Chinese scientists working on COVID-19 origins-tracing discuss latest findings, address data transparency controversy
Published: Apr 08, 2023 11:14 PM
coronavirus Photo:VCG

coronavirus Photo:VCG

Editor note: Amid waves of heated discussion about the origins of COVID-19 in the international community and China's recent release of new analysis collected at Wuhan's Huanan Seafood Market, the Global Times reporters on Friday conducted an interview with Liu Jun, a researcher from the China CDC who is also a member of the WHO-China joint expert team, and Qian Zhaohui from the Institute of Pathogen Biology, Chinese Academy of Medical Sciences, on their latest findings and discussions related to the tracing of the origins of COVID-19.

GT: Foreign media reports claimed that your team deleted the data uploaded on GISAID during the process of submitting a paper on the analysis of data collected at the Huanan Seafood Market, is that true?

Liu: We submitted the first draft of the paper to the Nature magazine in February 2022, and during the process of submission and revision, our teams uploaded the original data related to the paper on the GISAID data sharing platform (GISAID) in accordance with international practice for scientific paper publication. The uploaded data was only used for journal review and access, and it was agreed with Nature and GISAID that the data will be released publicly following the official publication of the paper. The data and access link have always been there and have not been deleted.

On March 11 2023, we found the data uploaded to the GISAID platform had been prematurely released by GISAID staff before the paper was published and without the knowledge of our team. Upon learning this, staff from our team called the GISAID platform to confirm the situation. We were told that the release was an error by GISAID staff. Thereupon, the platform shut down the data sharing function but the data remained on the platform. Neither our team nor the platform deleted the data, and the data access links for journal review have always been there. 

The latest version of our paper was published online in Nature on April 5, and all the original data has been released across four international and domestic databases simultaneously.

GT: what are the main conclusions of the paper? Have there been any new discoveries or content that contributes to the identification of the virus' origins?

Liu: The nucleic and gene sequencing on 1,380 environmental and frozen animal samples collected at Huanan market from January to March 2020 showed that all 457 animal samples collected in the market tested negative for COVID-19. And 73 out of 923 environmental samples were positive for COVID-19, with three strains of the virus isolated. The sequencing results showed that the genome was 99.9-100 percent homologous to the genome of the early cases, suggesting that these strains of virus were from patients infected with COVID-19.

The gene sequencing of environmental samples showed abundant human gene sequencing fragments, and those from common cold chain goods such as pigs, cows, chickens and ducks sold in the market, as well as a small number of gene fragments of animals such as mice and cats. It once again indicates that the presence of COVID-19 in the market was most likely from early patients. The Huanan market was only an outbreak site, not the origin. The data further supports the origins-tracing report jointly undertaken by the WHO-China expert team. 

GT: Based on the data your team uploaded on the GISAID, some international experts reached a different conclusion. Do you think the differences are out of different analysis methods or because of other reasons? 

Liu: We cannot rule out the possibility that different analyzing methods, software and parameters may end up with different results, but the DNA barcoding showed the highest abundance of human genes among the environmental samples, indicating the contamination within the market are most likely from early patients. The DNA barcoding also showed the existence of multiple animals including pigs, cows, chickens and ducks at the market before its closure. 

Some experts are concerned about the presence of presumed COVID-19 susceptible animal genes in the samples. However, existing research data does not support that animals in the market were infected with COVID-19. Even if animals had been infected, it cannot be ruled out that human-to-animal transmission occurred after humans were infected. Because our sampling time was in January 2020, later than the time when the COVID-19 cases were reported, we believe that the virus was likely to have entered the market through human infections or cold chain products, and the scientific basis for the so-called animal-to-human transmission at the market is obviously insufficient.  

GT: Some media reports said the data uploaded on GISAID should have been shared sooner. Why did the expert team not share this data before and is there any more still waiting to be shared? 

Liu: Since the COVID-19 outbreak, Chinese scientists have been carrying out a lot of work in an open, transparent and responsible manner to trace the origins of COVID-19, and share them in a timely manner. For example, in early stages of the outbreak, the whole genome sequence of the coronavirus was uploaded to the GISAID database platform, and epidemiological investigations of early cases were also published in the New England Journal of Medicine (NEJM).

At the beginning of 2020, experts from China CDC had collected both environmental and animal samples from the market, which showed all animal samples tested negative, and 73 environmental samples were positive. The virus gene sequencing showed they are highly homologous with that of early cases. The results indicated that the virus existed in the environment were from contamination of early cases and the market was an outbreak site in early stages of virus spread. 

All data we had at that time was reported to the WHO joint origins-tracing expert team between July 2020 and January 2021and they were fully discussed among experts.

The expert team had also visited the market in January 2021. They recognized the reliability and importance of the methods of sampling and testing, as well as that of the data and the results, and included the results within the WHO phase I origins-tracing report. 

The report suggested more investigations need to be undertaken, including the DNA barcoding of samples from the Huanan market. Based on the suggestions, Chinese experts carried out relevant research which showed the DNA barcoding failed to provide any new direct evidence over origins-tracing and proved the previous conclusion of the WHO-China joint origins-tracing report was scientific and objective. 

In February 2022, China CDC experts submitted the data of Huanan market to Nature for peer review, while it was also made public through the international preprint platform, and uploaded to GISAID in accordance with international practices. At present, relevant data has been released in four databases at home and abroad, and the paper has been officially published in Nature.

After the phase I joint report, Chinese scientists had carried out a great deal of work relevant to origins-tracing and the research had been published timely. Serological tests on blood donors in Wuhan in the second half of 2019 were published in the journal Protein and Cell. A study of the viral profiles of more than 17,000 bats in China, published in the journal National Science Review, did not find the sequence of novel coronavirus or its related coronaviruses.  

GT: Do you have any comment on the newly-released paper published by the China CDC? 

Qian: No direct evidence can prove the authentic origins of COVID-19, and the spread of the virus from bats to other animals and then from animals to humans is considered one of the possible origin hypotheses, but exactly where, when, and how the process occurred is not yet clear.

All the animal samples collected in the market as the paper mentioned were negative, and only some environmental samples were tested positive, which most likely came from contamination of human COVID cases. The data from the paper support the notion that Huanan market may have been just an amplifier of COVID-19 transmission, rather than the place where COVID-19 originated.

Chinese experts have been working very hard on studying the origins of the COVID-19, which is an extremely difficult task. Recently several countries also discovered some bat coronaviruses sharing very high homology in the virus genome sequence to SARS-CoV-2, indicating the importance of cooperation among countries to trace the origins of the virus. Currently, exactly where zoonotic transmission of the virus to human remains unknown and requires further study.

GT: Some officials in WHO assumed the lack of transparency from Chinese government over COVID-19 related data and claimed it may have affected global origins-tracing. What is your view on this, and has there been any difficulty in tracing the origins? 

Qian: As far as I know, the data referenced in the paper had actually been largely included in the WHO-China joint report in 2021 and the relevant report can be found online. Researchers in China have been working very hard to trace the origins and have continued to work closely with many international experts.

But tracing virus origins is an extremely difficult and complex task. The HIV outbreak began in the 1970s, but its zoonotic origins were only identified in 2014, and the virus jumped into humans around 1920. The Ebola virus was discovered in the 1970s, but it is still not entirely clear how it started. Places where outbreaks occurred often were not where the virus originated, such as the 1918 flu, HIV and so on. Bat coronaviruses highly similar to COVID-19 have been found in many places in the world and tracing the origins requires close cooperation among different countries and regions. 

GT: Some media reports claimed that WHO-China joint report on tracing COVID-19 origins received wide criticism because the lack of original data on early cases from China. What is your view on this? 

Qian: I noticed the opinion piece in Science mentioning these views, but from what I learned, the data were shared with the WHO team during WHO-China joint investigation. The main conclusions of the WHO-China joint report are that the laboratory origin of the pandemic was considered to be "extremely unlikely," and crossing over from bats to humans from an intermediary species was "most likely." These are largely considered as consensus among mainstream experts in field of virology.

I personally believe that the results of phase I origins-tracing and the professionalism and international reputation of the panel members and WHO should be fully respected. Tracing origins of the virus is an extremely difficult and professional task. We hope that experts at home and abroad can work together to solve this problem as soon as possible.