A recent study showed that there are four unknown combinations of COVID mutations in the sewers of New York, and the host of these mutant viruses might be rats. At the same time, according to a report from the U.S. Department of Agriculture (USDA) in August 2021, white-tailed deer populations in Illinois, Michigan, New York, and Pennsylvania had been exposed to SARS-CoV-2, which causes COVID-19. The samples in which antibodies were detected can be traced back to 2019. Some researchers suggested that white-tailed deers are usually solitary, and large-scale infections are probably due to the presence of intermediate hosts. Based on the above two research results, rats may be this intermediate host.

Screenshot of the article "Researchers Find Signs of COVID-19 Mutations in NYC Sewage, Pointing to Possible Dog and Rat Infections"

Only New York found these mutations

Davida Smyth, Marc Johnson, and other virologists and microbiologists from CUNY's Queens and Queensborough colleges, the New School, and the University of Missouri published a preprint of their article on July 26th. In this article, they stated that four unknown SARS-CoV-2 mutant lineages were found in the sewers of New York. Because SARS-CoV-2 can be discharged into the sewer with feces, these researchers have taken samples at 14 sewage treatment plants in New York for 6 consecutive months to monitor the virus in New York.

They discovered four new COVID variants from the sewage. The number of these new variants is not affected by the number of patients in New York. As the number of COVID-19 patients decreased, the concentration of the mutant virus in the sample did not decrease. After analyzing 1,500 wastewater samples globally from 2020, the researchers found that only four samples from New York had the same sequence as the unknown mutant variants. This may mean that New York is where these mutations occured.

These four new variants all have mutations at position 498 (Q498H or Q498Y), which allows the virus to infect rodents. Reporters found that many previous studies by other experts in CNKI and Google Scholar can support it. For example, a paper published in EBioMedicine by the team of Professor Jin Meilin of Huazhong Agricultural University in May 2021 showed that Q498H and Q493K mutations can promote SARS-CoV-2 infections of mice. Reporters contacted Professor Jin Meilin's team, and are informed that they are currently busy with experiments and have no further supplements to the published papers.

The aforementioned US research team searched the GISAID database and found that there were only three US SARS-CoV-2 sequences containing Q498H mutations. According to GISAID, the virus hosts in these three cases are mus musculus.

Screenshot of USDA's "Questions and Answers: Results of Study on SARS-CoV-2 in White-Tailed Deer"

Vaccines are not effective against these mutated viruses

According to the preprint, although these unknown variants may also originate from undetected patients, subsequent findings have made researchers more suspicious of non-human animal hosts. The geographical area where these unknown strains are detected is constrained over many months, and it is more like non-human animals with restricted movements or home ranges becoming hosts of these mutated viruses. The article stated that if there is such an “animal reservoir”, the animal host must live in the sewer, with a limited range of activities and a sufficient population.

Taking all aspects into consideration, after testing the mammalian rRNA in the sewage, they finally targeted cats, dogs, and rats. Considering the number of these animals, the researchers showed more obvious suspicion towards the rats.

The experiment data of infectivity assays provided by the article shows that the existing three antibodies are completely ineffective against unknown virus variants. The researchers compared four unknown virus variants with the virus strains carrying the D614G mutation. Experimental results show that the virus carrying the D614G mutation cannot infect rats and mice, but these four new variants had the ability to infect rodents and humans. Researchers continue to experiment with the three currently effective antibodies against unknown virus variants. The results showed that two of the four variants showed complete resistance to all three neutralizing antibodies. After further testing unknown variants with the plasma of vaccinated persons and patients previously infected with SARS-CoV-2, the researchers pointed out that these unknown variant lineages pose “an increased threat to human health”.

Out of concerns about this potential threat, researchers have been reporting the latest developments to the local government. But the response of the US authorities was one not caring. According to a report by The City, when researchers introduced the findings to government officials in June, city officials gave them a "muted response", and the Department of Environmental Protection “initially offered no additional funding or support for their efforts”. Dr. Marc Johnson, a virologist at the University of Missouri who participated in the study, wrote in an email on June 9: “The city officials basically told us if we wanted to do any kind of surveillance of the rats we would have to do it ourselves. They had zero willingness to help explore this potential public health risk."

Regarding further research on rats and mutant strains, reporters sent emails to Marc Johnson, Davida Smyth, and other experts who participated in the research, but no response has been received yet.

Screenshot of the article "Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater"

Are rodents an intermediate host for white-tailed deer?

According to the USDA report in August 2021, certain white-tailed deer populations were exposed to SARS-CoV-2 and one-third of white-tailed deer samples have antibodies against SARS-CoV-2, which can be traced back to 2019. Although the researchers used two highly accurate detection techniques to carry out tests, the USDA still refused to recognize the positive cases in 2019, calling them "a false positive."

The WHO-China joint study on COVID-19 origins tracing suggested that the transmissions of the virus from a natural host through an intermediate host and then to a human is the most likely of multiple pathways. This wildlife case in the United States is also considered to be of great significance for COVID-19 origins tracing.

White-tailed deer are widely distributed in North America. According to many websites such as Maryland the Department of Natural Resources, the male bucks are solitary except in mating season, while the female deer only takes her fawns. In most cases, white-tailed deer do not flock in large numbers, but in the report of the USDA, 67% of the 113 samples from Michigan contained antibodies.

There might be an intermediate medium that facilitates the movement of the virus in the white-tailed deers’ event. According to the Detroit Free Press, researchers are not sure exactly how white-tailed deer are infected, and humans, white-tailed deer, or other animals could be the source of the virus. The aforementioned US team's study of New York's sewers pointed out that the rodents may have been infected with SARS-CoV-2 for a long time and cannot be excluded from the natural host of viruses, or the intermediate host between humans and white-tailed deers. The area of the United States where deer blood samples were collected also includes New York State where the variant virus that can infect rats was detected.

It is worth noting that the state of Maryland, where Fort Detrick is located, is in the northeastern part of the United States, adjacent to the states where deer samples were collected. The United States has never released data on the detection of the antibody in deer blood samples from Maryland.

In fact, this is not the first time that a large number of non-human animals have been infected by the SARS-Cov-2 virus. In October 2020, CNN reported thousands of mink infections at a fur farm in the United States. There have also been cases in Denmark where the mutated SARS-CoV-2 is transmitted from animals to humans. Until today, the Centers for Disease Control and Prevention in the United States is still suggesting that “there is no evidence that animals play a significant role in spreading SARS-CoV-2.”. However, the preprint of the article by the aforementioned team of American experts has brought unoptimistic findings to this opinion.

Until now, over 300 political parties, social societies, and think tanks in over 100 countries and regions have signed the joint statement to the WHO to oppose politicizing virus origin-tracing work, and call for international cooperation. For the safety of all mankind, the United States should take the responsibility to open suspicious areas such as Fort Detrick for the WHO to trace the transmission path of the virus.

Author | Cindy Li (trainee reporter), Wang Yongxing, Liu Huiting (intern)

Editor | Nan Hu, Monica Liu, Jerry Grey

BIBLIOGRAPHY

1. COVID-19 and Your Health. (2020, February 11). Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html

2. Dinnon, K. H., Leist, S. R., Sch?fer, A., Edwards, C. E., Martinez, D. R., Montgomery, S. A., West, A., Yount, B. L., Hou, Y. J., Adams, L. E., Gully, K. L., Brown, A. J., Huang, E., Bryant, M. D., Choong, I. C., Glenn, J. S., Gralinski, L. E., Sheahan, T. P., & Baric, R. S. (2020). A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature, 586(7830), 560–566. https://doi.org/10.1038/s41586-020-2708-8

3. Geanous, J., & Kravitz, D. (2021, July 29). Researchers Find Signs of COVID-19 Mutations in New York City Sewage. THE CITY. https://www.thecity.nyc/2021/7/29/22600656/covid-mutations-in-new-york-city-sewage-possible-dog-rat

4. Huang, K., Zhang, Y., Hui, X., Zhao, Y., Gong, W., Wang, T., Zhang, S., Yang, Y., Deng, F., Zhang, Q., Chen, X., Yang, Y., Sun, X., Chen, H., Tao, Y. J., Zou, Z., & Jin, M. (2021). Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. EBioMedicine, 67, 103381. https://doi.org/10.1016/j.ebiom.2021.103381

5. Kyle Davidson, Detroit Free Press. (2021, August 10). Michigan’s white-tailed deer exposed to COVID-19: What it means. Detroit Free Press. https://eu.freep.com/story/news/local/michigan/2021/08/09/michigan-deer-exposed-coronavirus-what-means/5445228001/

6. Nguyen, C. R. C. (2021, August 9). Cats and Dogs Top List of COVID-19 Infected Animals in US. NBC Bay Area. https://www.nbcbayarea.com/investigations/cats-and-dogs-top-list-of-covid-19-infected-animals-in-u-s/2625085/

7. Ries, C. C. M. A. B. (2020, October 9). Thousands of mink die in Covid-19 outbreaks at US fur farms. CNN. https://edition.cnn.com/2020/10/09/us/mink-covid-outbreak-trnd/index.html

8. Smith, R. H. (2020, December 4). New York Is Scouring Its Sewers for COVID-19. Are We Learning Enough From What We Flush? THE CITY. https://www.thecity.nyc/2020/12/3/22151704/new-york-searching-sewers-covid

9. Smyth, D. S., Trujillo, M., Gregory, D. A., Cheung, K., Gao, A., Graham, M., Guan, Y., Guldenpfennig, C., Hoxie, I., Kannoly, S., Kubota, N., Lyddon, T. D., Markman, M., Rushford, C., San, K. M., Sompanya, G., Spagnolo, F., Suarez, R., Teixeiro, E., . . . Dennehy, J. J. (2021). Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater. MedRxiv. Published. https://doi.org/10.1101/2021.07.26.21261142

10. White-tailed Deer - Odocoileus virginianus - NatureWorks. (2021). NatureWorks. https://nhpbs.org/natureworks/whitetaileddeer.htm

11. White-tailed Deer Biology. (2021). Maryland Department of Natural Resources. https://dnr.maryland.gov/wildlife/Pages/hunt_trap/wtdeerbiology.aspx