Friday, May 22, 2020

This is where the virus is least deadly

Patterson Town Hall, (Wikicommons - Anthony22). Putnam County NY has the lowest IFR for COVID-19 in the United States.

SARS-CoV-2 is more virulent in southern Europe than in northern Europe. The reason, I’ve argued, is that the Mediterranean Basin is one of several regions where humans have coevolved for a longer time with crowded social environments. By "crowded" I mean not only proximity to other people but also proximity to domesticated animals. In such environments, which are prone to deadly pulmonary diseases like tuberculosis and pneumonia, natural selection may have favored susceptibility to infection by coronaviruses, which are normally mild in their effects, as a means to maintain a strong immune response to respiratory infections (Frost 2020). 

If we look at case fatality rates, Italy and Spain have been hit much worse than Germany, Switzerland, Austria, and Iceland. The United Kingdom falls between the two extremes, although a confounding factor is its large population of non-native origin (Singh 2020).

This pattern also shows up in a meta-study of infection fatality rates. Meyerowitz-Katz and Merone (2020) examined thirteen estimates of IFR from a wide range of countries. They came to two main conclusions:

- Mean IFR is 0.75% but varies considerably between countries;

- IFR has increased over time, being lower in February and March than in April and May.

Earlier estimates were based on the assumption that the average time lag between infection and death is two weeks on average. Actually, it's probably longer, perhaps a month. Later deaths may have thus been missed by estimates made in February and March.

If we look only at IFRs from April and May, the meta-study shows a north-south cline in the virulence of SARS-CoV-2:

Germany - 0.36%
France - 0.70%, 0.80%
Italy - 0.95%, 1.29%, 1.60%

For the same time period, the meta-study also presented three estimates from the United States:

New York City - 0.93%
California - 0.20%
United States - 1.30%

The last study provides estimates ranging from a low of 0.5% in Putnam County NY to a high of 3.6% in King County WA (Basu 2020). These numbers are so high because IFR is calculated only in relation to symptomatic cases. In my opinion, this study is not comparable to the others and should not have been included in the metastudy. It is nonetheless useful for charting the virulence of SARS-CoV-2 within the United States.

So why would the virus be less virulent in Putnam County NY than in King County WA? Let's consider the demographics in each case. The first county is 80% non-Hispanic White, 14% Hispanic, 3% Black, and 2% Asian. The second county is 65% non-Hispanic White, 15% Asian, 9% Hispanic, and 6% Black. Putnam County is whiter and probably less cosmopolitan than King County, which encompasses the Seattle area. This impression is strengthened by the voting pattern in Putnam County, which trends much more Republican than Democrat (Wikipedia 2020). The virus thus seems to be least virulent among "old stock" Euro Americans. I would also predict low virulence in Amerindian communities.

Virulence may also differ between west coast Hispanics and east coast Hispanics, as suggested by the difference between California and New York City. East Coast Hispanics are less often Mexican and more often Puerto Rican. They may thus be more vulnerable because they are more Mediterranean and less Amerindian by ancestry.


Basu, A. (2020). Estimating The Infection Fatality Rate Among Symptomatic COVID-19 Cases In The United States. Health affairs (Project Hope). 2020:101377hlthaff202000455.

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

Meyerowitz-Katz, G. and L. Merone. (2020).  A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates.  medRxiv, May 18, 2020 

Singh, S. (2020). BCG vaccines may not reduce COVID-19 mortality rates. medRxiv April 11, 2020

Wikipedia (2020). Putnam County, New York.,_New_York 


Anonymous said...

Putnam County is in the NYC metro area and not a very "old stock Euro" area. Like most of the NYC metro area, the white population there is mostly non-old stock Euro i.e. ethnic Catholics like Italians, Irish, and Jews.

Peter Frost said...

I realize there has been a shift toward the Republican party among Catholic and Jewish Americans, but the data on the wiki page show Putnam County as a Republican stronghold even forty years ago.

Anonymous said...

That's consistent with the white flight of white ethnics out of NYC and the closer suburbs beginning in the 60s. If you google around about the Putnam County Republican Party, you get lots of Italian, Irish, etc. names.

"Ms. Odell also pointed to historical trends to explain Republicans’ dominance in politics. She said that many public safety workers, particularly police officers and firefighters, moved to Putnam County in the 1960s from places like the Bronx, Queens and southern Westchester."

Peter Frost said...

The United States doesn't collect data on national origin. I did find data on religion. In Putnam County, 48.5% of the population identifies as Catholic and 1.2% as Jewish. The Catholic category would include the 14% who are Hispanic, as well as Americans of Irish descent. I don't see how the Italian proportion could be greater than 20%.

The point I'm trying to make is that Putnam County is more north European by origin than King County WA, where all non-Hispanic whites are down to 65%

Sean said...

What you are saying may well be right, but at present things seem too uncertain for taking any definite view on the matter, at least as far as I can see it. Anyway, here is what I thought a pertinent interview

Anonymous said...

1.2% Jewish would make it technically more Jewish than Miami-Dade and Los Angeles counties, which are regarded as Jewish strongholds.

None of the counties in the New York area, Putnam County included, have significant old stock north European populations. I suppose the Irish and Polish would be technically northern European, although the connotation of "northern European" in these sorts of discussions is usually northwestern European, German Protestant populations.

Peter Frost said...


The meta-analysis indicates that the IFR for COVID-19 is much higher than that for the flu. The world average seems to be 1% although there is much heterogeneity. I am open to changing my mind, and I believe that "views" should always be subject to change. But that's not an excuse for doing nothing and recommending nothing.


In this discussion I'm arguing that susceptibility to COVID-19, and to coronaviruses in general, should be higher in populations that have coevolved for a longer time with agriculture and urban or semi-urban environments. Broadly speaking, this coevolution would have been stronger among southern Europeans and Ashkenazi Jews.

From what I've seen (admittedly on the Internet), Putnam Country is described as being on the boundary between the New York City area and rural New York.

Bruce said...

Very confusing. If it's an evolved immune strategy wouldn't East Asian/Mediterranean populations have a higher tendency to be infected but a lower fatality rate (having evolved a tendency to get the virus but survive it)?

Peter Frost said...


Coronaviruses were always mild in their effects before the emergence of SARS in 2002. So there was no need to evolve a lower fatality rate. The fatality rate was already close to zero.

Sean said...

Sweden has done nothing, but the epidemic judged by deaths is fading out there as elsewhere, even though the number of people with antibodies is too low for herd immunity to be the reason. Some people never get influenza during an epidemic, others never catch a cold. As I understand Prof Gupta, she is saying that a lot of people must be immune without ever being infected; they don't acquire immunity to COVID-19 through surviving infection with it so they have no antibodies. And that explains why the pandemic is burning out where it apparently still has much of the population still to infect, them being not immune (judged by antibody tests).

"meta-analysis indicates that the IFR for COVID-19 is much higher than that for the flu". For those who got it, but there seems to be an assumption that a certain proportion of the population must be infected and survive with antibodies conferring immunity before herd immunity is reached. The adaptive immune system, which produces antibodies can produce general antibodies to fight off pathogens it has not encountered before.

Professor Gupta says the death rate is the only thing that should be taken into consideration, because the trajectory of the epidemic is similar in countries with very different responses to the pandemic, which indicates that the number of people with antibodies is not the crucial factor.

My reading is she says deaths should be falling far more drastically in Lombardy than anywhere else, but they are actually falling everywhere including Sweden which has no lockdown and too few people with antibodies for immunity through infection to be the answer. Conclusion: a substantial proportion of people cannot get infected in the first place.

Anonymous said...

I would also predict low virulence in Amerindian communities.

FWIW, apparently the Navajo nation has the highest infection rate in the US, and Amerindians have been a disproportionate number of the fatalities in places like Arizona:

Peter Frost said...

I suspect that fatalities in Sweden are largely among the immigrant population. I've even seen statements to that effect, but no solid data.

The infection case load is irrelevant to my argument. All people can be infected by coronaviruses. The relevant yardstick is the IFR. The second article says there have been 140 deaths in the Navaho nation. Fine. But what is the infection rate, including people who are asymptomatic or presymptomatic? Let's assume that 20% of the Navaho have been infected. That yields an IFR of 140/35,000 = 0.4%. That's a low IFR.

In addition, the Navaho have significant European admixture, mainly Spanish. So that factor should also be considered.

Anonymous said...

I wasn't really making an argument. Just pointing those articles out because I had been seeing articles recently in the news about Amerindians being hurt more than most by the virus.

Aren't the Navajo generally less admixed than most Amerindians in the US?

Peter Frost said...

I was able to find a reference to two studies on European admixture among the Navaho. One puts it at 1% and the other at 5%:

"The bloods analyzed in this study represent two segments of the [Navaho] population, a northern one centered at the Public Health Service Indian Hospital in Keams Canyon, Arizona, in which Caucasian admixture was estimated at 1.1 % (WILLIAMS et al. 1981; 1985), and a southern one based in Albuquerque, New Mexico, where individuals from a wider region of the reservation were sampled and Caucasian admixture was estimated at 5.0% (TROUP et al. 1982)."

Sean said...

Travel between China and Taiwan became common and it has the highest proportion of obese people in Asia. In addition 3.27 million people in Taiwan are over 65 years old. By any rational standard Taiwan ought to have a large number of dead from COVID-19, yet they are not even into double figures. Japan has a population of 126 million and it is the oldest in the world, and the population density in Japan is very high of course and the antibodies to SARS-CoV-2 are present in about 6% of Japanese. Yet only 900 have died of the disease in the entire county. The reason appears to be that the Japanese are the least overweight people in east Asia because there has been government mandated compulsory annual measuring of waistlines for individuals between 45 and 70 with sanctions for local government and companies whose people are overweight.

Sean said...

Something else I think is relevant: Japan has not had a lockdowwn.

Sean said...

"Opinion: Why we can't let our guard down in fight against the coronavirus Paul W. Ewald and Holly A. Swain EwaldCoronaviruses are moderately durable — they typically persist for a few days, though they sometimes can last for more than a week. Viruses with this persistence typically equilibrate at a level of harmfulness that causes about one death in 1,000 infected people. Death rates during the early phase of the pandemic are hard to come by because they fail to account for the total number of people infected.[...] On the basis of these consideration we expect that the COVID-19 viruses will shift toward a level of harmfulness that is below the one death per thousand where strong infection control measures are maintained.[...] If the virus is steadily becoming less harmful, then delaying infections may be especially important for individuals who have had inadequate health care opportunities. For example, in Kentucky and throughout the U.S., African Americans are disproportionately represented among COVID-19 cases and deaths. Being infected with milder variants of COVID-19 could be the difference between life and death for individuals whose infections are worsened by inequality of health care and preexisting conditions."

Sean said...

An article on Karl Friston from Wired so you know who he is. Anyway,

" Conventional models essentially fit curves to historical data and then extrapolate those curves into the future. They look at the surface of the phenomenon – the observable part, or data. Our approach, ..attempts to capture the mathematical structure of the phenomenon – in this case, the pandemic – and to understand the causes of what is observed. [...] A common type of epidemiological model used today is the SEIR model, which considers that people must be in one of four states – susceptible (S), exposed (E), infected (I) or recovered (R). Unfortunately, reality doesn’t break them down so neatly.

The answers are sometimes counterintuitive. For example, it looks as if the low German fatality rate is not due to their superior testing capacity, but rather to the fact that the average German is less likely to get infected and die than the average Brit. Why? There are various possible explanations, but one that looks increasingly likely is that Germany has more immunological “dark matter” – people who are impervious to infection, perhaps because they are geographically isolated or have some kind of natural resistance. This is like dark matter in the universe: we can’t see it, but we know it must be there to account for what we can see."

This seems to be very roughly in agreement with the conclusions of the susceptible-infected-recovered (SIR) model of:-

" "suspects that while physical distancing and the lockdown have helped suppress the epidemic, infections may have waned because of people’s natural resistance to the infection, for example through antibodies that fight related coronaviruses which cause common colds – but which would not necessarily show up in Covid-19 antibody tests. So a lot of people have the generalised action of antibodies making them not susceptible to being infected with Covid-19 in the first place, and so never getting the specific antibodies that are being taken as a sign of immunity through prior infection."

Figures for COVID-19 deaths in China may be unreliable, but bearing in mind the low number of deaths in Japan, Korea, and the astoundingly low number from Taiwan I wonder if it would be better to draw back a bit from lesser national differences (which I would not expect to be that big among Europeans) and comparing Chinese and European death. To my mind when we do this it indicates the likelihood of East Asians having more immunity to COVID-19.

Italy and Germany, for instance, are different in deaths, and while that may be partly due to different levels of preexisting immunity there is surely difference in administration and organisation in counter epidemic measures between the countries to explain the disparity. But Germany and no lockdown Japan, let alone Taiwan? Sorry in advance if I have misunderstood what you hypothesis would predict.

Peter Frost said...

Hi Sean,

There are cultural differences in compliance. This is why social distancing has worked so well in East Asia. In North America, especially in the U.S., the culture is too individualistic. Legally, Japan doesn't have a lockdown, but in practice that country is locked down, certainly as much as Canada.

I would like to believe that the virus will evolve into a less harmful form, but that's not what happened with the Spanish flu. COVID-19 seems to cause permanent damage to many of its hosts, but it kills only a small proportion, somewhere in the range of 0.5 to 2%. That may not be a strong enough selection pressure to make it less harmful.

The "average Brit" is partly South Asian and African.

Sean said...

Distancing cannot work where they do not have any, because there is no knowledge that the disease is a class A infection, ie one causing a wildfire pandemic. I think it is clear the Chinese national leadership did not know--because local party bosses swept the disaster under the carpet--that the novel Wuhan disease (COVID-19) had sustained transmissibility between humans until January 21st at the earliest. There was no kind of cordoning off of Wuhan, or lockdown or distancing anywhere in China until then. By the 23rd of January Wuhan was sealed off, the whole province of Hubei had no flights to elsewhere in China and Beijing had roadblocks. But that was two months without any measures, and Wuhan is a transport hub.

The Wuhan deaths constitute almost all of the deaths in China, and may have been due to local measures to sweep what was thought to be a class B infectious disease at most away under the carpet for all we know (eg just letting the infected die off or even speed them on their way). With such a head start for the virus, isn't under 5000 deaths total in mainland China a lot fewer than one would expect if the Chinese have greater susceptibility?

Antibodies that fight COVID-19 could be raised by simply catching a lot of colds (coronavirus is the cause of about 20% of cases of the common cold). The Covid-19 rate in Richmond is a third of Vancouver's, which seems to confirm what Gupta is saying, and what you are saying too, sort of. Although I think your theory is good, for what it's worth in my opinion you have it the wrong way round about the Chinese being innately more vulnerable to COVID-19 (that is my understanding of your hypothesis). The "average Brit" may be partly South Asian and African, but those Brits who are wholly non-European are on average not old.

I think how the virus evolves depends on whether there is an environment favouring virulence. The 1918 flu seems to have evolved the spectacular second wave virulence in crowded military camps and trenches and it was most dangerous to men of military age (the W shape age graph). Ewald has expressed concern about COVID-19 coming back in the October with specialised virulence for the ags of those in the Xinjiang detention camps. The totalitarian CCP government is one in which with a clean record a member of the party is guaranteed a rise to the top, but this entails avoiding being associated with anything going wrong. Careers are not made by subordinates bringing their boss bad news. Several weeks into the current crisis, Xi had to do a re-set, and make a special point of telling his regional bosses that they must not conceal cases of COVID-19.

As a result the supreme leadership actually know surprisingly little about egregious occurrences in the gigantic country they rule.Once having started to try and fix the problem or disappear the problem people, the regional and local officials cannot go to the leadership and explain they have covered up and created a disaster. So Xi may not really know what is going in in Xinjiang.

Anonymous said...

"Status of COVID-19

As of 19 March 2020, COVID-19 is no longer considered to be a high consequence infectious disease (HCID) in the UK.

The 4 nations public health HCID group made an interim recommendation in January 2020 to classify COVID-19 as an HCID. This was based on consideration of the UK HCID criteria about the virus and the disease with information available during the early stages of the outbreak. Now that more is known about COVID-19, the public health bodies in the UK have reviewed the most up to date information about COVID-19 against the UK HCID criteria. They have determined that several features have now changed; in particular, more information is available about mortality rates (low overall), and there is now greater clinical awareness and a specific and sensitive laboratory test, the availability of which continues to increase....."

Sean said...

covid-deaths-per-million-7-day-averages for nine countries

Santo's said...

You must learn to analyse all details as possible before formulate your often failed theories. Seems so many factors are not being counted there... I read somewhere in the rainbow that different levels of (corona)virus-exposure can affect how infected a person can be. In the end of day the major cultural differences may explain big part of these death rates infection, from % of older people who live with other generations in the same house (significantly in mediterranean nations than in nothern countries); cultural habit to kiss and touch other peoples in cumpliment; cultural habit to enjoy night's life; overwhelmed health system; smoking rates etc..

How big Greece has been affected?? also remember that corona is not measles. It's infectious but not exceptionally. Even because most of large scale infection events has been very locally from people who have direct contact with the vectors...

Santo's said...

Even that, if there is some biological suscetibility among ethnic groups maybe one hypothesis could be the fact northern europeans evolved and adapted in colder climates than southern europeans, more likely to be constantly exposed to respiratory diseases triggered by harsh winters. But, but, but...

Santo's said...

Santo's said...

Analyse mortality levels among ethnic minority individual subgroups who have no underlying conditions or have easily access to health service with whites (and east asians) before jump to big theorizations about it.

Santo's said...

Swimmers are less likely to get a strong flu??

Mediterranean subrace is known to be historically been breed on civilization while northern europeans had more time breeding in nature and developing physical and biological attributed to their environment they have adapted.

Also blacks are not on avg known to be great swimmers (those with great lung capacity).

Anonymous said...

northern italy is more affected than southern italy

deaths per age