Razib Khan One-stop-shopping for all of my content

March 28, 2020

COVID-19 and its environmental conditions

Filed under: coronavirus,COVID-19,Health,Health & Medicine,health care — Razib Khan @ 1:53 am

A friend of mine recently quipped that everyone seems to act like probability can be assigned two values 0 or 1. The same sort of logic seems to apply when it comes to talking about the environmental parameters which might affect the progress of COVID-19, such as temperature, humidity, and density. Many people seem to strenuously want to deny there is any plausible evidence that COVID-19 might exhibit seasonality. There is a fair amount of correlational work which suggests that there is an environmental factor shaping the spread and depth of COVID-19. And, we know three out of the four previous coronaviruses exhibit seasonality.

Well, I noticed this note on medRxiv today, Stability of SARS-CoV-2 in different environmental conditions. It’s a very short write-up of their experimental results. I don’t really know much about virology so I can’t evaluate it well, but you can see the figure above. As you increase the temperature the virus titer seems to drop much faster. At a very high temperature of 70 Celsius, they basically can’t detect anything after 1 minute.

Here is one of the better correlational analyses, using some sophisticated techniques, Causal empirical estimates suggest COVID-19 transmission rates are highly seasonal:

Nearly every country is now combating the 2019 novel coronavirus (COVID-19). It has been hypothesized that if COVID-19 exhibits seasonality, changing temperatures in the coming months will shift transmission patterns around the world. Such projections, however, require an estimate of the relationship between COVID-19 and temperature at a global scale, and one that isolates the role of temperature from confounding factors, such as public health capacity. This paper provides the first plausibly causal estimates of the relationship between COVID-19 transmission and local temperature using a global sample comprising of 166,686 confirmed new COVID-19 cases from 134 countries from January 22, 2020 to March 15, 2020. We find robust statistical evidence that a 1◦C increase in local temperature reduces transmission by 13% [-21%, -4%, 95%CI]. In contrast, we do not find that specific humidity or precipitation influence transmission. Our statistical approach separates effects of climate variation on COVID-19 transmission from other potentially correlated factors, such as differences in public health responses across countries and heterogeneous population densities. Using constructions of expected seasonal temperatures, we project that changing temperatures between March 2020 and July 2020 will cause COVID-19 transmission to fall by 43% on average for Northern Hemisphere countries and to rise by 71% on average for Southern Hemisphere countries. However, these patterns reverse as the boreal winter approaches, with seasonal temperatures in January 2021 increasing average COVID-19 transmission by 59% relative to March 2020 in northern countries and lowering transmission by 2% in southern countries. These findings suggest that Southern Hemisphere countries should expect greater transmission in the coming months. Moreover, Northern Hemisphere countries face a crucial window of opportunity: if contagion-containing policy interventions can dramatically reduce COVID-19 cases with the aid of the approaching warmer months, it may be possible to avoid a second wave of COVID-19 next winter.

To be clear. Does this mean weather/climate determine whether COVID-19 will spread or not? No. Rather, I think that weather/climate has some effect on the margin on the R0. I am not sure of the exact reason, but if the virus degrades much faster in hot climates, that could be one explanation of why spreading is more limited. It also does not seem to be the case that tropical countries are going to avoid mass healthcare crises. Rather, as these countries formulate policies to decrease R0, it may not be as long of a haul.

I believe that many are worried that if there is some relationship between temperature and COVID-19, people will think they are safe in a particular climate. The way to deal with this is not to ratchet up skepticism to an inordinately high extent. Rather, it is to be more clear and careful in how one presents the data.

Similarly, I think density has some impact. But, South Korea, Japan, and Taiwan show that density does not seal one’s fate.

March 27, 2020

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 8:34 pm

Talk about what you want. I assume even if you are dying of COVID-19 it will be something about Hindu/India vs. Muslims/Pakistan.

(we’ll be recording a podcast on COVID-19 with Kushal Mehra if you have any questions for him)

March 26, 2020

Browncast episode 88: Phillipe Lemoine, covid-19 “optimism”

Filed under: COVID-19,Health — Razib Khan @ 6:54 pm

Another BP Podcast is up. You can listen on LibsynAppleSpotify,  and Stitcher (and a variety of other platforms). Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe to one of the links above!

You can also support the podcast as a patron. The primary benefit now is that you get the podcasts considerably earlier than everyone else. This website isn’t about shaking the cup, but I have noticed that the number of patrons plateaued a long time ago. This month has been our biggest traffic month ever, and I think our corona-casts have been popular (patrons also get access to one that you can’t find on the public feed).

I would though appreciate more positive reviews! Alton Brown’s “Browncast” has 30 reviews on Stitcher alone! Help make us the biggest browncast! At least at some point.

This week I talked to Phillipe Lemoine about his blog post Are we headed toward an unprecedented public health disaster? A philosopher by training, Phillipe is now working as a data scientist, and he has been looking a the patterns of fatality in Europe for the past several weeks.

Cultural evolution at work!

Filed under: Religion — Razib Khan @ 1:44 pm


‘God Will Protect Us’: Coronavirus Spreads Through an Already Struggling Pakistan:

And the extremist clerics who often heckle or march against the civilian government, with the tacit approval of the military, are refusing to help. They largely ignored Mr. Khan’s call to limit Friday prayer gatherings. And even after the military deployed to try to enforce a lockdown, several clerics made videos that went viral in recent days, urging Pakistanis to come back to the mosques to worship.

To avoid mosques on Fridays would only invite God’s wrath at a time when people need his mercy, the clerics warned.

“We cannot skip Friday prayers because of fears of coronavirus,” said Shabbir Chand, a trader who attended a packed service in Karachi, the country’s biggest city. “Instead, we should gather in even larger numbers in mosques to pray to God to protect us from this fatal disease.”

One of the major aspects of Islam that some Hindu nationalists are obviously jealous of is its seeming unitary cohesion. A hadith attributed to Muhammad is that “the Ummah shall not agree upon error.” And Muslims famously come together weekly to pray together.

But in a time of coronavirus, the fractured and somewhat antisocial aspect of Hindu religion may have some benefits.

Version alpha of trying to understand East Asian population history is now out!

Filed under: Ancient DNA,East Asia,Han Chinese,Historical Genetics — Razib Khan @ 12:58 am

We’ve been waiting for ancient DNA to answer some questions about Eastern Eurasia for a while. I always thought Qiaomei Fu would spearhead it, but it doesn’t seem like it worked out that way. That’s bcause she’s not on a new preprint, The Genomic Formation of Human Populations in East Asia, which fills in a lot of gaps and confusing aspects of what has been reported from fragments of publications before (e.g., this clarifies a lot of things with Japan, see below). Since there has already been ancient DNA work on eastern Siberia and Southeast Asia, this is really focusing on the area in and around what is today the Peoples’ Republic of China. The first author has an affiliation with a university in Fujian.

Much of the analysis can be understood as language families. In this way, it goes back to L. L. Cavalli-Sforza’s correlations between gene trees and language trees, as well as his work on the agricultural Diasporas.

First, there isn’t something radically surprising here. As I suggest above, the mass of ancient DNA in the preprint and model-building just snap together a lot of what you can see in other work, some going back decades.

Let’s start with the “Onge-like/related ancestry. ”

Below you see the strange pattern of Y chromosomal haplogroup D. It’s common in Tibet, Japan, and among the Andamanese.

In the preprint the authors argue that there is a deep division among East Eurasian populations, going back further than 40,000 years, between a set of populations descended from groups related to Tianyuan man, and populations with affinities to the indigenous peoples of southeast Eurasia and Australia. Modern populations in East Asia can be thought of as a mix between these two groups, in various pulses and waves. The finding that some peoples in the Amazon had “Australo-Melanesian” affinity is very strange, but note that there’s no guarantee that the geographic distribution of the two clades was so skewed in the past.

The Onge-related ancestry is apparently found as the deepest layer in the Tibetan plateau and contributes 45% of the ancestry to the Jomon of Japan. Among ancient proto-Austronesian peoples of Taiwan, it contributed 14% of the ancestry. Earlier work on Southeast Asia indicated that even before the expansion of Austro-Asiatic farmers out of southern China they mixed with a basal East Eurasian lineage related to the Onge.

Chinese annals record the presence of dark-skinned peoples in Yunnan nearly into historical periods. These could very well be legends or rumors, or, they could be the last relic populations that had not been fully absorbed into the Tianyuan-descended farmer expansion.

Moving more recently into the past, the preprint findings that of the Tianyuan descended populations in East Asia there is a northern and southern grouping. The northern grouping has been discussed before, it is the classic Amur-river valley population. It turns out that a sample from 5,000 years ago in northern Shaanxi, just to the north of the hearth of classical Chinese civilization in Henan, resembles these Amur-river valley populations. Though the authors don’t have samples from southern China, or even the Yangzi, they use modern samples from southern Chinese peoples, as well as ancient samples from Taiwan, to infer that it is likely that the Yangzi river valley was inhabited by a somewhat different group during prehistory.

In the preprint, the argument is made that Austronesian, Tai-Kadai, and Austro-Asiatic all emerged out of the Yangzi valley and its rice cultures. As noted above, other papers have already outlined the peopling of Southeast Asia using ancient DNA, so I will ignore that. But, note that for Austro-Asiatic populations, ~1/3 of the ancestry is Onge-related. Some of this was mixed in while in southern China, but some of it probably accrued later on in Southeast Asia. Modern Austro-Asiatic populations can then be thought of as a compound of Tianyuan, and various  Onge-related groups.

China:  

The modern Han Chinese seem to be a fusion of the two idealized ancestral populations:


No great surprise. The Han have more of an affinity for northern East Asian populations than southern ones, with those in the south having more of an affinity for southerners than those in the north. A simple model might be expansion out of Shaanxi and Henan across a landscape with many southern agriculturalists. But that makes us ask: why is there “southern” ancestry among many northern Han today?

I think the explanation is that the expansion of the Han was characterized by reversals, as well as panmixia induced by political unification. Let me outline this explicitly:

– proto-Han identity is focused around Henan and Shaanxi between 2000 BC and 300 AD. As this culture expanded into the margins of the Yangzi and into Sichuan, it absorbed “southern” ancestry (as well as elements of culture).

– During the Han dynasty, 200 BC to 200 AD, the Chinese colonized portions of the far south, and aspects of panmixia occurred, as individuals moved across China north to south and vice versa

– The fall of the Han dynasty after 200 AD saw North China come to be ruled by “barbarians”, usually of Turkic provenance. South China maintained classical Han culture and political forms without external influence. Many northern families moved south between 200 AD and 600 AD. Many barbarians “became” Han, and mixed into the population. I believe this is when the 2-4% “West Eurasian” started to become prevalent in the north. This western ancestry was mediated through Turkic groups who were predominantly Siberian or Amur-river valley in ancestry. R1a1a is found in North China, so I believe that this ancestry is from Iranian groups absorbed into the Turco-Mongol populations.

– The reemergence of an integrated China after 600 AD sees the shift of the center of gravity of the Chinese economy move to the center and south, in particular the Yangzi river valley. Movement northward of South China repopulating areas that had been uninhabited moves “southern” ancestry north. Most of the population growth in the south is endogeneous, and not due to migration. There is very little to no West Eurasian ancestry in the south, as one might expect if large numbers of North Chinese moved south (the exception are probably the Hakka, who are known to be Northerners).

– There are still ethnic minorities in the South. Over the past 1,000 years, they have slowly been Sinicized and assimilated in many areas, so the proportion of “southern” ancestry in places like Guangdong has increased in part through such processes.

 Japan:

The Japanese are not entirely surprising. Using a two-way model with Han or Korean vs. Jomon, the Japanese are about 85% the former and 15% the latter. The proportion is a bit higher for Korean. The reason is straightforward: the Yayoi rice farmers probably derived from the Korean peninsula. Even into the edge of history Japan and the Baekje kingdom of Korea had close relations.

The interesting thing about Japan is this is an area where agriculturalists nearly overwhelmed the indigenous population, albeit absorbing them. The Jomon culture is unique because it was a sedentary hunter-gatherer society that also used pottery extensively. Previously analysis of Jomon remains produced “strange” results. In this preprint the authors give a good explanation of why: the Jomon are an even mixture of a population descended from the Onge-related clade and another one that is closer to the Amur river valley Northeast Eurasian populations, who descend from Tianyun.

Basically the Ainu are a fusion of a Siberian group, and, a population that has affinities with those indigenous to Southeast Asia before the arrival of agriculturalists. Before genetics archaeologists and anthropologists argued about the Ainu affinities. Despite sometimes looking “European” early blood group analysis quickly established an eastern affinity, but morphology and culture suggested connections to Siberia or Australia. The Australian Aboriginals descend from one of the Onge-related groups to a great extent, so the affinities are now intelligible.

Tibet:

Tibetans seem to be mixed between a small proportion of Onge-related, a larger proportion of an East Asian population descended from Tianyuan and closer to the Amur river valley groups than “southern” rice farmers, and finally a population similar to the Han. The latter mixed with the fusion of the first two ~3-4,000 years ago. This makes intelligible the “Sino-Tibetan” language family, whose validity I’m not clear on. But the linguistic affinity might date to this period.

Mongolia/Xinjiang:

This is the portion that is somewhat “controversial.” In Mongolia, they find that there was the arrival of an early western group, the post-Yamnaya Afanasievo, about 5,000 years ago. They flourished in and around the Altai. They are genetically almost exactly with the Yamnaya. Then, at some point in the Bronze Age, this group was totally replaced by another much more like the Sintashta-Andronovo. These groups were similar to the Yamnaya, but ~30% of their ancestry is like “European-farmers.” The conjecture you can make here is that there was reflux from Europe that came back onto the steppe. These were almost certainly Iranian.  This second wave clearly contributed much of the western ancestry into Mongols, judging by the high fraction of R1a1a-Z93 in the Altai.

But, the more intriguing aspect is south and east in Xinjiang, overlapping the zone occupied by the Indo-European Tocharians, the populations remained similar to the Afanasievo, albeit mixing with East Eurasian groups over time. The implication then is that the authors have “pegged” a separation date from the Tocharian Indo-European branch from the others, about ~5,000 years ago. Aside from Anatolian (e.g., Hittite), Tocharian is often seen to be the most basal.

Later Xinjiang also saw the arrival of Iranians. The western and southern oases of Xijiniang were Iranian, while the northern and eastern ones were Tocharian.

Genetic admixture:

They find that over time genetic distance between populations in East Asia declines over time. This is analogous to what happened in Western Eurasia.

This might be a generalized process, but I think there’s a specific thing driving this: the rise of the Chinese state-polity. Not only did the Han expand and absorb, but there was gene flow to neighboring groups. It is well known that Han Chinese have been moving into Vietnam, and assimilating, for 2,000 years. Similarly, many Han in the north have been known to “go barbarian.”

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