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Lancet ; 399(10329): 1070-1078, 2022 03 12.
Article in English | MEDLINE | ID: covidwho-1735071

ABSTRACT

BACKGROUND: Transmission of SARS-CoV-2 from humans to other mammals, including pet animals, has been reported. However, with the exception of farmed mink, there is no previous evidence that these infected animals can infect humans, resulting in sustained human-to-human transmission. Following a confirmed SARS-CoV-2 infection of a pet shop worker, animals in the shop and the warehouse supplying it were tested for evidence of SARS-CoV-2 infection. METHODS: In this case study, viral swabs and blood samples were collected from animals in a pet shop and its corresponding warehouse in Hong Kong. Nasal swab or saliva samples from human COVID-19 patients epidemiologically linked to the pet shop and from subsequent local cases confirmed to be infected by SARS-CoV-2 delta variant were collected. Oral swabs were tested by quantitative RT-PCR (RT-qPCR) for SARS-CoV-2 and blood samples were serologically tested by a surrogate virus neutralisation test and plaque reduction neutralisation test. The SARS-CoV-2 RT-qPCR positive samples were sequenced by next generation viral full genome sequencing using the ISeq sequencing platform (Illumina), and the viral genomes were phylogenetically analysed. FINDINGS: Eight (50%) of 16 individually tested Syrian hamsters in the pet shop and seven (58%) of 12 Syrian hamsters in the corresponding warehouse were positive for SARS-CoV-2 infection in RT-qPCR or serological tests. None of the dwarf hamsters (n=75), rabbits (n=246), guinea pigs (n=66), chinchillas (n=116), and mice (n=2) were confirmed positive for SARS-CoV-2 in RT-qPCR tests. SARS-CoV-2 viral genomes deduced from human and hamster cases in this incident all belong to the delta variant of concern (AY.127) that had not been circulating locally before this outbreak. The viral genomes obtained from hamsters were phylogenetically related with some sequence heterogeneity. Phylogenetic dating suggests infection in these hamsters occurred around Oct 14, 2021 (95% CI Sept 15 to Nov 9, 2021). Multiple zoonotic transmission events to humans were detected, leading to onward human-to-human transmission. INTERPRETATION: Pet hamsters can be naturally infected with SARS-CoV-2. The virus can circulate among hamsters and lead to human infections. Both genetic and epidemiological results strongly suggest that there was more than one hamster-to-human transmission event in this study. This incident also led to onward human transmission. Importation of SARS-CoV-2-infected hamsters was a likely source of this outbreak. FUNDING: US National Institutes of Health, Research Grants Council of Hong Kong, Food and Health Bureau, and InnoHK.


Subject(s)
COVID-19/veterinary , Cricetinae/virology , SARS-CoV-2 , Viral Zoonoses/transmission , Adult , Animals , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Child , Disease Outbreaks , Female , Hong Kong/epidemiology , Humans , Male , Pets/virology , Phylogeny
8.
Viruses ; 14(2)2022 01 19.
Article in English | MEDLINE | ID: covidwho-1625724

ABSTRACT

Bats are a reservoir for coronaviruses (CoVs) that periodically spill over to humans, as evidenced by severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. A collection of 174 bat samples originating from South Dakota, Minnesota, Iowa, and Nebraska submitted for rabies virus testing due to human exposure were analyzed using a pan-coronavirus PCR. A previously partially characterized CoV, Eptesicus bat CoV, was identified in 12 (6.9%) samples by nested RT-PCR. Six near-complete genomes were determined. Genetic analysis found a high similarity between all CoV-positive samples, Rocky Mountain bat CoV 65 and alphacoronavirus HCQD-2020 recently identified in South Korea. Phylogenetic analysis of genome sequences showed EbCoV is closely related to bat CoV HKU2 and swine acute diarrhea syndrome CoV; however, topological incongruences were noted for the spike gene that was more closely related to porcine epidemic diarrhea virus. Similar to some alphaCoVs, a novel gene, ORF7, was discovered downstream of the nucleocapsid, whose protein lacked similarity to known proteins. The widespread circulation of EbCoV with similarities to bat viruses that have spilled over to swine warrants further surveillance.


Subject(s)
Alphacoronavirus/classification , Alphacoronavirus/genetics , Chiroptera/virology , Disease Reservoirs/veterinary , Disease Reservoirs/virology , Phylogeny , Alphacoronavirus/isolation & purification , Animals , Genome, Viral , Iowa , Midwestern United States , Minnesota , Republic of Korea , Sequence Analysis, DNA , South Dakota , Viral Zoonoses/transmission
9.
Nature ; 602(7897): 481-486, 2022 02.
Article in English | MEDLINE | ID: covidwho-1585829

ABSTRACT

Humans have infected a wide range of animals with SARS-CoV-21-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.


Subject(s)
Animals, Wild/virology , COVID-19/veterinary , Deer/virology , Phylogeny , SARS-CoV-2/isolation & purification , Viral Zoonoses/transmission , Viral Zoonoses/virology , Amino Acid Sequence , Amino Acid Substitution , Animals , COVID-19/epidemiology , COVID-19/transmission , Evolution, Molecular , Humans , Male , Ohio/epidemiology , One Health/trends , SARS-CoV-2/chemistry , SARS-CoV-2/classification , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Viral Zoonoses/epidemiology
10.
Viruses ; 13(12)2021 12 16.
Article in English | MEDLINE | ID: covidwho-1580429

ABSTRACT

Several cases of naturally infected dogs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported despite the apparently low susceptibility of this species. Here, we document the first reported case of infection caused by the Delta (B.1.617.2) variant of concern (VOC) in a dog in Spain that lived with several household members suffering from Coronavirus Infectious Disease 2019 (COVID-19). The animal displayed mild digestive and respiratory clinical signs and had a low viral load in the oropharyngeal swab collected at the first sampling. Whole-genome sequencing indicated infection with the Delta variant, coinciding with the predominant variant during the fifth pandemic wave in Spain. The dog seroconverted, as detected 21 days after the first sampling, and developed neutralizing antibodies that cross-neutralized different SARS-CoV-2 variants. This study further emphasizes the importance of studying the susceptibility of animal species to different VOCs and their potential role as reservoirs in the context of COVID-19.


Subject(s)
COVID-19/veterinary , Dog Diseases/virology , SARS-CoV-2/isolation & purification , Animals , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19/diagnosis , COVID-19/transmission , COVID-19/virology , Dog Diseases/diagnosis , Dog Diseases/transmission , Dogs , Female , Genome, Viral/genetics , Pets/virology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Viral Zoonoses/diagnosis , Viral Zoonoses/transmission , Viral Zoonoses/virology
11.
J Med Virol ; 94(4): 1257-1260, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1568203

ABSTRACT

The ongoing discussion about the real origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) feeds acrimonious debates. Where did SARS-CoV-2 come from? Was SARS-CoV-2 transmitted in the wild from an animal to a person before exploding in Wuhan or was it an engineered virus that escaped from research or a laboratory in Wuhan? Right now, we still don't know enough whether SARS-CoV-2 is human-made or not, and lab-leak theories remain essentially speculative. Many recent studies have pointed out several plausible scenarios. Anyhow, currently, even if suspicions by some about the possibility of lab-leak hypothesis still remain, the consensus view is that the pandemic probably started from a natural source and, to determine the real origin of the SARS-CoV-2 virus, further research is needed.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Biological Evolution , COVID-19/epidemiology , COVID-19/transmission , Humans , Laboratories , SARS-CoV-2/isolation & purification , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Viral Zoonoses/virology
13.
Viruses ; 13(10)2021 09 25.
Article in English | MEDLINE | ID: covidwho-1438748

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), is responsible for the worst pandemic of the 21st century. Like all human coronaviruses, SARS-CoV-2 originated in a wildlife reservoir, most likely from bats. As SARS-CoV-2 has spread across the globe in humans, it has spilled over to infect a variety of non-human animal species in domestic, farm, and zoo settings. Additionally, a broad range of species, including one neotropical monkey, have proven to be susceptible to experimental infection with SARS-CoV-2. Together, these findings raise the specter of establishment of novel enzootic cycles of SARS-CoV-2. To assess the potential exposure of free-living non-human primates to SARS-CoV-2, we sampled 60 neotropical monkeys living in proximity to Manaus and São José do Rio Preto, two hotspots for COVID-19 in Brazil. Our molecular and serological tests detected no evidence of SAR-CoV-2 infection among these populations. While this result is reassuring, sustained surveillance efforts of wildlife living in close association with human populations is warranted, given the stochastic nature of spillover events and the enormous implications of SARS-CoV-2 spillover for human health.


Subject(s)
COVID-19/epidemiology , Epidemiological Monitoring/veterinary , Primates/virology , Alouatta/virology , Animals , Animals, Wild/virology , Brazil/epidemiology , COVID-19/veterinary , Callicebus/virology , Callithrix/virology , Pandemics , SARS-CoV-2/pathogenicity , Viral Zoonoses/transmission
14.
Viruses ; 13(10)2021 09 23.
Article in English | MEDLINE | ID: covidwho-1438741

ABSTRACT

Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus Infections/genetics , Epidemics/prevention & control , Animals , Animals, Domestic/virology , Animals, Wild/virology , Coronaviridae/metabolism , Coronaviridae/pathogenicity , Genome, Viral/genetics , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Pandemics/prevention & control , Phylogeny , SARS Virus/genetics , SARS-CoV-2/genetics , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission
16.
Science ; 373(6559): 1076-1077, 2021 Sep 03.
Article in English | MEDLINE | ID: covidwho-1403019

ABSTRACT

Cousins of the pandemic virus in animals help chart the path to humans.


Subject(s)
COVID-19/transmission , Chiroptera/virology , Pangolins/virology , SARS-CoV-2 , Viral Zoonoses/transmission , Animals , China , Humans
17.
PLoS Pathog ; 17(9): e1009883, 2021 09.
Article in English | MEDLINE | ID: covidwho-1398940

ABSTRACT

SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.


Subject(s)
COVID-19/veterinary , Mink/virology , Animals , COVID-19/epidemiology , COVID-19/genetics , COVID-19/transmission , Disease Outbreaks/veterinary , Environmental Microbiology , Farms , Female , Greece/epidemiology , Humans , Male , Mink/genetics , Occupational Exposure , Viral Zoonoses/transmission , Viral Zoonoses/virology
18.
Viruses ; 13(2)2021 02 23.
Article in English | MEDLINE | ID: covidwho-1389526

ABSTRACT

A challenging debate has arisen on the role of veterinary expertise in facing the SARS-CoV-2 pandemic. It seems totally unreasonable that in most countries, veterinary diagnostic and tracing forces were not deployed at the start to perform strategic tasks, which could have mitigated the outcome of this dramatic health emergency. Erasing the invisible line between human and veterinary virology will empower the response to future pandemics.


Subject(s)
Contact Tracing , Pandemics/prevention & control , Veterinary Medicine , Viral Zoonoses , Virus Diseases , Animals , Humans , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Virus Diseases/epidemiology , Virus Diseases/transmission , Virus Diseases/veterinary
20.
Nat Rev Immunol ; 21(12): 815-822, 2021 12.
Article in English | MEDLINE | ID: covidwho-1275932

ABSTRACT

Since the initial use of vaccination in the eighteenth century, our understanding of human and animal immunology has greatly advanced and a wide range of vaccine technologies and delivery systems have been developed. The COVID-19 pandemic response leveraged these innovations to enable rapid development of candidate vaccines within weeks of the viral genetic sequence being made available. The development of vaccines to tackle emerging infectious diseases is a priority for the World Health Organization and other global entities. More than 70% of emerging infectious diseases are acquired from animals, with some causing illness and death in both humans and the respective animal host. Yet the study of critical host-pathogen interactions and the underlying immune mechanisms to inform the development of vaccines for their control is traditionally done in medical and veterinary immunology 'silos'. In this Perspective, we highlight a 'One Health vaccinology' approach and discuss some key areas of synergy in human and veterinary vaccinology that could be exploited to accelerate the development of effective vaccines against these shared health threats.


Subject(s)
Communicable Diseases, Emerging/immunology , Communicable Diseases, Emerging/prevention & control , Cross Reactions/immunology , Vaccination , Vaccines/immunology , Viral Zoonoses/immunology , Viral Zoonoses/prevention & control , Animals , COVID-19/epidemiology , COVID-19/immunology , COVID-19/prevention & control , Humans , SARS-CoV-2/immunology , Species Specificity , Viral Zoonoses/transmission
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