The above map shows cumulative coronavirus cases. One of the things that I’m still confused by are some geographic patterns. For example, Thailand with 70 million people has had fewer than 4,000 cases and 60 deaths attributed to COVID-19. Bolivia with 11 million people has had 8,900 deaths. Why? There are many theories out there. One thing that is hard to deny: mainland Southeast Asia and Northeast Asia seem to be handling the pandemic “well” (at least after the Wuhan outbreak).
A new preprint on bioRxiv has gotten people even more curious, An ancient coronavirus-like epidemic drove adaptation in East Asians from 25,000 to 5,000 years ago:
The current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that started 25,000 years ago. These adaptive events were limited to ancestral East Asian populations, the geographical origin of several modern coronavirus epidemics. An arms race with an ancient corona-like virus may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to combat the pandemics of the future.
The evidence in the preprint is pretty persuasive. First, I need to communicate something the last author told me: there is no evidence in their results that East Asians have particular robustness or vulnerability to COVID-19. That is due to the fact that these selection sweeps can cut both ways with this particular virus. The GWAS themselves need to be done, and they haven’t been (something like the GWAS done in Europeans).
But, if you eliminate this possibility that makes us ask, why are diverse East Asian societies doing relatively well? Thailand is not Confucian. Vietnam is somewhat, and South Korea is a great deal. But all these nations have been doing well (Confucian South Korea actually has about 10 times more per capita deaths than Thailand).
Second, what was going on 25,000 years ago? One of the things I learned in a book like Fate of Rome is that pandemics are a feature of civilized dense global empires. So it seems unlikely that the ancient proto-Asians were subject to pandemics. But I have read that even endemic infectious diseases may have had issues at hunter-gather population densities. But the results from this preprint indicate a massive sweep for many generations right before the Last Glacial Maximum. Figure 1 in the preprint makes it obvious that this is restricted to East Asians. That being said, the signal in Japanese seems a bit attenuated compared to the Kinh and groups from China, so I wonder if this did not impact to the Jomon (25% or so of Japanese ancestry) but was restricted to somewhere in mainland East Asia?
wrt Thailand, more prosaic contributing factors ought not to be overlooked. Many people unfamiliar with Thailand might be surprised to learn that they have an excellent public healthcare system. Hong Kong’s is good, Thailand’s is better. Also, although they were initially too relaxed at the very start, they very quickly woke up to the threat, particularly from Chinese tourism, and closed their borders. And then of course there were no more Chinese tourists to keep out.
Vietnam – they were very fast in getting their borders closed, faster than Thailand. Probably faster than just about anyone.
In this pandemic, speed is everything – keeping the numbers low so that you can manage them with testing, tracing contacts and effectively quarantining them. That has worked for Australia and New Zealand, aside from one big unforced error in the state of Victoria in Australia (using untrained security guards to guard a quarantine hotel) which took months to get under control with heavy lockdowns. They are now free of it, though.
No one has noticed Macau – small population, but their total infected are only in double digits and zero fatalities, and they are contiguous with the Mainland, but border controls are tight – I can personally attest that border controls Macau/Mainland and HK/Mainland are very tight.
There are lots of apparent anomalies globally, so I’m not ruling anything out, but my feel is that this is at least a partial explanation.
“Second, what was going on 25,000 years ago?”
In Hunan, Jiangxi, Hubei that’s suspiciously close to when the first pottery was used. No idea what the where boiling in the Xianrendong Cave, at least wild rice.
https://www.theguardian.com/science/2012/jun/28/ancient-chinese-pottery-oldest-yet
I thought the Jomon were around 10% of Japanese ancestry, not 25%.
I’d say probably about 10-15% yeah. (Reasons pretty much the same as gave in comments here: https://www.gnxp.com/WordPress/2019/05/23/the-jomon-contributed-little-to-the-japanese/ … Though I think there might be some more published papers since this time that address the question more directly).
Not the most elegant example, but in the recent paper “Genomic Insights into the Demographic History of Southern Chinese”, Japanese have qpAdm model of 3.5% more of the “Early Branching with Onge Basal East Eurasian” (ugh what a moutful) ancestry than Koreans (who r similar in proportion of that to LN Coastal North China), and Jomon samples 38.7% more than Koreans so fits Japanese about 10% from Jomon. (Japanese modelled with about same total Early_Branching_Onge as North Chinese Han; Tibetans about same as Central Chinese Han groups. Table – https://imgur.com/a/ABb9sng).
My theory about East Asians is that they survived on the Eastern steppe, cut off from the West and North, under extreme climatic conditions, with very harsh, dry and cold winters, in which people spent a lot of time in closed dwellings. Both some physical, as well as psychological adaptations, point into that direction of selection in favour of people doing better if having to live together in a rather limited space.
Under these circumstances, an epidemic leaping from one habitation to the next seems to be very real, because I think also, that the fairly large groups living in close quarters had intensive contacts with each other. Just imagine a visitor coming to one of these dwellings in winter time, being himself still in the incubation period. Obviously this could have spread like wildfire and if there would have been good conditions for a respiratory virus to spread quickly in pre-Neolithic times, the best were in the refuge area for East Asians.
I also think that this kind of selection, physically, psychologically, immunological, was also part of the success story later, when the transition to the Neolithic happened. What other people had to adapt to newly, once they came into contact with the settled Neolithic way of life, East Asians in their larger scale dwellings had aleady done before, to a large degree. So the transition might have been much more fluent than for many other people in Eurasia, resulting in their successful, smooths transition with minimal to no replacement.
Also there is always the possibility of human ancestral components spreading with the help of pathogenes in a way which approaches “Co-evolution”. One notable example would be smallpox with European ancestry in America, another well known is Subsaharan ancestry with Malaria. Malaria is in some regions the single most important advantage Subsaharan Africans had in the competition.
And now we even have a new study digging deeper into this:
“Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ~22 generations. We estimate the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference.”
“We hypothesized that admixture has facilitated rapid adaptation to the malaria parasite Plasmodium vivaxvia the malaria-protective DARC locus (Duffy antigen receptor for chemokines; also known asAtypical Chemokine Receptor 1 (ACKR1)) in Santiago. The protective allele is almost fixed in West African populations and rare elsewhere.”
That kind of co-evolution will be seen even much more often, though probably not on such a high level. It was noticed in the historical accounts, that Malaria was directly introduced with black slaves into regions of America which didn’t had it before. Kind of an interesting that the disease helped to spread the associated, better adapted ancestral component.
“Interestingly, this hypothesis goesback to a voyage in 1721 in which Captain George Roberts reported that a disease in Santiago is “dangerous to strangers” during the rainy season (Roberts, 1745). Consistent with ancestry-mediated protection from malaria, the record has been interpreted by medical historians to suggest that “foreign visitors and residents of European descent seem to have suffered more than the African and Afro-Portuguese majority” from malaria in Santiago.”
Source:
https://www.biorxiv.org/content/10.1101/2020.09.01.278226v1
In Africa itself the distribution of Subsaharan or in more detail Niger-Kordofan/Negroid ancestry (Khoisan not) alligns very well with the distribution of Malaria.
The hypothesis may be true but China is faking it’s numbers. There hasn’t been real information out of China since February when they kicked out all foreign journalists. The Chinese population makes up most of south east asia. Other nations are relatively small, area wise and that makes implementing anything easier.
@superkuh: There are 1.4 billion Chinese most with access to smartphones and internet not to mention the innumerable number of foreign expats.
If the numbers were off by order of magnitude or coverups of subsequent outbreaks the CCP couldn’t hide it for long.
In fact you’re wrong ‘there hasn’t been any info since Feb’. Northern Manchuria, Xinjiang, Hainan, Beijing, Shanghai small outbreaks have been openly reported on and something you would be aware of if you were actually keeping track. What China has been able to demonstrate is the state capacity to contain and extinguish these outbreaks as they occur.
There is cognitive dissonance that CCP bad = lying/can’t possibly be doing better than US/Europe. Unfortunately facts don’t match up to your feelings. They’re doing better.
The big difference in Chinas response was that they managed to largely isolate the virus on the provincial level. Once it spreads throughout the country, you have to make a nation-wide lockdown to get the number down. The usual safety-measures don’t suffice any more and then you have a big economical damage done to your system, which you can’t keep up. Corona is bad, but its not the plague, so a years-long lockdown is no option.
We all saw the radical measures activated in on the provincial level, and the safety-measures nation-wide. The Chinese seem to have gotten the upper hand.
North America and Europe could have done so too, by similarily banning, sufficiently controlling (with isolation-quarantine) international traffice and shutting down on the provincial level immediately. They did not, so they couldn’t manage it.
If one of the vaccines is really safe & effective, China will be the big winner. If not, they can’t keep it up forever, but can at least ameliorate the effects.
Is anyone doing a GWAS study on COVID infections, severity, and deaths in the US?
Or are they afraid of the answers?
In 2019’s highly unreliable Global Health Security Index, Thailand was the highest ranked nonwhite country (even higher than South Korea), so it doing well at countering COVID is not too surprising. Recall that Thailand was the first country to record a COVID case outside of China. Vietnam is a country with a ruling Communist party, as are Laos and Cuba. Mongolia and Taiwan responded quickly with travel restrictions because they’re neighbors of China. The outbreaks in Malaysia, Burma, the Philippines, and especially Indonesia should put to rest any theories that Asians are immune to the virus. Cambodia seems to have avoided any major outbreak for much the same reasons Burma managed to for the first few months of the pandemic -travel restrictions combined with its general unimportance.
Hadn’t heard of it, so I looked it up:
https://www.ghsindex.org/
Some of it makes for strange reading after the event, so to speak. The ‘most prepared’ countries? USA a long way first, followed by the UK. Highly unreliable was a reasonable description.
Looking at the OP map, and wondered what it would look like per capita. The best we can do right now is this: https://tinyurl.com/y458sdak
As a periodic review thing, here’s where India, Pakistan, Iran stands on coronavirus relative to some comparison countries: https://tinyurl.com/y58qyb32
Bommer and Vollmer suggested that, purely going on demography and age, IFR should be about 1:3 between India:EU/USA, and about 5:6 between India:Brazil, and 1:1 Iran.
Actual peak of death rates between India:EU / India:USA is about 1:10, peak of death rate relative to Brazil about 6.25x, peak of death rate relative to Iran 7x.
Ratio of cumulative deaths, India:US/Brazil – 1:8, India:EU – 2:11.
Pakistan has done better than India (death ratio about 1:3 between them) and is now “returned to normal” (since September) as far as Google Mobility data shows – https://ourworldindata.org/covid-mobility-trends
Indication that Indian and Pakistani public health state capability higher than EU, since demographically adjusted performance better? E.g. deaths lower than expected. sing Tiger of Pakistan more competent generally?
On the other hand, Iranian public health state capability very low relative to Pakistan… (Iran deaths picking up very rapidly)?
GWAS studies have reported a genetic susceptibility to severe COVID-19 that is associated with Neanderthal-related parts of the genome. Is that a factor in the near absence of reports from Africa?
Re genetic v. cultural/political adaptations, I’d think it would be helpful to look at East Asians who don’t live in East Asia. Some left many generations ago and are pretty assimilated.
@Matt
Interesting observation. I totally missed that chart.
However the preliminary analysis of southeastern ancient Korean remains(~7000 years BP and onward) seems to suggest that they had some Jomon-like components already and Yayoi Japanese already had Jomon like elements before they entered Japan. So the actuall Jomon admixture inside Japan may have been even lower.
This also means that not all “Andaman HG” portion of Koreans came from LN China. Likewise for Devil’s Gate.
The Koean remains were submitted to Max Planck Inst. by more sensible and realistic Korean scholars(finally) who knew their limations and you will see the results in the next few years.
@superkuh: “but China is faking it’s numbers”
The paper from 2 experts in fraud detection, Koch (Research Department, Federal Reserve Bank of Dallas) and Okamura (Saïd Business School, University of Oxford):
Do you think you know more than them??
Blood group A has been shown to affect covid infection, though SES, cultural, health care facilities also matter. Globally Thailand ranks third in low blood group A percentage, so are many other East Asian countries. Note SKorea actually has higher %GroupA than UK. India seems to be an outlier as they also have less GroupO which is less susceptable to covid and they also have more Neanderthal gene variants that are more susceptable to covid. GroupO is dominant in China but Wuhan and Beijing have exceptional higher %GroupA due to more descendents from the ancent assimilated northerners.
Rank | %BloodA | Country
3 | 16.9 | Thailand
8 | 20.8 | India
13 | 21.9 | Vietnam
21 | 23.9 | Singapore
27 | 25.9 | Taiwan
30 | 26.1 | Macao
32 | 26.13 | HongKong
38 | 27.2 | Cambodia
40 | 27.42 | World
44 | 27.8 | China
49 | 29.45 | Bolivia
54 | 30.35 | Malaysia
60 | 32.0 | UnitedKingdom
71 | 33.87 | SouthKorea
81 | 35.7 | UnitedStates
83 | 36.0 | Italy
83 | 36.0 | Spain
90 | 37.0 | Sweden
The clades of SARS2 also show quite distinct geo distribution, like the clade 19’s in the Pacific rim regions and Clade 20’s in the Atlantic rim countries. Higher %Clade19’s regions tended to have less covid fatalities, a very obvious example is between US west coast California which have significant clade19’s and east cost NewYork which is mostly clade20’s. The Rsq of the single factor regressions are a bit low but that could be improve with additional factors like SES, etc.
LogFatalPMC = +0.025*Pct20A+2.22; #n=73; Rsq=0.0946; p=0.008111 ** (VSig)
LogFatalPMC = +0.027*Pct20B+2.43; #n=73; Rsq=0.0912; p=0.009425 ** (VSig)
LogFatalPMC = -0.026*Pct19A+3.77; #n=73; Rsq=0.147; p=0.0008315 *** (VVSig)
LogFatalPMC = -0.035*Pct19B+3.35; #n=73; Rsq=0.0745; p=0.01949 * (Sig)
Poor SKorea is currently being ravaged by clade20C which Nextstrain had asserted to be originated from US and therefore the YankFlu, either from the fleeing Korean Americans or the presence of the US troops in SKorea. The SKorea covid epicenter is Daegu which is a major US military base. The White House cluster is also Clade20C.
https://i.ibb.co/S7bV4dY/CladeKR.png
I don’t think South Korea is “being ravaged”:
http://ncov.mohw.go.kr/en/bdBoardList.do
The SKorea covid epicenter is Daegu which is a major US military base.
Daegu is the “covid epicenter” because of the superspreader religious sect whose members evaded government quarantine efforts, not because of “a major military base.” The largest American military base (indeed, often claimed the largest overseas American military base anywhere) in Korea is Camp Humphreys in Pyongtaek, in just about the opposite corner of the country from Daegu.
By the way, where is Japan on that type-A blood rank?
The religious sect outbreak is distinguishable on dux.ie’s plot in green, attributed to Wuflu Clade 19B. The subsequent big increase is differentiated in red, attributed to Yankflu Clade 20C.
Twinkie, you can find Japan here:
https://www.babymed.com/pregnancy/blood-type-and-rh-rhesus-status-countries#
Thanks.
The subsequent big increase is differentiated in red, attributed to Yankflu Clade 20C.
That’s not what I critiqued. What I questioned was his remark about Daegu. Daegu’s infamy as covid outbreak area is from the earlier strain from China as far as I know. Everyone and his dog know that the recent cases have been later imports from the U.S.
The U.S. base in Daegu has something like 5000 people. Camp Humphreys near Pyongtaek probably has 40,000 Americans now.
It is not difficult to guess dux.ie’s nationality or at least his political alignment.
His argument is pseudo-science. No one should be worked up from what he said. As others pointed out Taegu is not the epicenter right now. When it was, a religious sect or a Chinese community there was blamed but the leftist China-loving Moon government tried to blame it all on Jesus freaks which I am not terribly fond of either but they are no worse than Moon freaks.
Later a call center near a Chinese enclave in Seoul became a sencondary epicenter but the government tried to suppress any guess linking it to Chinese because if that ever happened they would lose election, which they should have.
Korea should have shut down China much the way Taiwan did. No more blood type pseudo science please. China should be quarantined from the rest of humanity.
China should be quarantined from the rest of humanity.
strong disagree. the old delusions are over. but we can’t give in to hopelessness about humanity (yes, i’m saying this…)
@EastAsianMan, fair enough. While it looks like the Japanese would be predicted to have about 10% excess Jomon related ancestry relative to Korean people today (based on the Andaman HG in that model!), some of that may have happened outside the islands, *if* there was some later dilution and turnover in Korea today from other sources with less “Andaman HG” related (like Devil’s Cave). Will need some adna from Korea to see if any early samples show slightly higher “Andaman HG” related /more Japanese like ancestry than present day people.
Matt, Razib: Any idea why compared to India, its neighbours have so far fared quite well?
For example, just now the count of deaths from JHU’s website shows:
Pakistan: 7696
Bangladesh: 6416
Burma: 1765
Nepal: 1337
Sri Lanka: 90
which, even when adjusted for the population sizes are tiny compared to India’s 133,738 deaths. (Sri Lanka’s population ~22 millions, Nepal pop. ~28 millions, thus Nepal has about the half of per capita rate to that of India’s, and Pakistan’s almost a third).
Are there some cultural factors for this?
At first I though India might have the same SARS2 clade profile as that for SKorea. But no, there is little trace of clade20C YankFlu there, later stage SARS2 infections are mostly from Europe and westcoast US like Washington state (i.e. Amazon and MSoft) which have noticable traces of subclade 20A/18877T IndianFlu.
https://i.ibb.co/dW82QkP/CladeIN.png
https://i.ibb.co/Mp4yHty/nxclade1108b.png
There are surprisingly significant subclade 19A/13730T SingFlu in India which could be the origin but that subclade is dominant in Singapore and Malaysia at over 60% but negligible in HK and China and so that subclade could have an afinity for SAsian. India and Malaysia have previous bouts of bat based diseases like Nipah virus. A Nipah virus expert had pointed out that the likely medium for transmission of the bat virus is the large scale collection of sugary palm sap in pots in open air where the bats also feed on, as well as urinating and defecating in them. So those workers who drank the raw palm sap or processing them into palm wine have close absorption of the bat bodily fluids.
https://en.wikipedia.org/wiki/Palm_wine
http://www.fao.org/3/t0681E/t0681e11.htm
Palm wine is rare for East Asians, they prefer rice wine which is prepared in-house and might have problem with rats.
https://en.wikipedia.org/wiki/Palm_wine#Consumption_by_animals
“Megabats have been known to drink from containers of harvested palm sap and then urinate into the containers, leading to the transmission of the Nipah virus.”
Hence the frequently heard exclamation: “This palm wine tastes like bat’s piss!”
As others pointed out Taegu is not the epicenter right now.
That’s what I was saying – that and the idea of Daegu being an epicenter due to an American military base.
When it was, a religious sect or a Chinese community there was blamed but the leftist China-loving Moon government tried to blame it all on Jesus freaks which I am not terribly fond of either but they are no worse than Moon freaks.
Later a call center near a Chinese enclave in Seoul became a sencondary epicenter but the government tried to suppress any guess linking it to Chinese because if that ever happened they would lose election, which they should have.
Korea should have shut down China much the way Taiwan did. No more blood type pseudo science please. China should be quarantined from the rest of humanity.
You certainly seem to have very overwrought and sweeping views on some topics. I’m not exactly a Sinophile, and even I find such a call unhinged.
And is blood type difference and related implications pseudoscience? And I’m not talking about some astrology-like stereotype common in Japan and Korea (“O-types are warmer people and A-types are hyperactive!”).
Here is a partial list of papers on SARS2 and bloodgroup from non-Chinese institutions.
https://doi.org/10.1101/2020.05.31.20114991 “The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis”
https://doi.org/10.1101/2020.04.08.20058073 “Testing the association between blood type and COVID-19infection, intubation, and death”
https://doi.org/10.1101/2020.07.13.20152637 “Modelling suggests blood group incompatibility may substantially reduce SARS-CoV-2”
Very early the NY Governor Coumo asserted that “Coronavirus came to New York from Europe, not China”.
https://www.reuters.com/article/healthcare-coronavirus-usa-new-york/coronavirus-came-to-new-york-from-europe-not-china-governor-idUSKCN2262NJ
There are scientific results backing Cuomo’s assertion. A New York City study by Gonzalez-Reiche et al from Icahn School of Medicine at Mount Sinai (US institution) showed that out of the 85 sequenced cases of SARSCov2 found there only 1/85 was from Asia and that was from Oceania, not even China.
https://doi.org/10.1101/2020.04.08.20056929
“Introductions and early spread of SARS-CoV-2 in the New York City area”
The data in table 1 is very telling, which I reproduced below with my emphasis in color,
https://i.ibb.co/8BLLjHy/nysp1.png
The much talked about western US flight Marginot line was partially effective against the milder SARCov2 clade 19’s strain from Asia which resulted in mild fatality rate for the US west coast. Just compare the SARS2 fatality rate for California and NewYork. Instead NYC was ravaged either by direct native variants or savagely reared by the more virulent strains from the European sources from the east of NYC. The current COVID surge in California is from subclade 20A/20268G (SpainishFLu) most probably the spread from Mexico. The NY SARS2 cesspool produces the new killer mutant clade 20C which is the clade of the White House cluster as asserted by Bedford and most probably infected Trump himself.
There is a more recent edited paper (August 19, 2020) from NYU confirming that results,
If your adult child committed mass murder, is the parent totally responsible?? Does US have total authority to control incoming visitors?? Does US have the ability to suppress SARS2 inside the country?? If US has eliminated the SARS pool like NZ there will be no killer descendant clade 20C and US will be a safer place.
https://i.ibb.co/DVcWP5v/Clade-US-CA.png
“And is blood type difference and related implications pseudoscience?”
No, but touting it as a major factor in the spread of the Chinese virus certainly is.
I am not calling for mass extermination of Chinese or anything like that. I am just advocationg what Taiwan and Vietnam, two of the most successful countries in controlling the disease, did to China.
China was bullying Korea not to impose a travel ban on Chinese in the beginning but after the outbreak in Korea, PRC went ahead with travel restriction on Koreans. PRC is the most morally reprehensible country imaginable in modern world.
I hate to live in a world where she is the most dominant country. To prevent it drastic measures may be necessary even if it sounds racist. I voted for Trump even though I think he is scum, because a hundred years from now he may be remembered as a great president who tried to stop China; all his moral faults will seem petty.
@EastAsianMan: “No, but touting it as a major factor in the spread of the Chinese virus certainly is.”
Did I?? Go read my first sentence: “Blood group A has been shown to affect covid infection, though SES, cultural, health care facilities also matter.” Don’t put words into my mouth.
Anyway go do some reading yourself. From Wikipedia, also the first sentence,
You do know what are antibodies and antigenic substances ?? And from the Italian-Spanish study
Are all those numbers confused you and too difficult for you to understand ??
@dux.ie
I am smarter than you. Actually we are not even in the same league.
@Matt
I read the paper again and it appears that there were only 4-5 Koreans in the sample and one of them appears to be either mislabeled or admixed(probably with Han Chinese). Koreans are relatively homogeneous and such a variation is very unlikely.
Excluding him/her Andaman_HG component in Koreans will be lower and Jomon admixture in Japanese will be higher.
Since Koreans have some Jomon, the cumulative Jomon component in Japanese may exceed 15 percent.