key: cord-0707095-017lib9m authors: Chan, Jasper Fuk-Woo; Siu, Gilman Kit-Hang; Yuan, Shuofeng; Ip, Jonathan Daniel; Cai, Jian-Piao; Chu, Allen Wing-Ho; Chan, Wan-Mui; Abdullah, Syed Muhammad Umer; Luo, Cuiting; Chan, Brian Pui-Chun; Yuen, Terrence Tsz-Tai; Chen, Lin-Lei; Chik, Kenn Ka-Heng; Liang, Ronghui; Cao, Hehe; Man Poon, Vincent Kwok; Chan, Chris Chung-Sing; Leung, Kit-Hang; Tam, Anthony Raymond; Tsang, Owen Tak-Yin; Chan, Jacky Man-Chun; To, Wing-Kin; Lam, Bosco Hoi-Shiu; Lee, Lam-Kwong; Lo, Hazel Wing-Hei; Wong, Ivan Tak-Fai; Leung, Jake Siu-Lun; Wong, Evelyn Yin-Kwan; Chu, Hin; Yip, Cyril Chik-Yan; Cheng, Vincent Chi-Chung; Chan, Kwok-Hung; Tse, Herman; Lung, David Christopher; Ng, Kenneth Ho-Leung; Au, Albert Ka-Wing; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung; To, Kelvin Kai-Wang title: Probable Animal-to-Human Transmission of SARS-CoV-2 Delta Variant AY.127 Causing a Pet Shop-Related COVID-19 Outbreak in Hong Kong date: 2022-03-02 journal: Clin Infect Dis DOI: 10.1093/cid/ciac171 sha: 80c0b6feb52bc1f7f817751fbb638bb246c48be8 doc_id: 707095 cord_uid: 017lib9m BACKGROUND: SARS-CoV-2 can infect human and other mammals, including hamsters. Syrian (Mesocricetus auratus) and dwarf (Phodopus sp.) hamsters are susceptible to SARS-CoV-2 infection in the laboratory setting. However, pet shop-related COVID-19 outbreaks have not been reported. METHODS: We conducted an investigation of a pet shop-related COVID-19 outbreak due to Delta variant AY.127 involving at least three patients in Hong Kong. We tested samples collected from the patients, environment, and hamsters linked to this outbreak and performed whole genome sequencing analysis of the RT-PCR-positive samples. RESULTS: The patients included a pet shop keeper (Patient 1), a female customer of the pet shop (Patient 2), and the husband of Patient 2 (Patient 3). Investigation showed that 17.2% (5/29) and 25.5% (13/51) environmental specimens collected from the pet shop and its related warehouse, respectively, tested positive for SARS-CoV-2 RNA by RT-PCR. Among euthanized hamsters randomly collected from the storehouse, 3% (3/100) tested positive for SARS-CoV-2 RNA by RT-PCR and seropositive for anti-SARS-CoV-2 antibody by ELISA. Whole genome analysis showed that although all genomes from the outbreak belonged to the Delta variant AY.127, there were at least 3 nucleotide differences among the genomes from different patients and the hamster cages. Genomic analysis suggests that multiple strains have emerged within the hamster population, and these different strains have likely transmitted to human either via direct contact or via the environment. CONCLUSIONS: Our study demonstrated probable hamster-to-human transmission of SARS-CoV-2. As pet trading is common around the world, this can represent a route of international spread of this pandemic virus. Coronaviruses are a diverse group of positive-stranded RNA viruses belonging to the family Coronaviridae in the order Nidovirales found in a wide range of mammals and birds [1] . Coronaviruses are known to have repeatedly crossed species barriers with some emerging as important human pathogens. SARS-CoV-1 was likely originated in bats with subsequent amplification in civets before jumping into human [2, 3] . Dromedary camels (Camelus dromedarius) play an important role in the transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) [4] . Bats and rodents are generally considered as the animal reservoirs of alphacoronaviruses and betacoronaviruses, whereas birds are the likely reservoirs of deltacoronaviruses and gammacoronaviruses [1] . As of today, there are seven coronaviruses known to cause disease in humans. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the Coronavirus Disease 2019 (COVID- 19) pandemic, was first discovered in patients in Wuhan, China, in late 2019, and was soon found to be highly transmissible in the human population [5, 6] . This pandemic virus can be transmitted via the droplet and contact routes, and airborne transmission may also be important [7, 8] . Various animal species have been reported to be infected by SARS-CoV-2, including companion animals like pet dogs and cats, zoo animals, mink on mink farms, and wild white-tailed deer [9] . The World Organization for Animal Health (OIE) reported that infection with SARS-CoV-2 has been documented in at least 17 animal species, and outbreaks have been documented in 15 animal species as of 31 st December 2021 [10]. However, animal-to-human transmission has been generally considered to be rare [11] . Mink (the American mink, Neogale vison)-associated COVID-19 human cases have been documented in Europe in late 2020, resulting in mass culling of 17 million of minks in November 2020 [12] . A c c e p t e d M a n u s c r i p t 6 Hong Kong Special Administrative Region, China, has adopted a "zero tolerance" policy for COVID-19 and there were only sporadic locally-acquired cases. Alarmingly, in January 2022, three local patient-cases of COVID-19 caused by the SARS-CoV-2 Delta variant AY.127 which has not been found in the local community in Hong Kong previously. All three patients were epidemiologically linked to either a local pet shop or to each other. Investigations showed that the environment of the pet shop as well as the warehouse supplying the hamsters to the pet shop were contaminated with SARS-CoV-2. Epidemiological and virological investigations demonstrated that the index patient was possibly infected by contact with SARS-CoV-2-infected animals or the contaminated environment in the pet shop, and then transmitted the virus to the others. Herein, we report the details of the epidemiological and virological investigations of this pet shop-related outbreak. Whole genomes sequencing of patient specimens were performed using Nanopore (Nanopore protocol -PCR tiling of COVID-19 [Version: PTC_9096_v109_revH_06Feb2020] according to the manufacturer's instructions with minor modifications (Oxford Nanopore Technologies) as we described previously [13] . Illumina sequencing was used for environmental specimens. For bioinformatics analysis, the recommended ARTIC bioinformatics workflow was used with minor modifications applied as described previously [13] . Maximum-likelihood whole genome phylogenetic tree was constructed using IQ-TREE2 [14] . (See supplementary methods for details). The genome sequences have been deposited in GISAID database (Supplementary Table S1 ) Enzyme immunoassay (EIA) was performed as previously described [15, 16] . Briefly, The index patient (Patient 1) was a 23-year old female who worked as a shopkeeper in a pet store. On January 11 2022, she developed rhinorrhea, sore throat and cough ( Figure 1 ). Table 2 ). The hamster cage swab 1 from the pet shop was also different from the human cases (4 bp difference from case 1, 2 or 3 contact residues are highly similar to those of human [17, 18] . Moreover, transmission of SARS-CoV-2 among hamsters by either contact or non-contact are highly efficient [17, 19] . The clinical manifestations of the hamsters may be mild when the exposure dose is low [20] . Hamsters usually develop a self-limiting illness and recover by 1-2 weeks after exposure to SARS-CoV-2, which allows silent transmission to other hamsters and possibly human [17] . Live infectious virus particles could be detected in the respiratory tract of SARS-CoV-2- A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t Interspecies transmission and emergence of novel viruses: lessons from bats and birds Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster Lessons learned one year after SARS-CoV-2 emergence leading to COVID-19 pandemic SARS CoV-2 Variant of Concern in a designated quarantine hotel for travelers: a challenge of elimination strategy of COVID-19 Nosocomial outbreak of COVID-19 by possible airborne transmission leading to a superspreading event Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 SARS-CoV-2 in animals -situation report 8 Animals and COVID-19 Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans False COVID-19 cases due to contamination by inactivated virus vaccine IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era Beneficial effect of combinational methylprednisolone and remdesivir in hamster model of SARS-CoV-2 infection Clofazimine broadly inhibits coronaviruses including SARS-CoV-2 Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility The Roborovski Dwarf Hamster Is A Highly Susceptible Model for a Rapid and Fatal Course of SARS-CoV-2 Infection Surgical mask partition reduces the risk of noncontact transmission in a golden Syrian hamster model for Coronavirus Disease 2019 (COVID-19) Oral SARS-CoV-2 Inoculation Establishes Subclinical Respiratory Infection with Virus Shedding in Golden Syrian Hamsters A thermostable, closed SARS-CoV-2 spike protein trimer Cocirculation of two SARS-CoV-2 variant strains within imported pet hamsters in Hong Kong Chinchillas, Guinea Pigs and Rabbits to be culled after 11 tested positive A c c e p t e d M a n u s c r i p t 16