Spillover infection of common animal coronaviruses to humans
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Bibliographic record
Abstract
Porcine deltacoronavirus, part of the Deltacoronavirus genus, was first discovered in pigs in Hong Kong, China, in 2012.1Woo PC Lau SK Lam CS et al.Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.J Virol. 2012; 86: 3995-4008Crossref PubMed Scopus (921) Google Scholar Initially, its clinical importance was not acknowledged by governments and veterinarians. Until 2014, several studies from the USA showed that porcine deltacoronavirus could cause severe diarrhoea in piglets. Subsequently, it was reported in China, South Korea, Thailand, Japan, Viet Nam, Laos, Canada, Mexico, and Peru. Porcine deltacoronavirus can infect non-porcine hosts, including near-term Angus–Jersey cross-bred gnotobiotic calves, turkeys, and chickens, in experimental conditions. Besides animal hosts, embryonated chicken eggs and human cell lines, including human hepatoma cells and human lung carcinoma cells, were also susceptible to porcine deltacoronavirus in experimental conditions. Data from studies since 2017 have revealed cross-species transmission and potential zoonosis of porcine deltacoronavirus from pigs to humans.2Kong F Wang Q Kenney SP Jung K Vlasova AN Saif LJ Porcine deltacoronaviruses: origin, evolution, cross-species transmission and zoonotic potential.Pathogens. 2022; 11: 79Crossref PubMed Scopus (5) Google ScholarGenerally, coronaviruses infecting humans belong to the genera Alphacoronavirus (including human coronavirus 229E and human coronavirus NL63) and Betacoronavirus (including human coronavirus OC43, human coronavirus HKU1, SARS-CoV, SARS-CoV-2, and MERS-CoV; appendix p 1). However, this group became larger as of 2021. Lednicky and colleagues3Lednicky JA Tagliamonte MS White SK et al.Independent infections of porcine deltacoronavirus among Haitian children.Nature. 2021; 600: 133-137Crossref PubMed Scopus (56) Google Scholar reported spillover of porcine deltacoronavirus to children in Haiti with symptoms of acute undifferentiated febrile illness. Genetic analysis suggested that three strains of porcine deltacoronavirus originating from humans were similar to porcine deltacoronavirus strains found in China and the USA originating from pigs,3Lednicky JA Tagliamonte MS White SK et al.Independent infections of porcine deltacoronavirus among Haitian children.Nature. 2021; 600: 133-137Crossref PubMed Scopus (56) Google Scholar which further supports the zoonosis of porcine deltacoronavirus from pigs to humans. Thus, porcine deltacoronavirus could be considered the eighth coronavirus infecting humans.Canine coronavirus is a clinically significant cause of acute diarrhoea in dogs, especially in puppies. Although it belongs to the Alphacoronavirus genus, few reports on human infections are available. However, since 2021, two independent studies have reported canine coronavirus infection in humans with symptoms of mild fever and pneumonia, in Malaysia and the USA.4Lednicky JA Tagliamonte MS White SK et al.Isolation of a novel recombinant canine coronavirus from a visitor to Haiti: further evidence of transmission of coronaviruses of zoonotic origin to humans.Clin Infect Dis. 2021; (published online Oct 28.)https://doi.org/10.1093/cid/ciab924Crossref PubMed Google Scholar, 5Vlasova AN Diaz A Damtie D et al.Novel canine coronavirus isolated from a hospitalized patient with pneumonia in east Malaysia.Clin Infect Dis. 2022; 74: 446-454Crossref PubMed Scopus (48) Google Scholar These viruses underwent recombination. For example, CCoV-HuPn-2018 was a recombinant alphacoronavirus between canine coronavirus and feline coronavirus, and HuCCoV_Z19Haiti was a recombinant alphacoronavirus among different strains of canine coronavirus. Perhaps canine coronavirus could be considered the ninth coronavirus infecting humans.Raising animals (such as pigs, chickens, and cattle) is the main income source for farmers in low-income countries and regions. Because of poor biosafe measures, such as not wearing masks and gloves, farmers and veterinarians were usually exposed to porcine deltacoronavirus, canine coronavirus, and animals infected with these viruses. Most patients in previous studies were children living in rural areas with frequent exposure to domesticated animals and wildlife. Therefore, we think that urging more studies to step up surveillance of porcine deltacoronavirus and canine coronavirus and evaluate the effects of these viruses on public health is essential. Porcine deltacoronavirus, part of the Deltacoronavirus genus, was first discovered in pigs in Hong Kong, China, in 2012.1Woo PC Lau SK Lam CS et al.Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.J Virol. 2012; 86: 3995-4008Crossref PubMed Scopus (921) Google Scholar Initially, its clinical importance was not acknowledged by governments and veterinarians. Until 2014, several studies from the USA showed that porcine deltacoronavirus could cause severe diarrhoea in piglets. Subsequently, it was reported in China, South Korea, Thailand, Japan, Viet Nam, Laos, Canada, Mexico, and Peru. Porcine deltacoronavirus can infect non-porcine hosts, including near-term Angus–Jersey cross-bred gnotobiotic calves, turkeys, and chickens, in experimental conditions. Besides animal hosts, embryonated chicken eggs and human cell lines, including human hepatoma cells and human lung carcinoma cells, were also susceptible to porcine deltacoronavirus in experimental conditions. Data from studies since 2017 have revealed cross-species transmission and potential zoonosis of porcine deltacoronavirus from pigs to humans.2Kong F Wang Q Kenney SP Jung K Vlasova AN Saif LJ Porcine deltacoronaviruses: origin, evolution, cross-species transmission and zoonotic potential.Pathogens. 2022; 11: 79Crossref PubMed Scopus (5) Google Scholar Generally, coronaviruses infecting humans belong to the genera Alphacoronavirus (including human coronavirus 229E and human coronavirus NL63) and Betacoronavirus (including human coronavirus OC43, human coronavirus HKU1, SARS-CoV, SARS-CoV-2, and MERS-CoV; appendix p 1). However, this group became larger as of 2021. Lednicky and colleagues3Lednicky JA Tagliamonte MS White SK et al.Independent infections of porcine deltacoronavirus among Haitian children.Nature. 2021; 600: 133-137Crossref PubMed Scopus (56) Google Scholar reported spillover of porcine deltacoronavirus to children in Haiti with symptoms of acute undifferentiated febrile illness. Genetic analysis suggested that three strains of porcine deltacoronavirus originating from humans were similar to porcine deltacoronavirus strains found in China and the USA originating from pigs,3Lednicky JA Tagliamonte MS White SK et al.Independent infections of porcine deltacoronavirus among Haitian children.Nature. 2021; 600: 133-137Crossref PubMed Scopus (56) Google Scholar which further supports the zoonosis of porcine deltacoronavirus from pigs to humans. Thus, porcine deltacoronavirus could be considered the eighth coronavirus infecting humans. Canine coronavirus is a clinically significant cause of acute diarrhoea in dogs, especially in puppies. Although it belongs to the Alphacoronavirus genus, few reports on human infections are available. However, since 2021, two independent studies have reported canine coronavirus infection in humans with symptoms of mild fever and pneumonia, in Malaysia and the USA.4Lednicky JA Tagliamonte MS White SK et al.Isolation of a novel recombinant canine coronavirus from a visitor to Haiti: further evidence of transmission of coronaviruses of zoonotic origin to humans.Clin Infect Dis. 2021; (published online Oct 28.)https://doi.org/10.1093/cid/ciab924Crossref PubMed Google Scholar, 5Vlasova AN Diaz A Damtie D et al.Novel canine coronavirus isolated from a hospitalized patient with pneumonia in east Malaysia.Clin Infect Dis. 2022; 74: 446-454Crossref PubMed Scopus (48) Google Scholar These viruses underwent recombination. For example, CCoV-HuPn-2018 was a recombinant alphacoronavirus between canine coronavirus and feline coronavirus, and HuCCoV_Z19Haiti was a recombinant alphacoronavirus among different strains of canine coronavirus. Perhaps canine coronavirus could be considered the ninth coronavirus infecting humans. Raising animals (such as pigs, chickens, and cattle) is the main income source for farmers in low-income countries and regions. Because of poor biosafe measures, such as not wearing masks and gloves, farmers and veterinarians were usually exposed to porcine deltacoronavirus, canine coronavirus, and animals infected with these viruses. Most patients in previous studies were children living in rural areas with frequent exposure to domesticated animals and wildlife. Therefore, we think that urging more studies to step up surveillance of porcine deltacoronavirus and canine coronavirus and evaluate the effects of these viruses on public health is essential. S-LZ, M-FS, and J-FZ contributed equally. We are supported by grants from the Guangdong Academy of Agricultural Sciences (XTXM202202, R2020PY-JC001, and 202122TD to ML); the Guangdong Provincial Department of Science and Technology (2020B0202080004 and 2021B1212050021 to M-FS); Guangzhou Science and Technology Bureau (202103000096 to J-FZ and 202206010192 to S-LZ); Maoming Laboratory (2021ZZ003 to J-FZ); and the Department of Agriculture and Rural Affairs of Guangdong Province (2021KJ114 and 2021KJ119 to S-LZ). Supplementary Material Download .pdf (.12 MB) Help with pdf files Supplementary appendix Download .pdf (.12 MB) Help with pdf files Supplementary appendix
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it