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Thread: Novel Coronavirus (2019 n-cov) thread

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    Novel Coronavirus (2019 n-cov) thread

    Since its been slow for ancient DNA, I thought I'd start a thread on the coronavirus.

    Check out this Indian paper analyzing the genetic composition of the virus: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag. It makes the shocking inference that the virus was engineered, based on unique insertions related to HIV virus (!).

    We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.
    bioRxv emphasizes this paper has not been peer-reviewed and suddenly that the paper "has been withdrawn", but is still available as of now.

    Last week, the head of Harvard's chemistry dept researcher was arrested for failing to disclose his recruitment by Chinese intelligence, there are multiple other cases that have popped up in the US and Canada (some of which have since been scrubbed from the news).

    This article, like many others, have emphasized that Wuhan was the site of a level 4 lab for studying the most virulent diseases:
    The scientist who worked at the National Microbiology Lab in Winnipeg made at least five trips to China between 2017-18, including one to train scientists and technicians at China’s newly certified Level 4 lab, which does research with the most deadly pathogens. Xiangguo Qiu, who was escorted out of the Winnipeg lab in July amid an investigation into what’s being described by Public Health Agency of Canada as a possible “policy breach”, was invited to go to the Wuhan National Biosafety Laboratory of the Chinese Academy of Sciences twice a year for two years, for up to two weeks each time. Several of Mrs Qiu’s co-workers say there have always been questions about her trips to China, and what information and technology she was sharing with researchers there.
    What does everyone here think about all this? Was this virus just a random event, was it an unfinished vaccine that escaped, an attempt at a bioweapon that escaped??
    Last edited by K33; 02-06-2020 at 04:18 PM.

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    The "similarities" were in reality biased because the sequences selected could match thousands of different virus and yet they choose the "HIV" arbitrarily.

    4 short sequences that can match everything.

    However there are new possibilites about cure made of HIV drugs.

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    The source of the coronavirus outbreak is traced to wild bats (Zhou et al. 2020). The new coronavirus is a zoonotic viral disease and the first patients who were infected acquired these viruses directly from wild animals. Bat dishes are known in Wuhan, where the bat meat is considered an exotic dish, which made Wuhan the epicenter of the new coronavirus outbreak.

    Abstract
    Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.
    https://www.biorxiv.org/content/10.1...01.22.914952v2
    Coronaviruses are endemic in China because of their peculiar culinary culture. Hu et al. (2017) previously traced SARSr-CoV to a single bat cave in Yunan, where the SARS outbreak originated from. The data show that frequent recombination events have happened among those SARSr-CoVs in the same cave. The nearest village to the bat cave is only 1.1 km away, which indicates a potential risk of exposure to bats for the local residents.

    Abstract
    A large number of SARS-related coronaviruses (SARSr-CoV) have been detected in horseshoe bats since 2005 in different areas of China. However, these bat SARSr-CoVs show sequence differences from SARS coronavirus (SARS-CoV) in different genes (S, ORF8, ORF3, etc) and are considered unlikely to represent the direct progenitor of SARS-CoV. Herein, we report the findings of our 5-year surveillance of SARSr-CoVs in a cave inhabited by multiple species of horseshoe bats in Yunnan Province, China. The full-length genomes of 11 newly discovered SARSr-CoV strains, together with our previous findings, reveals that the SARSr-CoVs circulating in this single location are highly diverse in the S gene, ORF3 and ORF8. Importantly, strains with high genetic similarity to SARS-CoV in the hypervariable N-terminal domain (NTD) and receptor-binding domain (RBD) of the S1 gene, the ORF3 and ORF8 region, respectively, were all discovered in this cave. In addition, we report the first discovery of bat SARSr-CoVs highly similar to human SARS-CoV in ORF3b and in the split ORF8a and 8b. Moreover, SARSr-CoV strains from this cave were more closely related to SARS-CoV in the non-structural protein genes ORF1a and 1b compared with those detected elsewhere. Recombination analysis shows evidence of frequent recombination events within the S gene and around the ORF8 between these SARSr-CoVs. We hypothesize that the direct progenitor of SARS-CoV may have originated after sequential recombination events between the precursors of these SARSr-CoVs. Cell entry studies demonstrated that three newly identified SARSr-CoVs with different S protein sequences are all able to use human ACE2 as the receptor, further exhibiting the close relationship between strains in this cave and SARS-CoV. This work provides new insights into the origin and evolution of SARS-CoV and highlights the necessity of preparedness for future emergence of SARS-like diseases.
    https://journals.plos.org/plospathog...l.ppat.1006698
    Last edited by ThirdTerm; 02-06-2020 at 10:39 PM.
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    I've heard that non-Asian populations may have a degree of immunity to coronavirus; however, I'm yet to hear anything concrete.
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    Quote Originally Posted by ThirdTerm View Post
    The source of the coronavirus outbreak is traced to wild bats (Zhou et al. 2020). The new coronavirus is a zoonotic viral disease and the first patients who were infected acquired these viruses directly from wild animals. Bat dishes are known in Wuhan, where the bat meat is considered an exotic dish, which made Wuhan the epicenter of the new coronavirus outbreak.



    Coronaviruses are endemic in China because of their peculiar culinary culture. Hu et al. (2017) previously traced SARSr-CoV to a single bat cave in Yunan, where the SARS outbreak originated from. The data show that frequent recombination events have happened among those SARSr-CoVs in the same cave. The nearest village to the bat cave is only 1.1 km away, which indicates a potential risk of exposure to bats for the local residents.
    I read a year or so ago that bats are considered the biggest reservoir of viruses that endanger humans. You would think the Chinese govt would ban eating bats.

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    Quote Originally Posted by alan View Post
    I read a year or so ago that bats are considered the biggest reservoir of viruses that endanger humans. You would think the Chinese govt would ban eating bats.
    The chinese does not want to rock the boat with its population by banning traditional practices

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    Quote Originally Posted by mildlycurly View Post
    I've heard that non-Asian populations may have a degree of immunity to coronavirus; however, I'm yet to hear anything concrete.
    What about this study?
    Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov
    https://www.biorxiv.org/content/10.1....919985v1.full

    We also noticed that the only Asian donor (male) has a much higher ACE2-expressing cell ratio than white and African American donors (2.50% vs. 0.47% of all cells). This might explain the observation that the new Coronavirus pandemic and previous SARS-Cov pandemic are concentrated in the Asian area.

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    Quote Originally Posted by eastara View Post
    What about this study?
    Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov
    https://www.biorxiv.org/content/10.1....919985v1.full

    We also noticed that the only Asian donor (male) has a much higher ACE2-expressing cell ratio than white and African American donors (2.50% vs. 0.47% of all cells). This might explain the observation that the new Coronavirus pandemic and previous SARS-Cov pandemic are concentrated in the Asian area.
    I saw that, it looks like it was RNA and not DNA, so they required actual live tissue samples? They had 4 Africans/Afro-Americans, 3 Europeans, and only 1 East Asian sample. But the Asian did have a 5x susceptibility vs the whites and blacks.

    Would really like to see this analysis re-run with a larger sample size and more diverse populations...

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    My wife is from Kaifeng which is about 6 hours north of Wuhan. Eating bats is not as common in China as is being reported. While Corona Viruses may originate with bats, there is probably an intermediate species of animal that passes it along to humans. MERS-CoV passed from bats to camels to people. SARS-CoV passed from bats, to possibly civet cats to people. So one would have to assume that it is a similar case with nCoV-2019.

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    Quote Originally Posted by Webb View Post
    My wife is from Kaifeng which is about 6 hours north of Wuhan. Eating bats is not as common in China as is being reported. While Corona Viruses may originate with bats, there is probably an intermediate species of animal that passes it along to humans. MERS-CoV passed from bats to camels to people. SARS-CoV passed from bats, to possibly civet cats to people. So one would have to assume that it is a similar case with nCoV-2019.
    Pangolins are now being suggested as an intermediate.

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