Co-circulation of two SARS-CoV-2 variant strains within imported pet hamsters in Hong Kong.
Kin-Hang Kok1,2
Shuk-Ching Wong3
Wan-Mui Chan1
Lei Wen1
Allen Wing-Ho Chu1
Jonathan Daniel Ip1
Lam-Kwong Lee4
Ivan Tak-Fai Wong4
Hazel Wing-Hei Lo4
Vincent Chi-Chung Cheng1,3,5
Alex Yat-Man Ho6
Bosco Hoi-Shiu Lam6
Herman Tse7
David Lung8
Ken Ng Ho-Leung Ng9
Albert Ka-Wing Au9
Gilman Kit-Hang Siu4
Kwok-Yung Yuen1,2,5
Affiliations9 institutions
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
bCentre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China.
Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, People's Republic of China.
Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, People's Republic of China.
Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China.
Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China.
Department of Pathology, Hong Kong Children's Hospital, Hong Kong Special Administrative Region, People's Republic of China.
Department of Pathology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, People's Republic of China.
Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, People's Republic of China.
During the investigation of a pet shop outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) with probable hamster-to-human transmission, the environmental and hamster samples in epidemiologically linked pet shops were found positive for SARS-CoV-2 Delta variant AY.127 strains which are phylogenetically closely related to patients and reported European strains. This interspecies' spill-over has triggered transmission in 58 patients epidemiologically linked to three pet shops. Incidentally, three dwarf hamsters imported from the Netherlands and centralized in a warehouse distributing animals to pet shops were positive for SARS-CoV-2 spike variant phylogenetically related to European B.1.258 strains from March 2020. This B.1.258 strain almost disappeared in July 2021. While no hamster-to-human transmission of B.1.258-like strain was found in this outbreak, molecular docking showed that its spike receptor-binding domain (RBD) has a similar binding energy to human ACE2 compared to that of Delta variant AY.127. Therefore, the potential of this B.1.258-related spike variant for interspecies jumping cannot be ignored. The co-circulation of B.1.258-related spike variants with Delta AY.127, which originated in Europe and was not previously found in Hong Kong, suggested that hamsters in our wholesale warehouse and retail pet shops more likely have acquired these viruses in the Netherlands or stopovers during delivery by aviation than locally. The risk of human-to-hamster reverse zoonosis by multiple SARS-CoV-2 variants leading to further adaptive spike mutations with subsequent transmission back to humans cannot be underestimated as an outbreak source of COVID-19. Testing imported pet animals susceptible to SARS-CoV-2 is warranted to prevent future outbreaks.
Phylogenetic analysis showed that SARS-CoV-2 Delta AY.127 and B.1.258 lineages co-circulated in imported hamsters in Hong Kong and were closely related to European strains, supporting viral evolution and cross-regional introduction.
Environmental and hamster samples were found positive for SARS-CoV-2 Delta variant AY.127 strains which are phylogenetically closely related to patients and reported European strains. Three dwarf hamsters imported from the Netherlands were positive for SARS-CoV-2 spike variant phylogenetically related to European B.1.258 strains.
Genes or proteins
spike
Analysis methods
phylogenetic analysis
Genomic EvolutionExtraction confidence 0.85
Key finding
Genomic and molecular docking analysis of the B.1.258 spike variant from infected hamsters revealed phylogenetic relatedness to European strains and comparable binding affinity of RBD to human ACE2, indicating evolutionary potential for interspecies transmission.
Three dwarf hamsters imported from the Netherlands and centralized in a warehouse were positive for SARS-CoV-2 spike variant phylogenetically related to European B.1.258 strains from March 2020. Molecular docking showed that its spike receptor-binding domain (RBD) has a similar binding energy to human ACE2 compared to that of Delta variant AY.127.
Genes or proteins
spike; receptor-binding domain
Analysis methods
phylogenetic analysis; molecular docking
Outbreak Investigation2 records
Outbreak InvestigationExtraction confidence 0.95
Key finding
Hamsters in pet shops were infected with SARS-CoV-2 Delta AY.127, associated with probable hamster-to-human transmission.
During the investigation of a pet shop outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) with probable hamster-to-human transmission, the environmental and hamster samples in epidemiologically linked pet shops were found positive for SARS-CoV-2 Delta variant AY.127 strains which are phylogenetically closely related to patients and reported European strains.
Transmission direction
animal-to-human
Geographic raw
Hong Kong
Country inferred
Hong Kong
Outbreak setting
pet shop
Outbreak scale
58 patients epidemiologically linked to three pet shops
Outbreak InvestigationExtraction confidence 0.90
Key finding
B.1.258-related SARS-CoV-2 was found in imported hamsters, but no transmission to humans occurred in this outbreak.
Incidentally, three dwarf hamsters imported from the Netherlands and centralized in a warehouse distributing animals to pet shops were positive for SARS-CoV-2 spike variant phylogenetically related to European B.1.258 strains from March 2020. While no hamster-to-human transmission of B.1.258-like strain was found in this outbreak, molecular docking showed that its spike receptor-binding domain (RBD) has a similar binding energy to human ACE2 compared to that of Delta variant AY.127.
Method
molecular docking
Transmission direction
animal-to-human
Geographic raw
Hong Kong
Country inferred
Hong Kong
Outbreak setting
warehouse distributing animals to pet shops
Outbreak time
March 2020
Receptor Usage1 records
Receptor UsageExtraction confidence 0.80
Key finding
Molecular docking indicated that the SARS-CoV-2 B.1.258-like variant spike RBD binds human ACE2 with similar affinity to the Delta AY.127 variant.
Molecular docking showed that its spike receptor-binding domain (RBD) has a similar binding energy to human ACE2 compared to that of Delta variant AY.127.
Method
molecular docking
Receptors
human ACE2
Spillover Event1 records
Spillover EventExtraction confidence 0.95
Key finding
Probable hamster-to-human spillover of SARS-CoV-2 Delta variant AY.127 occurred in pet shops in Hong Kong, leading to infection in 58 humans.
During the investigation of a pet shop outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) with probable hamster-to-human transmission, the environmental and hamster samples in epidemiologically linked pet shops were found positive for SARS-CoV-2 Delta variant AY.127... This interspecies' spill-over has triggered transmission in 58 patients epidemiologically linked to three pet shops.
Method
phylogenetic analysis; molecular docking
Study design
outbreak investigation
Transmission direction
animal-to-human
Geographic raw
Hong Kong
Country inferred
China
Zoonotic Surveillance1 records
Zoonotic SurveillanceExtraction confidence 0.95
Key finding
Environmental and hamster samples collected from pet shops and a central warehouse in Hong Kong were positive for SARS-CoV-2 Delta AY.127 and B.1.258 variant lineages during outbreak surveillance.
During the investigation of a pet shop outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) with probable hamster-to-human transmission, the environmental and hamster samples in epidemiologically linked pet shops were found positive for SARS-CoV-2 Delta variant AY.127 strains... Incidentally, three dwarf hamsters imported from the Netherlands and centralized in a warehouse... were positive for SARS-CoV-2 spike variant phylogenetically related to European B.1.258 strains.
Method
testing; epidemiological investigation
Sample type
environmental samples; hamster samples
Geographic raw
Hong Kong
Country inferred
China
Citation context
References
34 references
Reference network
Force-directed citation graph. OmniVira-indexed references are prioritized and recursively expanded up to three steps.
Probable Animal-to-Human Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant AY.127 Causing a Pet Shop-Related Coronavirus Disease 2019 (COVID-19) Outbreak in Hong Kong.
Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study
Chu
2020
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SARS-CoV-2 in animals – situation report 8 [cited 2022 Jan 29]
