Is the SHC014 chimeric coronavirus "eerily similar" to Covid-19 in anything but a journalistic sense?

Question

Gulf News writes:

In the virology community, their project is known as "chimeric coronavirus", eerily similar to COVID-19. This chimera is created in a petridish, reportedly with the "surface spike protein (S protein) of a coronavirus found in horseshoe bats, called SHC014, and the backbone of a SARS virus that could be grown in mice".

Here's the scary bit: In the lab (we don't know which one), this new coronavirus was found so potent it could infect and replicate in human airway cells naturally. It also infected mice lung cells. It's one of the experiments which prompted Prof Simon Wain-Hobson, a virologist at the Pasteur Institute in Paris, to warn that such research is "misleading" and "irrational", stating thus: “The consequence of any accident would be anywhere from a handful of infections to a catastrophic pandemic.”

Is this SHC014 chimeric coronavirus "eerily similar to COVID-19" in a scientific (not just journalistic) sense? Have any scientific publications drawn a parallel between the two viruses?

(I know that SARS-CoV-2 is most closely similar to RaTG13 at whole genome level and at RBD level [most likely] to Pangolin-CoV. I'm asking what if any scientific relevance does SHC014 have to Covid-19.)

Answer 1

The "similarity" of this specific chimera was addressed in a recent paper concerning the lack of evidence that SARS-CoV-2 is lab-grown:

Another claim in Chinese social media points to a Nature Medicine paper published in 2015 [7], which reports the construction of a chimeric CoV with a bat CoV S gene (SHC014) in the backbone of a SARS CoV that has adapted to infect mice (MA15) and is capable of infecting human cells [8]. However, this claim lacks any scientific basis and must be discounted because of significant divergence in the genetic sequence of this construct with the new SARS-CoV-2 (>5,000 nucleotides).

Liu, S. L., Saif, L. J., Weiss, S. R., & Su, L. (2020). No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2. Emerging Microbes & Infections, 9(1), 505-507.

The "eerily similar" nature seems at most to be something well recognized by virologists, particularly in the wake of SARS: coronaviruses circulating in bats could become dangerous to humans if mutations occur in key parts of their genome or recombinations occur with other coronaviruses in bats or intermediate hosts. That's more or less what happened with the first SARS and more or less what happened with SARS-CoV-2, as best as can be told right now.

I'd also take a bit of umbrage at the language used in that article:

this new coronavirus was found so potent it could infect and replicate in human airway cells naturally

seems like a bit of fear-mongering. Any virus that affects humans can "naturally replicate" in human cells: the author could have merely written that instead of calling it "so potent".

Answer 2

Coronavirus main lineages

• alphacoronavirus : bats and many mammals including 229E and NL63 (ACE2), Feline-CoV, TGEV

• betacoronavirus : bats and many mammals, 15% similarity to the previous, need to look at the RNA polymerase and the general structure to establish a phylogenetic relation

  • Mers (Camel) plus a bat lineage

  • MHV, OC43, HKU1, plus a rat and a bat lineage. Humanity probably had a great influence on this lineage

  • Sarbecovirus

    • SARS-CoV (ACE2) and SHC014 (ACE2, 93% similarity) and many non-(ACE2) bat viruses (90% similarity)

    • SARS-CoV-2 (ACE2) 80% similarity to the previous and 96% to RaTG13 (ACE2) and 92% to Pangolin (ACE2)

• gammacovonavirus (avian, beluga)

• deltacovonavirus (avian and swine)

As you see SARS-CoV-2 is very very close to the virus you are mentioning, even if there are enough difference (and bat and Pangolin viruses) to be 100% sure its emergence is totally unrelated to the SARS-CoV and SHC014 experiments. Until this year everybody would have considered SARS-CoV-2 as too distant to SARS to be a danger.

Wuhan's lab is specialized in ACE2 Sarbecoviruses. But the chimeric CoV and the controversy and condamnation of gain-of-function researches was about Baric lab in Chapel Hill, North Carolina, to which Wuhan participated by providing SHC014, the bat virus using ACE2 they found 2 years before. Note everything was published in Nature, there was nothing hidden. Also the chimeric study proved that SHC014 wasn't able to infect human cells, not because of its spike but its backbone, which was reassuring for a possible reemergence of SARS. On the Neertheland, USA and Japan side there was a similar story about H5N1 mutants and chimera.