Recent data and maps to help find the origin of COVID-19

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Dr. Daniel Lucey, who has responded to, and monitored information on outbreaks since 2001, has provided a series of updates and analysis on what is now the COVID-19 pandemic in Science Speaks posts first published Jan. 7. Recently returned from a trip to Shanghai, Hong Kong and Egypt, he continues to break down developments and data on the spread of the virus.This is his 15th update on questions raised by the continued spread of, and responses to the virus that causes COVID-19.

What new information on the origin(s) of the novel coronavirus causing COVID-19 has appeared following the Jan. 25 Science Speaks post  putting forth the evidence-based hypothesis that the outbreak did not begin in the Huanan seafood market and occurred before December 2019’?

Much information has appeared and will be discussed below. The first bookend of this new information is the interview with this writer by Jon Cohen of SCIENCE published Jan. 26: ‘Wuhan seafood market may not be the source of novel virus spreading globally”.

The most recent bookend is the March 13 article in the South China Morning Post: “Coronavirus: China’s first confirmed Covid-19 case traced back to November 17.”

What is the primary goal of this March 15 IDSA update # 15 posting?

To integrate this new information into a way forward in terms of how to find the origin(s) of this virus and the pandemic it has caused.  We propose use of maps, literally of the Wuhan Seafood Market once thought to be the sole source of the virus, and also conceptual maps to trace back the virus to November and earlier, in locations of relevance rather than this “Red Herring” Seafood Market.

Since Jan. 25 what has been reported in the medical literature as to the earliest known human-to-human transmission of this novel coronavirus?

In a paper published Jan, 29 in the New England Journal of Medicine by 45 Chinese authors on the early transmission dynamics of the initial 425 patients in Wuhan it was concluded that: “there is evidence that human-to-human transmission has occurred among close contacts has occurred since the middle of December 2019.”

Q: Since Jan. 25 what has been reported in terms of “environmental testing” of this Wuhan Huanan Seafood Market?

On or about Jan. 26 the China Center for Disease Control in Beijing issued a press release (in Chinese) stating that environmental samples of this Market were collected on two dates: January 1st and January 12. The English-language version was shorter than the Chinese version, and can be read at this “China Daily” newspaper link.

How many samples were collected on each date?

On Jan. 1, a total of 515 samples were collected. On Jan. 12, an additional 70 samples were collected.

Were any from animals in the market?

None of these 585 samples were reported to be from animals in the market.

How many of these 585 environmental samples were positive for the virus nucleic acid?

33 of these 585 samples were reported positive.

Have any virus-positive samples from any animals in this market ever been reported?

No.

Has it ever been reported exactly what type of “environmental samples” were obtained? (e.g., swabs from floors)

No.

Where in this market were the 33 virus-positive samples located?

No data has been published in a medical journal; however, China CDC reported in a press release that 31 of the 33 samples were in the western part of this market, one sample was from a garbage truck linked with the market, and no location was provided for one sample.

What additional information was provided about the western part of the market and about the 31 virus-positive samples?

The western part of the market is reported to be where many of the live animals (non-seafood) were sold. At least 14 of the 31 positive samples were from 22 “Stalls” from a specific area of the market between ‘7th and 8th street’ (google-translated from the Chinese in the original press release and verified with a Mandarin-fluent colleague).

 What interpretation of these data was given in the press release by the CDC?

The conclusion by the China CDC was that this was evidence that the virus had been transmitted from animals in the market to humans in the market.

What equally valid hypothesis is there to explain the 31 positive samples?

That the virus was not in any of the animals in the market, but only in humans working or visiting the market, who transmitted it to other humans. In this hypothesis humans alone were responsible for the positive environmental samples.

Is there a 3rd possible hypothesis to explain these data?

Yes, a third possible hypothetical explanation is that there were both humans and animals infected with the virus in this part of the market, and both could have accounted for the positive environmental samples.

What happened to the many animals in this market?

The only public reference to the fate of these animals is in the Report of the Joint WHO-China Mission February 16-24 that was posted on the WHO website February 28.  It is somewhat cryptically stated that the animals were at an  unnamed) “destination” away from the market.

 What is the verbatim information in this WHO Report regarding animals?

On page 8 of the report it is stated:

“Zoonotic origins COVID-19 is a zoonotic virus. From phylogenetic analyses undertaken with available full genome sequences, bats appear to be the reservoir of COVID-19 virus, but the intermediate host(s) has not yet been identified. However, three important areas of work are already underway in China to inform our understanding of the zoonotic origin of this outbreak. These include early investigations of cases with symptom onset in Wuhan throughout December 2019, environmental sampling from the Huanan Wholesale Seafood Market and other area markets, and the collection of detailed records on the source and type of wildlife species sold at the Huanan market and the destination of those animals after the market was closed.”

What information on the market investigation of the purported animal source of the virus in this Market was provided in this WHO mission report?

Almost nothing.

Instead, in the very first section of Annex D titled “Knowledge Gaps” included:

“Knowledge gaps and key questions to be answered to guide control strategies include: Source of infection

  • Animal origin and natural reservoir of the virus
  • Human-animal interface of the original event
  • Early cases whose exposure could not be identified”

On March 3rd, what information regarding this market was provided in another statement by Chinese authorities?

The Chinese media report stated that beginning 3 March and ending by 5 March apparently a team returned to the Market to complete removal of any remaining material that might be infectious and complete decontamination of the Market. Read at Beijing News and hit translate.

Was any mention made in this 3 March China CDC announcement about animals in, or linked to, the market?

No.  Presumably no animals are still in the market.

What is a ‘Way Forward” in the search for the origin(s) of this virus and initial patient(s) e.g., patient zero or index case(s)?

One way forward, that very likely has already been accomplished by the many brilliant epidemiologists and scientists of the China CDC, headed by George F. Gao, MD, DVM, but not yet released publicly (and not seen by this writer), is to create overlapping maps of the Market and outside the Market of all positive and negative virus locations for:

  • Environments
  • Humans
  • Animals

What would such a map of the market look like for environmental samples?

The locations of at least 14 of the positive virus environmental samples has been reported to be in the western section of the Market, specifically between 7th and 8th streets, involving 22 “stalls” in the Market.  Thus, on a map of the market place a symbol such as a closed triangle for the precise location of each of the 31 positive environmental samples.

In addition, place an open triangle for the location of the positive sample in the garbage truck and the location of the 1 other sample of unnamed location. Importantly, the precise location on the map of the Market for the virus-negative environmental samples, totaling 553 of the total 585 samples obtained on January 1, and January 12, should be placed on the map.  (585 total-33 positive = 552 negative samples).

What would this map of the market look like for humans?

There are 27 patients with Covid-19 with “an exposure to the market” out of the 41 initial patients reported in the Lancet paper Jan. 24  by Huang C.  and 28 Chinese co-authors.

(Prof. Bin Cao, MD is the corresponding author). Thus, map the precise location of where these 27 persons worked and/or visited the Market. Also, map precisely where the 14 persons listed as having “no exposure to the market” in this Jan. 24 Lancet paper.  For example, place a symbol on the map, such as a closed square, for virus-positive humans. If any other humans working or visiting the market who tested negative for the virus, then their locations in the Markets should be added to the map with open squares.

How would thus visualizing overlap, if any, in the market of virus-positive environmental samples and infected humans?

If overlap exists on this map of the locations of the 27 infected humans “exposed to the Market” and the 33 virus-positive environmental samples, then some support could be given for any of the 3 hypotheses stated above, namely:

-Only the infected humans accounted for the positive environmental samples.

-Only infected animals accounted for the positive environmental samples.

-Both humans and animals accounted for the positive environmental samples.

 What would this map of the Market look like for animals and their samples?

No data are available regarding the test results and locations of any positive (or negative) samples from any animals whether from respiratory, intestinal, blood, skin or other anatomical sites of the animals in the Market or any other markets in Wuhan or elsewhere in Hubei province or any of the other 30 provinces or regions in China, or Hong Kong, Macau, or elsewhere in the world. If any animal samples were positive, then the precise location within the Market could be placed using a third symbol such as a closed circle. Likewise, the precise location on the map of the Market of animals that tested negative for the virus should be shown using an open circle.

On March 13 what key information was reported in the South China Morning Post (SCMP), a highly respected newspaper based in Hong Kong?

A: An article in the SCMP yesterday March 13, under the byline of Josephine Ma, is cited (in quotes only) below:

“The first case of someone in China suffering from Covid-19, the disease caused by the novel coronavirus, can be traced back to November 17, according to government data seen by the South china Morning Post. Chinese authorities have so far identified at least 266 people who were infected last year, all of whom came under medical surveillance at some point. Some of the cases were likely backdated after health authorities had tested specimens taken from suspected patients…”

“According to the government data seen by the Post, a 55 year-old from Hubei province could have been the first person to have contracted Covid-19 on November 17. From that date onwards, one to five new cases were reported each day. By December 15, the total number of infections stood at 27–the first double-digit daily rise was reported on December 17—and by December 20, the total number of confirmed cases had reached 60…”

“By the final day of 2019, the number of confirmed cases had risen to 266. On the first day of 2020 it stood at 381.While the government records have not been released to the public, they provide valuable clues about how the disease spread in its early days and the speed of its transmission, as well as how many confirmed cases Beijing has recorded…”

“Of the first nine cases to be reported in November—four men and five women—none has been confirmed as being “patient zero”. They were all aged between 39 and 79, but it is unknown how many were residents of Wuhan, the capital of Hubei and the epicenter of the outbreak…”

“It is possible that there were reported cases dating back even earlier than those seen by the Post. According to the World Health organization’s website, the first confirmed Covid-19 case in China was on December 8, but the global body does not track the disease itself but relies on nations to provide such information. A report I the medical journal The Lancet by Chinese doctors from Jinyintan Hospital in Wuhan, which treated some of the earliest patients, put the data of the first known infection at December 1…”

“As late as January 11, Wuhan’s health authorities were still claiming there were just 41 confirmed cases.”

How could antibody tests, IgM and IgG, be helpful to identify both humans and animals who were in the autumn, September-December, of 2019?

China has IgM and IgM antibody tests that they included in their March 3rd update (the 7th overall) of their national guidelines on the diagnosis and treatment of Covid-19.

Thus, these antibody tests could be used to identify both infected humans and animals (if validated for animals as well as humans), regardless of time and place e.g., from September through December 2019 and in many animal markets, restaurants, animal farms, illegal animal trade supply chains, and elsewhere in Wuhan, Hubei province, and other provinces in China and even in other nations nearby and distant.

Q:  What is the overwhelmingly likely origin of this outbreak-become-pandemic of the three possible ways an outbreak could begin: Naturally occurring, accidental, or intentional?

This outbreak was naturally occurring, arising from a still unidentified animal or more than one animal species. This coronavirus then infected humans and most likely over several months, e.g., between September and December, was able to acquire the ability to be transmitted from human-to-human. Whether it began in Wuhan, elsewhere in Hubei province or in China remains to be proven.

Looking toward the future, what is another reason to determine the animal origin, location, timing, and potential environmental change or trigger for this coronavirus outbreak-become-pandemic?

Looking forward, because we (humans) must prepare for the 4th and 5th contagious novel coronavirus pneumonia following on the initial three: SARS, MERS, and this “SARS-CoV-2”. The next one may or may not be officially named “SARS-CoV-3” or “MERS-CoV-2”. The name is not so important, compared with the suffering, death, economic and all-of-society damage and destruction it might cause, just as this Covid-19 pandemic is doing around the world now.

Dr. Daniel Lucey

Daniel Lucey, M.D. MPH, FIDSA, FACP, is an infectious diseases physician and adjunct professor of infectious diseases at Georgetown University Medical Center, a senior scholar at the Georgetown University O’Neil Institute, Anthropology Research Associate, Smithsonian Museum of Natural History and a member of the Infectious Diseases Society of America Global Health Committee.He has served as a volunteer medical responder to outbreaks that included the West Africa Ebola crisis. He has collected information on outbreaks starting in 2001 with cases of anthrax in 2001, and including smallpox vaccination 2002, SARS 2003, H5N1 Flu 2004, MERS in 2013, and Ebola in April, 2014, He has gathered, and  updated information on the spread of the coronavirus Jan. 6.

53 thoughts on “Recent data and maps to help find the origin of COVID-19

  1. t smith

    Best coverage of the issue I have read so far. Points to obvious flaws in the CP of China’s huge surveillance program…and doubts that this could occur

    Reply
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