On January 30, local time, the world’s leading medical journal, The Lancet, published a new paper online, revealing that the genome sequence of the new coronavirus (2019-nCoV) is very different from SARS-CoV and can be considered a new type of human infectious coronavirus. But the original host of the virus is the same as SARS-CoV, and it is a bat.
(Original title: Lancet Disclosure: New Coronavirus is very different from human SARS, 4 details to be noted)
Journalist Zhang Ruyu He Liping
At the same time, the paper found that the new coronavirus into human cells used molecular “channels”, that is, human receptors, may also be the same as SARS virus, are angiotensin conversion enzyme 2 (ACE2).
It is worth noting that the paper also reveals four details:
First, the outbreak was first reported in late December 2019, when most bats in Wuhan were hibernating.
Second, no bats have been found or sold in the South China seafood market, but there are many non-aquatic animals, including mammals.
Third, the genetic sequence between 2019-nCoV and its close relatives, bat-SL-CoVZC45 and bat-SL-CoVZXC21, is less than 90%, meaning that these two coronaviruses originating from bats are not direct ancestors of 2019-nCoV.
Fourth, in SARS and MERS, bats are their natural hosts, another animal is the intermediate host, and humans are the ultimate hosts.
The study found 2019-nCoV in all 10 genetic samples taken from patients, including eight complete genomes and two partial genomes. The genetic sequences of each sample are almost identical (more than 99.98 percent of the gene sequences are the same), indicating that the virus is the only recent infestation of humans.
“It is interesting to note that this study found that the gene sequence of the 2019-nCoV virus from different patients is almost identical,” said Professor Shi Weifeng, one of the authors of the paper, Shandong First Medical University and Shandong University’s Laboratory for Epidemiology of The Etiology of New Infectious Diseases. The findings suggest that the isolated 2019-nCoV originated from the same source, that the transmission occurred for a short time and was detected relatively quickly. However, as the virus spreads to more people, it is necessary to continuously monitor the occurrence of mutations. “
The paper was presented with researchers from china’s Centers for Disease Control and Prevention, Shandong University, Shandong First Medical University and Shandong Academy of Medical Sciences, Hubei Province Center for Disease Control and Prevention, Shenzhen Huada Inyuan Medical Technology Co., Ltd., Chinese Academy of Sciences, PLA General Hospital, Wenzhou Medical University, University of Sydney, Shandong First Medical University Affiliated First Hospital.
Samples taken from 9 people, 1 person staying at a hotel near the seafood market
The paper sequenced samples of broncholar alveoli irrigation and cultured separators from nine hospitalized patients.
The researchers say the systematic evolutionary analysis of these 2019-nCoV genomes and other coronavirus genomes is intended to determine the evolutionary history of the virus and to help infer its possible origin. To explore the possible receptor binding properties of viruses, the researchers modeled homologous.
Sample information on nine patients infected with the new 2019 coronavirus
Nine patients had viral pneumonia and a common respiratory pathogen was negative, and at least three hospitals in Wuhan were admitted. Eight of them had been to the South China Seafood Market before developing symptoms, while the other (WH04) had not been to the market but stayed at a hotel near the market from 23 December to 27 December 2019.
Samples of 5 of the 9 people (WH19001, WH19002, WH19004, WH19008, YS8011) were collected by the CDC, and the CDC tested the samples negative for all common respiratory pathogens screened.
Samples from the remaining 4 patients (WH01, WH02, WH03, WH04) were collected by Huada gene and the results showed that they were also negative for common respiratory pathogens.
By analyzing samples from nine patients, the researchers obtained eight complete and two-part genome sequences for 2019-nCoV.
This data has been stored in China’s National Microbiology Data Center (login number NMDC10013002, genome login number NMDC60013002-01 to NMDC60013002-10), while data from Huada gene has been stored in China’s national gene bank (login number CNA0007332- 35)。
Based on these genomes, the researchers developed a real-time PCR analysis method and retested the original clinical samples of huada gene (WH01, WH02, WH03, and WH04) to determine its threshold cycle (Ct) values. The remaining samples were tested by another real-time fluorescence quantitative PCR developed by the China Center for Disease Control and Prevention, with Ct values ranging from 22.85 to 32.41.
These results confirm the presence of 2019-nCoV in the patient.
The virus is the latest to infect humans and is genetically different from SARS-CoV
The 10 groups of 2019-nCoV genome sequences obtained by the researchers from nine patients were highly similar, exhibiting more than 99.98 percent of the sequence homologousness. As a typical RNA virus, the average evolutionary rate of coronaviruses is about 10 to 4 nucleotides per site per year, with mutations produced in each replication cycle.
The researchers believe this suggests that the virus has only recently appeared in human groups.
A source sequence search of the 2019-nCoV complete genome shows that The most closely related viruses in GenBank (DNA sequence database established by the U.S. National Biotechnology Information Center) are bat-SL-CoVZC45 (homologous 87.99 percent; query coverage 99 percent), and sars-like coronavirus bat-SL-CoVZXC21 (login MG77) 2934; homologous 87.23%; query coverage 98%). Both of the most closely related viruses were collected in the eastern Chinese city of Zhoushan in 2018.
In the five gene regions (E, M, 7, N and 14), the sequence homologous is greater than 90%, the highest in the E gene (98.7%). The 2019-nCoV S gene has the lowest sequence of homologous ness with bat-SL-CoVZC45 and bat-SL-CoVZXC21, at only about 75%. In addition, the sequence homologousness in 1b (about 86%) is lower than the sequence homologousness in 1a (about 90%).
2019-nCoV and SARS-CoV GZ02 (SARS coronavirus, The sequence of search number AY390556) and the sequence of bat SARS-like coronavirus bat-SL-CoVZC45 (MG772933) and bat-SL-CoVZXC21 (MG772934)
Most encoded proteins show a high degree of sequence homologousness between 2019-nCoV and the associated bat-derived coronavirus (see figure above). One notable exception, however, is the protrusion protein, which has only about 80% of the sequence homologous.
Compared to the two most closely related, 2019-nCoV is farther away from SARS-CoV (SARS coronavirus, about 79% homologous) and MERS-CoV (MERS coronavirus, about 50% of homologous).
Systematic developmental analysis of the full-length genome of the 2019-nCoV and B coronaviruses as representative viruses
The system development analysis shows that 2019-nCoV belongs to the sarbecovirus subgenite of the B-type coronavirus, with the relatively long branch length of the closest bat-SL-CoVZC45 and bat-SL-CoVZXC21, and genetically different from SARS-CoV.
Importantly, homologous modeling shows that 2019-nCoV has a receptor binding domain structure similar to SARS-CoV, although amino acid differences exist at some key residues.
The researchers note that 2019-nCoV may bind to human angiotensin-converting enzyme 2 (ACE2) receptors, while serum ACE assays are mainly used for the diagnosis of lung disease, and have some value in the diagnosis of liver disease, thyroid disease and other systemic diseases.
Bats go to hibernation, who is the intermediate host?
From an epidemiological perspective, eight of the nine patients studied by the researchers had a history of exposure to the South China Seafood Market in Wuhan, suggesting that they may have been in close contact with the source of the infection on the market. But one patient had never been to the market, even though he lived in a home near the market before the outbreak. This indicates that the patient may have contracted the virus due to droplet transmission or from currently unknown sources.
Available data suggest that the 2019-nCoV virus infected humans from bat libraries, but it is not clear whether an animal that is currently unknown acts as an intermediate host between bats and humans. Although the researchers’ systematic developmental analysis also suggests that bats may have been the original host of the virus, an animal sold at the South China Seafood Market in Wuhan may have been an intermediate host that prompted the virus to appear in the human body.
The researchers stress that some facts suggest that another animal is acting as an intermediate host between bats and humans.
First, the outbreak was first reported in late December 2019, when most bat species in Wuhan were hibernating.
Second, bats are not sold or found at the South China Seafood Market, and a variety of non-aquatic animals, including mammals, are available for purchase.
Third, the sequence homogeneity between 2019-nCoV and its close relatives, bat-SL-CoVZC45 and bat-SL-CoVZC21, is less than 90%, so bat-SL-CoVZC45 and bat-SL-CoVZC21 are not direct ancestors of 2019-nCoV.
Fourth, according to previous studies, in SARS-CoV and MERS-CoV, bats are natural virus banks (sources of viruses), while another animal (SARS-CoV’s fruit beaver and MERS-CoV’s single-peak camel) is the intermediate host, and humans are end-hosts.
So, based on current data, researchers believe the 2019-nCoV virus that caused the outbreak in Wuhan may have initially been hosted by bats and may have been transmitted to humans by some or more of the currently unknown wildlife sold at the South China Seafood Market.