The traceability of the new coronavirus has yielded the latest results. On February 18, local time, pre-printed this website bioRxiv (without peer review) published a paper “The identification of the Malay pangolin 2019-nCoV-related coronavirus in southern China”, the author of the communication is Professor Guan Wei of the National Key Laboratory of The School of Public Health of the University of Hong Kong, Professor Hu Yanling of Guangxi Medical University.
(Original title: Stop eating pangolins!) The tube team found a new coronary-related coronavirus from the pangolin)
Journalist He Liping
He is currently the Director of the National Key Laboratory for Emerging Infectious Diseases at the University of Hong Kong and the Director of the Influenza Research Centre. During the SARS period in 2003, the tube team was the first to isolate the SARS virus and confirmed that the beaver was the intermediate host of SARS and a direct source of human infection with SARS. Based on the clarity of the intermediate host and the reporting of the pipe-to-tube, Guangdong Province then cleared the beavers on the market, thus effectively curbing the spread of SARS outbreak.
In this latest study, Guan Qi et al. reported the discovery of the 2019-nCoV-related coronavirus in pangolins (lactation),” detected during anti-smuggling operations in southern China. They found that pangolin-related coronaviruses belong to two subtypes of the 2019-nCoV-related coronavirus, one of which has a receptor binding domain very close to the 2019-nCoV.
The authors argue that the study’s findings on the multiple pangolin coronavirus lineage and its similarity to 2019-nCoV suggest that pangolins should be considered as a potential intermediate host for the new coronavirus and should be removed from the vegetable market to prevent zoonotic transmission.
On February 7, researchers such as Professor Shen Yongyi and Professor Xiao Lihua of South China Agricultural University, Lingnan Modern Agricultural Science and Technology Guangdong Province Laboratory, and the Chinese People’s Liberation Army Academy of Military Sciences and the Guangzhou Zoo Research Department also published their research results: pangolins are potential intermediate hosts of the new coronavirus.
By analyzing more than 1,000 macro genomic samples, the team targeted pangolins as potential intermediate hosts of the new coronavirus, then detected a 70% positive rate for beta-coronaviruses in pangolins through molecular biology tests, and further isolated the virus, which was observed under a typical coronavirus particle structure under an electric mirror Finally, through the genome analysis of the virus, it is found that the isolated strains are as similar as those in the current infected human strains.
However, Shen Yongyi et al.’s research results have not yet been officially published.
It is worth mentioning that pangolins are the most serious of all mammals, illegally trafficked, used as a food source, and scales are also drugged. As a result, pangolins have received increasing attention in recent years, and pangolin species such as Chinese pangolins are now on the IUCN Red List of Endangered Species.
Multi-batch pangolin sample tested positive for coronavirus
The outbreak of the new crown outbreak is temporarily thought to be linked to The South China Seafood Market in Wuhan, where wild animals sold may be the source of zoonotic infections. Although the bat is likely to be the host of the 2019-nCoV, it is not clear that the intermediate host of the metastatic virus.
The team previously collected samples of 18 frozen tissue (lungs, intestines, blood) from 18 Malay pangolins between August 2017 and January 2018. These pangolins were obtained during the Guangxi Customs anti-smuggling operation.
System development analysis describes the evolutionary relationship between 2019-nCoV, pangolin coronavirus sequences obtained in this study, and other coronaviruses.
It is worth noting that RNA high-throughput sequencing of these samples showed the presence of coronaviruses in 6 out of 43 samples (2 lungs, 2 intestines, 1 pulmonary intestinal mixture, 1 blood). The team then obtained six full- or near-full-length genome sequences labeled GX/P1E, GX/P2V, GX/P3B, GX/P4L, GX/P5E, GX/P5L. These viruses also have a genome structure similar to the 2019-nCoV, with nine predictive open reading boxes. The team also successfully isolated the virus.
Based on the new genome sequence, the team designed qPCR detection primers to confirm that the original samples were positive for coronaviruses.
Next, the team conducted further qPCR testing of another batch of pangolin samples collected between May and July 2018. Of the 19 samples of 12 pangolins (9 intestinal tissues, 10 lung tissues), 3 were positive for coronavirus.
In addition to these pangolins from Guangxi, after the outbreak, the Guangzhou Customs Technology Center also re-examined five archived pangolin samples (2 skin tissues, 1 unknown tissue, 1 scale) they seized during an anti-smuggling operation in March, which also found coronavirus.
Using high-throughput sequencing, the team found that the scale samples contained coronavirus sequences and used the data to assemble a 2155bp partial genome sequence (labeled GD/P2S), which represents 72% of the 2019-nCoV genome.
Notably, another study on diseased pangolins in Guangdong in 2019 also found a virus overlap similar to 2019-nCoV in lung samples. Through different assembly methods and manual screening, a partial genome sequence (labeled GD/P1L) of approximately 86.3% of the total length of the viral genome was obtained.
The genomes of these coronaviruses found in pangolins are similar to the genomes of new coronaviruses at 85.5%-92.4%, and represent two subtypes of the new coronavirus in the system evolution tree, of which GD/P1L and GD/P2S are closely related to the new coronavirus.
Pangolins may be long-term hosts of coronaviruses, but are not the closest to 2019-nCoV
The new coronavirus belongs to the Sarbecovirus subspecies of beta-coronavirus, and several studies have noted that members of the Sarbecovirus subspecies have undergone extensive genetic recombination.
To test this view, the team further recombined the virusEs ZC45 and ZCS21, which showed that the bat coronaviruses ZC45 and ZCS21 may be recombinant, containing genomic fragments of multiple SARS-CoV-related genealogy (genomic regions 2, 5, 7) and 2019-nCoV-related genealogy. Includes genomic fragments from this pangolin (regions 1, 3, 4, 6, 8).
More notable, however, is the team’s observation of a presumed recombinant signal between pangolin coronavirus, bat coronavirus RaTG13, and 2019-nCoV. In particular, although 2019-nCoV is most closely related to the bat coronavirus RaTG13 in the rest of the virus genome, the receptor binding domain (RBD) amino acid homologous nature of 2019-nCoV and Guangdong pangolin is 97.4%, The amino acid homologousity of RaTG and 2019-nCoV receptor binding domain is only 89.2%
In fact, Guangdong Pangolin coronavirus and 2019-nCoV have the same amino acids on the RBD’s five key residues, while RaTG13 and 2019-nCoV have only one amino acid the same. However, the development algellant system development analysis for RBD only shows that the Guangdong Pansama coronavirus is not the closest kinship to 2019-nCoV.
Therefore, the team speculated that the amino acid homologousness between the Guangdong pangolin coronavirus and the new coronavirus may have been caused by the convergence of selective mediaage, rather than recombination. Of course, it is still difficult to judge based on available data.
The paper notes that while any drivers of convergent evolution are unknown, its likeness of recombination will further highlight the role of intermediate animal hosts in human virus outbreaks.
So far, pangolins are the only mammals, except bats, identified as infected with 2019-nCoV-related coronavirus infections.
For the study, the team found two related coronavirus lineage in pangolins, all related to 22019-nCoV. This suggests that pangolins may be the long-term hosts of these viruses.
Or get 2019-nCoV-related viruses from other animal hosts such as bats
But surprisingly, pangolins are single-living animals with relatively small populations and endangered status. However, it cannot be ruled out that pangolins independently obtained the 2019-nCoV-related virus from bats or other animal hosts.
It is worth noting that both types of pangolin coronaviruses were obtained from smuggled Malay pangolins, most likely from Southeast Asia, where the virus diversity they maintain is currently unknown.
The team believes there is no doubt that the extent of the spread of the coronavirus in the pangolin population needs further investigation, but repeated infections of the 2019-nCoV-related coronavirus in Guangxi and Guangdong province suggest that pangolins may be potentially important hosts for the emergence of coronaviruses.
The team noted that coronaviruses, including those associated with the 2019-nCoV-related viruses, are evident in many wild mammals in Asia. Although the epidemiology, pathogenicity, inter-species infectiousness and spread of pangolin coronavirus has yet to be studied, the data provided in this study strongly suggest that the treatment of these animals requires considerable care and that the sale of the animals should be strictly prohibited.
They also noted that further monitoring of pangolins in the natural environment of China and South-East Asia was also clearly necessary to understand their role in the emergence of 2019-nCoV and the risk of future human and zoonotic disease transmission.