in a human population for some time to evolve those characteristics. The question has where that population is?

There is a nice (but pay walled) article in the Economist that looks at this.

One of the great questions of the past six months is where sarscov-2, the virus that causes covid-19, came from. It is thought the answer involves bats, because they harbour a variety of sars-like viruses. Yunnan, one of China’s southernmost provinces, has drawn the attention of virus hunters, as the closest-known relatives of sarscov-2 are found there. But some think the origins of the virus are not to be found in China at all, but rather just across the border in Myanmar, Laos or Vietnam.

This is the hunch of Peter Daszak, head of EcoHealth Alliance, an organisation which researches animals that harbour diseases that move into people. Since the outbreak, in 2003, of the original sars (now known as sarscov), scientists have paid close attention to coronaviruses. Dr Daszak says that around 16,000 bats have been sampled and around 100 new sars-like viruses discovered. In particular, some bats found in China are now known to harbour coronaviruses that seem pre-adapted to infect people. The chiropteran hosts of these viruses have versions of a protein called ace2 that closely resemble the equivalent in people. This molecule is used by sars-like viruses as a point of entry into a cell.

That such virological diversity has so far been found only in China is because few people have looked at bats in countries on the other side of the border. Yet these places are likely to be an evolutionary hotspot for coronaviruses—one that mirrors bat diversity (see map). The horseshoe bats in Yunnan which harbour close relatives of sarscov-2 are found across the region. Other countries are thus likely to have bats with similar viral building blocks. Dr Daszak believes it is “quite likely that bats in Myanmar, Laos and Vietnam carry similar sars-related coronaviruses, maybe a huge diversity of them, and that some of them could be close to sarscov-2”.

Economist: “SARS-CoV-2 will look beyond China

One of the strong supporting arguments to support this has been the very low rates of infection in Vietnam (412 confirmed cases) and Cambodia (198 confirmed cases). Relative to the population levels of 95+ million and 16+ million respectively, these have been extraordinarily low.

Both states are authoritarian and, especially in the case of Vietnam, have been intensely proactive with dealing with COVID-19. While there don’t appear to have been any excessive mortality level studies on these states, there also haven’t been evidence of hiding of cases either.

Vietnam is an authoritarian, one-party state which is notoriously secretive about sharing information.

But most experts believe Vietnamese authorities are being honest about coronavirus statistics.

Huong Le Thu, an analyst at the Australian Strategic Policy Institute, told the ABC that given international organisations, foreign epidemiologists and even Australia’s ambassador to Hanoi have expressed confidence in the data, she had “no reason” to doubt the figures.

The Reuters news agency reported none of the 13 funeral homes it contacted in Hanoi have seen an increase in funerals amid the pandemic.

“I know I sound like I’ve drunk the Kool-Aid, but I don’t see any alarm bells ringing about the accuracy or lack of transparency in the numbers,” said Sharon Kane, Vietnam country director at Plan International, an NGO that works on public health.

Radio New Zealand: “How has Vietnam, a developing nation, had no Covid deaths?

When you look at the list of COVID-19 cases in Vietnam or Cambodia, what does become obvious that they have excessive representation in people who grew up in other areas of the world.

John Bell, a professor of medicine at the University of Oxford, says everyone thought there would be a flood of cases in Vietnam because the country is right across the border from China. Yet Vietnam has reported only 300 in a population of 100m, and no deaths. The country did not have a great lockdown either, he adds. Nobody could work out what was going on.

One explanation, he suggests, is that Vietnam’s population is not as immunologically “naive” as has been assumed. The circulation of other sars-like viruses could have conferred a generalised immunity to such pathogens. So, if a new one emerged in the region, it was able to take hold in the human population only when it travelled all the way to central China—where people did not have this natural resistance.

This would tie in with the idea that infection with one coronavirus can provide protection against others, and that even in countries away from the evolutionary cauldron of South-East Asia part of the population may have some protection against the current pandemic. In particular, there are suggestions that protection might be conferred mainly via part of the immune system called t-cells (which work by killing virus-infected cells) rather than via antibodies (which work by gumming up pathogens). If that is the case, then serological studies which look at antibodies may be underestimating natural immunity.

All of which means that searching the reservoirs of bats of Vietnam, Cambodia, and Laos for a exact or very closer match for COVID-19 would be a good idea. Since the identification of the human corona virus in the common cold viruses back in the 1960s, we have had a number of identified epidemic outbreaks. SARS. MERS, and now COVID-19.

Each has caused a flurry of activity in various regions of the world and now at a global level. Two of these (SARS and MERS) were pretty obviously recent and ill-adapted hops from a host (probably a bat) directly or indirectly to humans. But COVID-19 appears to be exceptionally well adapted to humans and spreading in human societies. It is causing immense amounts of damage when it managed to spread out of whatever enclave where it was already endemic.

It’d appear to me that proactively knowing what is out there in the wild is the best way to prevent the next corona virus from the same enclave. It’d be rare for single virus variant to be endemic. Where there is one, there are likely to be more sharing similar characteristics.

Finding out the intermediate vector species or practices that allow the spread to a human population would also be very useful in preventing future epidemics. Because we’re going to see them as our population and practices keep expanding into wild areas, and as we keep shutting human hosts around the world to assist in their spread.

As for the mystery of the origin of covid-19, more answers will come when the who mission takes place, perhaps in August. The critical steps that led a South-East Asian bat virus to start a pandemic could have happened inside or outside of China—whether in wild-animal markets or farms, or in traders or hunters. The virus may have jumped directly from bats into people, or come via an intermediate species. The story is waiting to be told. 

Economist: “SARS-CoV-2 will look beyond China


As a side note, the wacky conspiracy theories that any human was capable of designing these characteristics into a virus are pretty ludicrous. As a technical species, we simply don’t have the genetic subtlety to design something like COVID-19. Much the same applies to the idea that a release of the naturally occurring sample of the virus from a lab being of significance is just stupid and ignorant. At some stage the virus would would have escaped from whatever human enclave it was in – and infected the rest of the world.

23 comments on “COVID-19: A human adapted virus ”

  1. ianmac 1

    Presumably Trump will declare from his position as an eminent scientist that the above is impossible. His gut continues to tell him that this was a Chinese designed virus.

    On a serious note it seems possible that not only is the above column possible, but it does raise the probability that there will emerge more lethal viruses. I Health System needs serious upgrading.

    • lprent 1.1

      … it does raise the probability that there will emerge more lethal viruses.

      I'd bet on it within the current decade, and I don't gamble on anything less than a sure bet.

    • Draco T Bastard 1.2

      A more lethal virus is inevitable. Evolution happens all the time and, as viruses have a really short life cycle, viruses evolve damn fast.

      The problem is that many people seem to think that everything is as it has always been and that it will always be this way and thus think that we don't need any more than what we have as far as necessary protections (like a good health system) go.

      • JohnSelway 1.2.1

        Not to mention how quickly bacteria are evolving to resist antibiotics which, in my opinion, is a far scarier proposition. A resistant strain of the Bubonic Plague would be an absolute nightmare

        • Draco T Bastard 1.2.1.1

          And the answer to that is to stop using antibiotics as much as we do. Which never seems to go down well:

          Sick person: But, I need antibiotics for this common cold.

          Doctor: No, you don't – you need bed rest

          Sick person: But, I need to go to work…

          See the problem?

          • JohnSelway 1.2.1.1.1

            I agree – some doctors throw antibiotics in when they aren't even needed. My father was a practicing GP and he always prescribed antibiotics sparingly

  2. Andre 2

    I've spent a while wondering if maybe the virus made the jump to humans and became endemic in some isolated population of humans quite a while ago, allowing it to evolve its improved adaptation to humans, then some intrepid traveler finally ended up catching it and bringing it out of its isolation.

    In which case Wuhan just had the bad luck to be where the first superspreading event occurred in the chains of transmission.

    • ianmac 2.1

      Wasn't there an obscure report that a Covid infection was discovered in France last year?

      • Andre 2.1.1

        Yeah. But IIRC that was late enough in the year that it could still be consistent with the Wuhan outbreak as the point of transfer to humans. Or not.

    • AB 2.2

      "endemic in some isolated population of humans quite a while ago, allowing it to evolve its improved adaptation to humans"

      Wouldn't it require a fairly large population of humans for the virus to work through over time in order to acquire those adaptations? A couple of hundred people up a remote valley somewhere presumably wouldn't be enough – and therefore – do sufficiently large isolated populations actually exist for this scenario?

      • Draco T Bastard 2.2.1

        A couple of hundred people up a remote valley somewhere presumably wouldn't be enough

        It would be enough if the virus had several human generations to evolve over. They're pretty much immune, remember.

  3. Drowsy M. Kram 3

    Thanks for an excellent summary of that Economist article which makes a (much) more convincing case for the likely origin of sars–cov-2 (–> Covid-19) than Sørensen and Dalgleish, or the much touted Chris Martenson who has shifted to 'safer' ground.

    A few will continue to insist that evil fiends in the CCP must (somehow) be to blame, because they're evil fiends. There is, however, plenty of evidence that the CCP's 'methods' would be inimicable to NZ's way of life without resorting to speculative fearmongering.

    https://en.wikipedia.org/wiki/Misinformation_related_to_the_COVID-19_pandemic#Bio-engineered_virus

    • mauī 3.1

      Side with the so called 'experts' why don't you, although they're far from convincing, doing their best to say it's inconceivable.

      Martenson puts forward a reasonable theory that it could be an artificial virus, yet scientific people such as yourself dismiss him out of hand. Perhaps it's because he was miles ahead of the WHO in calling this disease a pandemic, and that mask use was essential to stop the spread, among other things. We can't have an outsider being proven right can we.

      • Drowsy M. Kram 3.1.1

        I've no problem with so-called outsiders being proven right – scientific discovery is sprinkled with examples of outsider opinion overturning expert consensus, but it's not a common occurrence. What really interests me is why some on-lookers favour outsider opinion over expert consensus – might there be other, non-science 'factors' at play?

        For example, wouldn't it have been great if climate change deniers (all outsiders now) had been proven right. But now we know, and that truth will set us free, eventually.

        • Andre 3.1.1.1

          … scientific discovery is sprinkled with examples of outsider opinion overturning expert consensus, but it's not a common occurrence.

          "Not a common occurence" gives the impression it happens far more frequently than actually happens. A better description is "extremely rare occurrence".

          When it does happen, it's almost always the result of an enormous amount of work to first show the flaws in the existing consensus, then convincingly demonstrating the alternative that overthrows the previous consensus.

          Random off the cuff reckons from someone not actively working in that particular field are a very unlikely source of overthrowing the expert consensus. So yeah, it is indeed a very interesting question as to why some people immediately choose to believe the random off-the-cuff reckons over the considered expert consensus.

          • Drowsy M. Kram 3.1.1.1.1

            Fair enough Andre – hoped that use of the word "sprinkled", as opposed to 'littered', would give a clue as to how (extremely) uncommon / rare these 'game-changing' (urgh) 'paradigm shifts' (double urgh) are, although quantitation is problematic.

            Specific examples that sprang to mind were the efforts of Nobel prize winners in Physiology or Medicine 1997 (Prusiner) and 2005 (Marshall and Warren).

        • mauī 3.1.1.2

          "What really interests me is why some on-lookers favour outsider opinion over expert consensus.."

          I'm thinking there's probably a correlation between the prevalence of conspiracy theories and bullshit expert explanation where the facts aren't supportive or have large gaps.

  4. Adrian 4

    Last week I heard a report ( sorry don't remember when but probably NatRad as out in a paddock working ) that sewage samples from around the world have reportedly identified Covid -19 as having been around for at least 2 years. The assumption was that it needed the right enviroment to go rogue involving temperature, humidity and a suitable human host and Wuhan market may have just fitted the bill.

  5. Editractor 5

    Given this discussion, this pre-proof essay from a science journal may be of interest to some:

    "On the evolutionary epidemiology of SARS-CoV-2"

    • Wairua 5.1

      I clicked the link and got an automatic download rather than an open document. .I prefer to have some control over downloads. Cheers ..

      • Brigid 5.1.1

        Because it's a pdf. Perhaps have a look at your browser settings see if you can disable this function.

      • Incognito 5.1.2

        Always hover your cursor over a link before you click. Once you click it is up to your system and its settings as to what happens next.

      • Editractor 5.1.3

        The file is a pdf. If you want it to open automatically in your browser you will need a browser pdf reader.

        I would have left the raw link but as I have a pdf reader extension the file contents were automatically being displayed inside the post, which made it too small to read.

        The file comes from cell.com, Cell being a major publisher of scientific journals, but you are right to be cautious anyway.

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