Thursday, June 23, 2022

Ancestral East Asians and adaptation to coronaviruses

 



Early farming village in China (Wikicommons – Xinyang City Museum, Gary Todd)

 

Respiratory viruses began to propagate more easily when hunting and gathering gave way to farming and as settlements grew larger. Humans may have then evolved to use coronaviruses as a natural vaccine against deadlier respiratory diseases, like tuberculosis and pneumonia.

 

 

A new genomic study has found that East Asians had to adapt to epidemics of coronaviruses some 25,000 years ago. The authors looked at gene variants for proteins that interact with coronaviruses in five East Asian populations: Han Chinese (Beijing); Han Chinese (South China); Dai (Yunnan, China); Japanese; and Vietnamese. There were three main findings:

 

·         Ancestral East Asians had to adapt to coronavirus epidemics around 25,000 years ago

·         They adapted by acquiring mutations that are close to genes that regulate the development of lung tissue and other tissues affected by COVID-19

·         Those mutations either promote or block infection by coronaviruses (Souilmi et al. 2021, p. 3505).

 

The last finding is puzzling. Did those ancestral East Asians become more vulnerable or less vulnerable to coronaviruses? The authors simply say that half of those mutations from 25,000 years ago have “anti- or proviral effects” versus 29% of all proteins that interact with coronaviruses (Souilmi et al. 2021, p. 3509). Fine. But how many of those mutations were antiviral and how many proviral?

 

It might seem strange that natural selection would actually make people more susceptible to coronavirus infections. Yet such susceptibility could be beneficial. A viral infection can boost immunity to other pathogens, including deadly ones that cause tuberculosis, pneumonia, or pneumonic plague. Until recently, coronaviruses were typically mild in their effects, producing what we call the “common cold.” They may thus act as a natural vaccine against deadlier respiratory diseases (Frost 2020).

 

Respiratory diseases are believed to have become serious for humans when hunting and gathering gave way to farming. People became sedentary and their settlements grew larger with time, thus providing respiratory viruses with better conditions for propagation (Comas et al. 2013). This theoretical model is in conflict, however, with the above finding that ancestral East Asians began adapting to coronaviruses some 25,000 years ago, long before they adopted farming and became sedentary. We’re thus left with the unlikely conclusion that coronavirus epidemics began among scattered bands of hunter-gatherers.

 

The estimate of 25,000 years ago is probably wrong. The authors arrived at that figure by calculating the latest date when the ancestors of the four East Asian groups were still a single population. But East Asians are not descended from a single population. Their origins are best described by the "Two-Layer" (TL) hypothesis:

 

·         Modern humans spread into East Asia through a northern route and a southern route.

·         The southerners were then replaced to varying degrees by northerners who spread out of northeast Asia and successively occupied northern China, southern China, and Southeast Asia (Oxenham and Buckley 2016; Xu et al. 2006).

·         Thus, as you go farther south in East Asia, the population has a greater admixture from the earlier southern “layer”—from hunter-gatherers who closely resemble the relic groups that still exist in parts of Southeast Asia, i.e., the Andaman Islanders, the Aeta of the Philippines and the Maniq and Semang of the Malayan Peninsula.

 

Admixture from that older southern substrate pushes back in time the latest common ancestors, who never existed. Adaptation to coronaviruses therefore happened at a later date, probably when the “northerners” pushed into what is now northern China and adopted farming. They then grew in population, pushed farther south, and intermixed with the hunter-gatherers who lived there. 

 

 

References

 

Comas, I., M. Coscolla, T. Luo, et al. (2013). Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics 45: 1176–1182. https://doi.org/10.1038/ng.2744

 

Frost, P. (2020). Does a commensal relationship exist between coronaviruses and some human populations? Journal of Molecular Genetics 3(2): 1-2. https://researchopenworld.com/does-a-commensal-relationship-exist-between-coronaviruses-and-some-human-populations/

 

Frost, P. (2022). A natural vaccine. Evo and Proud, February 21 http://evoandproud.blogspot.com/2022/02/a-natural-vaccine.html

 

Oxenham, M., and H.R. Buckley. (2016). The population history of mainland and island Southeast Asia, in M. Oxenham and H.R. Buckley (eds) The Routledge Handbook of Bioarchaeology in Southeast Asia and the Pacific Islands. Routledge.

 

Souilmi, Y., M.E. Lauterbur, R. Tobler, C.D. Huber, A.S. Johar, S.V. Moradi, W.A. Johnston, N.J. Krogan, K. Alexandrov, and D. Enard. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Current Biology 31(16), 3504–3514.e9. https://doi.org/10.1016/j.cub.2021.05.067

 

Xue, Y., T. Zerjal, W. Bao, S. Zhu, Q. Shu, J. Xu, R. Du, S. Fu., P. Li, M.E. Hurles, H. Yang, C. Tyler-Smith. (2006). Male demography in East Asia: A north-south contrast in human population expansion times. Genetics 172: 2431-2439, https://doi.org/10.1534/genetics.105.054270

8 comments:

Santocool said...

''It might seem strange that natural selection would actually make people more susceptible to coronavirus infections.''

Evolution doesn't always mean ''improving a function'' and selective processes can be extremely slow, even more so for large populations and when is not an epidemic of a very serious disease.

Another possibility is that not all east asians populations have been equally exposed to thesecorona virus epidemics.

Also these epidemics must also be more severe in children and adolescents to have a stronger effect on the selection of the most adapted.

''This theoretical model is in conflict, however, with the above finding that ancestral East Asians began adapting to coronaviruses some 25,000 years ago, long before they adopted farming and became sedentary. We’re thus left with the unlikely conclusion that coronavirus epidemics began among scattered bands of hunter-gatherers.''

...began adapting...

Consumption of contaminated meat?

https://www.apmresearchlab.org/covid/deaths-by-race

Peter Frost said...

Santocool,

"Evolution doesn't always mean ''improving a function'"
In Darwinian theory, evolution means becoming better adapted to your environment. There are cases of balanced selection, where an organism becomes less adapted for one trait in order to become more adaptive for another trait. But that wouldn't apply here.

In the past, children died of pneumonia and tuberculosis.

With respect to COVID-19, Asian Americans take more precautions than do most other ethnic groups. Also, the category "Asian American," like the category "White American," is far too broad to be useful.

Santocool said...


''In the past, children died of pneumonia and tuberculosis.''

But I mean specific diseases.

We are all exposed to common flu viruses, but when the new coronavirus appeared, the vast majority of people who died from it could have easily survived a flu.

And you're talking about specific variants, right?


''is far too broad''

Not so much. To say that is not possible to conjecture with these definitions seems to me to be an exaggeration. Of course, the ideal is always to specify, to enrich with more information.

Relative to Native Indians, Blacks, Pacific Natives, and Hispanics, it seems less vague to me.

It is surprising that Hispanics have died below their average in the general population. But it is always important to take factors other than genetics into account.


''In Darwinian theory, evolution means becoming better adapted to your environment. There are cases of balanced selection, where an organism becomes less adapted for one trait in order to become more adaptive for another trait. But that wouldn't apply here.''

Ideally, but evolution is synonymous of change or transformation, which can go in any direction, including a less ideal direction.

How are you sure?

Anonymous said...

sorry, but pneumonia, tuberculosis and (pneumonic) plague are deseases not caused by VIRUSES, but by BACTERIA.
it may happen, that (some) corona viruses also could act/infect bacteria in human organic tissue? or simply boost human immune systems.
...
santocool's blaant starement: 'covid-19 victims would have overcome/survuved easily any flu' is nonsense. covid was/is mortal for people over 80plus, extreme obese, suffering from multiple desease, diabetes/cancer. in all waves of flu infections, these groups also were victims of flu. . germany about 25 000 in 2018.(if the recent covid-methods to count would have applied then, certainly 50-100 000 )

Santocool said...

Completely incoherent comment. I know very older people have comparatively higher rates of mortality by flu but you're putting in the same pocket these people with younger or overweight adults or with commorbities like diabetes. Likely different/comparatively lower rates of mortality. If a common flu was as deadly as covid, we would have seen an excess of deaths every year without a new strain circulating around us.

Santocool said...

The first stat about mortality rate for 80 years or more by covid in China was 15% or more of likelihood. So covid still not (totally) mortal to this demographic segment. But because very older people is so rare even today when they died in higher rates it is more noticiable.

Peter Frost said...

Santocool,

Viral infections seem to boost the immune response to any infection. So I'm not talking about specific respiratory pathogens.

Human evolution accelerated after the formation of large geographical races. Most of the interesting differences are between smaller groups of more recent origin.

Actually, maladaptive change is much more likely than adaptive change. On the other hand, maladaptive change is much, much less likely to survive.

Anon,

Sorry, that was a big blooper on my part. I should have written "respiratory pathogens" instead of "respiratory viruses." Pneumonia can be caused by respiratory viruses, however.

Santocool said...

''Viral infections seem to boost the immune response to any infection. So I'm not talking about specific respiratory pathogens.''

So how have many people, including young people without comorbidities, dying of covid-19, before vaccines were available,if they have also been exposed annually to these nonspecific viral strains throughout their lives??

Your logic doesn't seem to make sense in this current pandemic scenario.

I think that the fact that Asians are less prone to obesity, diabetes, or cardiovascular disease, as a genetic or biological explanation, apparently contributes to having fewer deaths from covid-19.

Not to mention their tendency to respect rules, especially those of a sanitary nature, also contributed to less people being exposed to contamination.

Do East Asians have, on average, more robust health in general?


''Human evolution accelerated after the formation of large geographical races. Most of the interesting differences are between smaller groups of more recent origin.''

Agree.

''Actually, maladaptive change is much more likely than adaptive change. On the other hand, maladaptive change is much, much less likely to survive.''

All populations carry some level of mutation burden or genetic diversity relatively independent of selective events, which are related to their own probability of combinations during or since conception and which originated before or from a primordial founder effect.

We not only inherit traits from our parents and their genealogical subbranches, but also combinations of these traits.
Traits, when inherited, are not inherited individually, especially complexes, which are often part of a larger phenotype, as in the case of personality.

This is why certain minority conditions, whether very negative or neutral, manifest, regardless of whether there is some prior selective process at work to increase or decrease their phenotypic expression.

My opinions.