The question of the origin of the new coronavirus remains a mystery in the scientific community. On March 26 local time, nature, a top academic journal, published an online paper identifying sars-cov-2 related coronaviruses in Malaysia pangolins. The authors of this study are Professor Guan Yi, National Key Laboratory of new infectious diseases, School of public health, Hong Kong University, and Professor Hu Yanling, Guangxi Medical University. It is worth noting that the achievement is online in the form of accelerated article preview, and the receiving time is March 17 local time.
Guan Yi is now director of the National Key Laboratory for emerging infectious diseases and director of the influenza research center at the University of Hong Kong. During the period of SARS in 2003, Guan Yis team took the lead in isolating the SARS virus and confirmed that civet cat was the intermediate host of SARS and the direct source of human infection. Based on the clearness of intermediate hosts and the report of Guan Yi, the civets in the market were removed in Guangdong Province, which effectively curbed the spread of SARS.
In this latest study, Guan Yi and others reported that new coronavirus related coronaviruses were found in pangolins (Mammalia Lepidoptera) found in anti smuggling operations in southern China. They found that the pangolin associated coronavirus belongs to two subtypes of the new coronavirus associated coronavirus, one of which has a receptor binding domain very close to the new coronavirus.
The authors believe that novel coronavirus coronavirus lineages and their similarity to the new crown viruses found in the study suggest that pangolin should be considered as the potential intermediate host of the new coronavirus and should be removed from the vegetable market to prevent the spread of human zoonotic disease.
Of course, according to the current research, the team does not think it is enough to show that pangolin is the intermediate host directly involved in the outbreak. But to date, pangolin is the only mammal other than bats found to be infected by the new coronavirus associated coronavirus. They may at least play an important role in the ecology of coronavirus community.
In the outbreak caused by the new coronavirus, the first to express or play an important role in pangolin is South China Agricultural University, Professor Shen Yongyi and Professor Xiao Lihua of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and technology, and the team of the Military Academy of the peoples Liberation Army and the research department of Guangzhou zoo. They announced the research results on February 7: pangolin The novel coronavirus is a potential intermediate host.
It is worth mentioning that pangolin is the most illegally trafficked of all mammals. It is used as a source of food and scales are also used as medicines. Therefore, pangolin has attracted more and more attention in recent years. Pangolin species such as Chinese Pangolin have been listed as the most endangered species on the red list of endangered species by the World Conservation Union (IUCN).
Multiple batches of pangolin samples were positive for coronavirus
The outbreak of the new crown outbreak is temporarily considered to be related to the South China seafood market in Wuhan, where the wild animals sold may be the source of zoonoses. Although bats are likely to host the new coronavirus, it is not clear which intermediate hosts are responsible for the transfer of the virus.
Guan Yi and others previously collected frozen tissue (lung, intestine, blood) samples from 18 pangolins from August 2017 to January 2018. These pangolins were obtained in Guangxi customs anti smuggling operations.
Phylogenetic analysis described the evolutionary relationship among the new coronavirus, the pangolin coronavirus sequence obtained in this study, and other coronaviruses.
Notably, high-throughput RNA sequencing of these samples revealed the presence of coronavirus in 6 of 43 samples (2 lungs, 2 intestines, 1 mixture of lungs and intestines, 1 blood). The research team then obtained six full-length or near full-length genome sequences, labeled GX / P1E, GX / P2V, GX / P3b, GX / p4l, GX / P5E and GX / p5l. These viruses also have a genome structure similar to the new coronavirus, with 11 predictive open reading frames. The team also successfully isolated the virus.
Based on the new genome sequence, the team designed qPCR primers to confirm that the original samples were positive for coronavirus.
Next, the team conducted further qPCR tests on another group of pangolin samples collected between May and July 2018. Of the 19 samples (9 intestinal tissues and 10 lung tissues) from 12 pangolins, 3 were positive for coronavirus.
In addition to these pangolins from Guangxi, after the outbreak, Guangzhou Customs Technical Center also retested five archived pangolin samples (2 skin tissues, 1 unknown tissue, 1 scale) that they seized during the anti smuggling operation in March. The same coronavirus was found in these samples.
Through high-throughput sequencing, the research team found that the scale samples contained coronavirus sequences. With these data, a 21505bp partial genome sequence (labeled GD / p2s) was assembled, which can represent 72% of the new coronavirus genome.
It is worth noting that another study on the prevalence of pangolin in Guangdong Province in 2019 also found overlapping groups of viruses similar to the new coronavirus in lung samples. Through different assembly methods and artificial screening, 86.3% of the total genome of the virus (labeled GD / P1l) was obtained.
The genomes of these coronaviruses found in pangolin are 85.5% - 92.4% similar to those of new coronavirus, and represent two subtypes of new coronavirus related viruses in phylogenetic tree, among which the subtypes GD / P1l and Gd / p2s are closely related to new coronavirus.
Pangolin may be a long-term host of coronavirus, but it is not closely related to new coronavirus
The new coronavirus belongs to the subgenus sarbecovirus of u03b2 - coronavirus. Previously, some studies have noted that the members of the subgenus sarbecovirus have undergone extensive gene recombination.
In order to verify the above view, the research team further carried out recombination analysis and recombination. The analysis showed that bat coronavirus zc45 and zcs21 may be recombinants, including multiple SARS CoV related genealogies (genome regions 2, 5, 7) and genome fragments of new coronavirus related genealogies, including those from pangolin (regions 1, 3, 4, 6, 8).
More significantly, however, the team observed putative recombination signals between pangolin coronavirus, bat coronavirus ratg13 and new coronavirus. In particular, although neocoronavirus and bat coronavirus ratg13 are most closely related in the rest of the virus genome, the amino acid homology of the receptor binding domain (RBD) of neocoronavirus and pangolin in Guangdong is 97.4%, while the amino acid homology of the receptor binding domain of rATG and neocoronavirus is only 89.2%
In fact, Guangdong pangolin coronavirus and new coronavirus have the same amino acid on the five key residues of RBD, while ratg13 and new coronavirus have only one amino acid. However, phylogenetic analysis of synonymous loci only for RBD showed that Guangdong pangolin coronavirus was not the closest relative of new coronavirus.
Therefore, the team speculated that the amino acid homology of RBD between Guangdong pangolin coronavirus and new coronavirus might be caused by selective mediated convergent evolution rather than recombination. Of course, it is still difficult to judge based on the existing data. The similarity of ACE2 sequence between human and pangolin (84.8%) was higher than that between human and bat (80.8% - 81.4%).
The occurrence of recombination or convergent evolution further emphasizes the role of intermediate animal hosts in the emergence of human viruses. However, it is important to note that the spike protein (S-protein) of all the pangolin coronaviruses found so far has not seen the insertion of multiple bases (similar to Flynn) at the S1 / S2 junction. This insertion feature can now distinguish the new coronavirus from the beta coronavirus (including ratg13), which may also promote the rapid spread of the new coronavirus in the population.
So far, pangolin is the only mammal infected by the new coronavirus associated coronavirus except bats.
In this study, the team found two related coronavirus lineages in pangolin, all related to the new coronavirus. This suggests that pangolin may be a long-term host of these viruses.
Or get new coronavirus related viruses from bats and other animal hosts
But surprisingly, pangolin is a solitary animal with a relatively small population size and is endangered. However, it can not be excluded that pangolin obtained new coronavirus related virus independently from bat or other animal hosts. Therefore, their role in the emergence of new coronavirus remains unclear.
It is worth noting that both of these two kinds of pangolin coronaviruses are obtained from the smuggled Malay pangolin, which is likely to come from Southeast Asia, and the virus diversity they maintain in their native areas is currently unknown.
The research team believes that there is no doubt that the transmission degree of coronavirus in pangolin population needs further investigation, but the repeated infection of new coronavirus related coronavirus in Guangxi and Guangdong Province shows that pangolin may play an important role in the ecology of coronavirus community.
The team noted that coronaviruses, including those associated with the new coronavirus, are evident in many wild mammals in Asia. Although the epidemiology, pathogenicity, interspecific infectiousness and transmissibility of pangolin coronavirus still need to be studied, the data provided by this study strongly shows that the handling of these animals needs to be very careful and should be strictly prohibited from being sold in the vegetable market. They also noted that further monitoring of pangolins in the natural environment of China and Southeast Asia is clearly necessary to understand their role in the emergence of new coronavirus and the risk of future zoonotic transmission. Original paper link: https://www.nature.com/articles/s41586-020-2169-0 source: surging news editor in charge: Wang Fengzhi ufe64 nt2541
The team noted that coronaviruses, including those associated with the new coronavirus, are evident in many wild mammals in Asia. Although the epidemiology, pathogenicity, interspecific infectiousness and transmissibility of pangolin coronavirus still need to be studied, the data provided by this study strongly shows that the handling of these animals needs to be very careful and should be strictly prohibited from being sold in the vegetable market.
They also noted that further monitoring of pangolins in the natural environment of China and Southeast Asia is clearly necessary to understand their role in the emergence of new coronavirus and the risk of future zoonotic transmission.
Link to the original paper: https://www.nature.com/articles/s41586-020-2169-0