Late Edit: Pangolins with this viral infection have been found from smuggled ones from both Guangxi and Guangdong provinces, but do not show up in wild pangolin populations in general.
Despite the virus being characterized in pangolins, after looking into this, I now think it is basically incorrect to think of this as primarily a “pangolin virus.” The pangolins were a dying canary in a coal mine, and probably caught it from something else that serves as the real reservoir species for this nCOV precursor*.
These pangolins were being smuggled when they were captured by the authorities in Guangxi. They were dying of probably several diseases; they had lesions in their skin, intense congestion, and were in generally atrocious condition when they got sequenced for viruses. They turned up positive for all manner of things (herpes out the wazoo, but also a sendai virus which was most closely related to the sequence of a human-taken sample, a paramyxovirus, and yes, several coronaviruses).
Given that so many of the pangolins died, the pangolins look more like a highly-susceptible secondary species, than a mostly-asymptomatic primary reserve species* to me.
* GD/PIL or GD/P2S is thought of as a possible nCOV progenitor, alongside bat-virus RaTG13. GD/PIL’s receptor-binding motif (RBM) in particular is identical to SARS-2′s, although nCOV otherwise appears more closely related to RaTG13.
** On educated priors, I think the true reservoir is probably rats, bats, or (less likely) humans in the Guanxi, Hunan, and/or Hubei province.
Personally, I assign >90% on either rats (strong priors + skin lesions) or bats (strong priors + simplest story). But these were exotic animal smugglers; there is a small chance that the original reservoir species could be any animal.
Late Edit: Pangolins with this viral infection have been found from smuggled ones from both Guangxi and Guangdong provinces, but do not show up in wild pangolin populations in general.
Despite the virus being characterized in pangolins, after looking into this, I now think it is basically incorrect to think of this as primarily a “pangolin virus.” The pangolins were a dying canary in a coal mine, and probably caught it from something else that serves as the real reservoir species for this nCOV precursor*.
These pangolins were being smuggled when they were captured by the authorities in Guangxi. They were dying of probably several diseases; they had lesions in their skin, intense congestion, and were in generally atrocious condition when they got sequenced for viruses. They turned up positive for all manner of things (herpes out the wazoo, but also a sendai virus which was most closely related to the sequence of a human-taken sample, a paramyxovirus, and yes, several coronaviruses).
Here’s the original article on the pangolins whose virome they sequenced, and the article noting its relatedness to nCOV.
Given that so many of the pangolins died, the pangolins look more like a highly-susceptible secondary species, than a mostly-asymptomatic primary reserve species* to me.
* GD/PIL or GD/P2S is thought of as a possible nCOV progenitor, alongside bat-virus RaTG13. GD/PIL’s receptor-binding motif (RBM) in particular is identical to SARS-2′s, although nCOV otherwise appears more closely related to RaTG13.
** On educated priors, I think the true reservoir is probably rats, bats, or (less likely) humans in the Guanxi, Hunan, and/or Hubei province.
Personally, I assign >90% on either rats (strong priors + skin lesions) or bats (strong priors + simplest story). But these were exotic animal smugglers; there is a small chance that the original reservoir species could be any animal.