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Earnest R, Hahn AM, Feriancek NM, Brandt M, Filler RB, Zhao Z, Breban MI, Vogels CBF, Chen NFG, Koch RT, Porzucek AJ, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber HR, Cantoni JL, Pitzer VE, Olarte Castillo XA, Goodman LB, Wilen CB, Linske MA, Williams SC, Grubaugh ND. Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559030. [PMID: 37808797 PMCID: PMC10557615 DOI: 10.1101/2023.09.22.559030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Diverse mammalian species display susceptibility to and infection with SARS-CoV-2. Potential SARS-CoV-2 spillback into rodents is understudied despite their host role for numerous zoonoses and human proximity. We assessed exposure and infection among white-footed mice (Peromyscus leucopus) in Connecticut, USA. We observed 1% (6/540) wild-type neutralizing antibody seroprevalence among 2020-2022 residential mice with no cross-neutralization of variants. We detected no SARS-CoV-2 infections via RT-qPCR, but identified non-SARS-CoV-2 betacoronavirus infections via pan-coronavirus PCR among 1% (5/468) of residential mice. Sequencing revealed two divergent betacoronaviruses, preliminarily named Peromyscus coronavirus-1 and -2. Both belong to the Betacoronavirus 1 species and are ~90% identical to the closest known relative, Porcine hemagglutinating encephalomyelitis virus. Low SARS-CoV-2 seroprevalence suggests white-footed mice may not be sufficiently susceptible or exposed to SARS-CoV-2 to present a long-term human health risk. However, the discovery of divergent, non-SARS-CoV-2 betacoronaviruses expands the diversity of known rodent coronaviruses and further investigation is required to understand their transmission extent.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nicole M Feriancek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Matthew Brandt
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhe Zhao
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nicholas F G Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Abbey J Porzucek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Alexa Garbiel
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Claire Keanna
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Hannah Litwak
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Heidi R Stuber
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Jamie L Cantoni
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Ximena A Olarte Castillo
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Laura B Goodman
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Megan A Linske
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Scott C Williams
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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2
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Narat V, Salmona M, Kampo M, Heyer T, Rachik AS, Mercier-Delarue S, Ranger N, Rupp S, Ambata P, Njouom R, Simon F, Le Goff J, Giles-Vernick T. Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis. Nat Commun 2023; 14:3674. [PMID: 37339968 DOI: 10.1038/s41467-023-39455-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, MNHN/CNRS/Univ. Paris Cité, Paris, France
| | - Maud Salmona
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Mamadou Kampo
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | | | | | | | - Noémie Ranger
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Stephanie Rupp
- Department of Anthropology, City University of NewYork - Lehman College, NewYork, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Virology, AP-HP, Hôpital Saint Louis, Paris, France.
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France.
| | - Tamara Giles-Vernick
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France.
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3
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Pruvot M, Denstedt E, Latinne A, Porco A, Montecino-Latorre D, Khammavong K, Milavong P, Phouangsouvanh S, Sisavanh M, Nga NTT, Ngoc PTB, Thanh VD, Chea S, Sours S, Phommachanh P, Theppangna W, Phiphakhavong S, Vanna C, Masphal K, Sothyra T, San S, Chamnan H, Long PT, Diep NT, Duoc VT, Zimmer P, Brown K, Olson SH, Fine AE. WildHealthNet: Supporting the development of sustainable wildlife health surveillance networks in Southeast Asia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160748. [PMID: 36513230 DOI: 10.1016/j.scitotenv.2022.160748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Wildlife and wildlife interfaces with people and livestock are essential surveillance targets to monitor emergent or endemic pathogens or new threats affecting wildlife, livestock, and human health. However, limitations of previous investments in scope and duration have resulted in a neglect of wildlife health surveillance (WHS) systems at national and global scales, particularly in lower and middle income countries (LMICs). Building on decades of wildlife health activities in LMICs, we demonstrate the implementation of a locally-driven multi-pronged One Health approach to establishing WHS in Cambodia, Lao PDR and Viet Nam under the WildHealthNet initiative. WildHealthNet utilizes existing local capacity in the animal, public health, and environmental sectors for event based or targeted surveillance and disease detection. To scale up surveillance systems to the national level, WildHealthNet relies on iterative field implementation and policy development, capacity bridging, improving data collection and management systems, and implementing context specific responses to wildlife health intelligence. National WHS systems piloted in Cambodia, Lao PDR, and Viet Nam engaged protected area rangers, wildlife rescue centers, community members, and livestock and human health sector staff and laboratories. Surveillance activities detected outbreaks of H5N1 highly pathogenic avian influenza in wild birds, African swine fever in wild boar (Sus scrofa), Lumpy skin disease in banteng (Bos javanicus), and other endemic zoonotic pathogens identified as surveillance priorities by local stakeholders. In Cambodia and Lao PDR, national plans for wildlife disease surveillance are being signed into legislation. Cross-sectoral and trans-disciplinary approaches are needed to implement effective WHS systems. Long-term commitment, and paralleled implementation and policy development are key to sustainable WHS networks. WildHealthNet offers a roadmap to aid in the development of locally-relevant and locally-led WHS systems that support the global objectives of the World Organization for Animal Health's Wildlife Health Framework and other international agendas.
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Affiliation(s)
- Mathieu Pruvot
- Wildlife Conservation Society, Health Program, Bronx, NY, USA; University of Calgary, Faculty of Veterinary Medicine, Calgary, AB, Canada.
| | - Emily Denstedt
- Wildlife Conservation Society, Lao PDR Country Program, Vientiane, Laos
| | - Alice Latinne
- Wildlife Conservation Society, Viet Nam Country Program, Hanoi, Viet Nam
| | - Alice Porco
- Wildlife Conservation Society, Cambodia Country Program, Phnom Penh, Cambodia
| | | | - Kongsy Khammavong
- Wildlife Conservation Society, Lao PDR Country Program, Vientiane, Laos
| | | | | | - Manoly Sisavanh
- Wildlife Conservation Society, Lao PDR Country Program, Vientiane, Laos
| | | | - Pham Thi Bich Ngoc
- Wildlife Conservation Society, Viet Nam Country Program, Hanoi, Viet Nam
| | - Vo Duy Thanh
- Wildlife Conservation Society, Viet Nam Country Program, Hanoi, Viet Nam
| | - Sokha Chea
- Wildlife Conservation Society, Cambodia Country Program, Phnom Penh, Cambodia
| | - Sreyem Sours
- Wildlife Conservation Society, Cambodia Country Program, Phnom Penh, Cambodia
| | - Phouvong Phommachanh
- National Animal Health Laboratory, Department of Livestock and Fisheries, Vientiane, Laos
| | - Watthana Theppangna
- National Animal Health Laboratory, Department of Livestock and Fisheries, Vientiane, Laos
| | - Sithong Phiphakhavong
- National Animal Health Laboratory, Department of Livestock and Fisheries, Vientiane, Laos
| | - Chhuon Vanna
- Department of Wildlife and Biodiversity, Forestry Administration, Phnom Penh, Cambodia
| | - Kry Masphal
- Department of Wildlife and Biodiversity, Forestry Administration, Phnom Penh, Cambodia
| | - Tum Sothyra
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Sorn San
- General Directorate of Animal Health and Production, Phnom Penh, Cambodia
| | - Hong Chamnan
- General Directorate of Natural Protected Areas, Phnom Penh, Cambodia
| | - Pham Thanh Long
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Nguyen Thi Diep
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Vu Trong Duoc
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Patrick Zimmer
- Canadian Wildlife Health Cooperative, Saskatoon, SK, Canada
| | - Kevin Brown
- Canadian Wildlife Health Cooperative, Saskatoon, SK, Canada
| | - Sarah H Olson
- Wildlife Conservation Society, Health Program, Bronx, NY, USA
| | - Amanda E Fine
- Wildlife Conservation Society, Health Program, Bronx, NY, USA
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4
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Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Roy S, Ayukekbong JA, Saylors KE, Joly DO, Wolfe ND, Rubin EM, Lange CE. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110. [PMID: 35233291 PMCID: PMC8867583 DOI: 10.1093/ve/veab110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/05/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
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Affiliation(s)
- Nkom F Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Amethyst Gillis
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Centre Region Route de Kribi, Yaoundé, BP 1364, Cameroon
| | - Joseph Le Doux Diffo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Jean-Michel Takuo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Julius Nwobegahay
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
| | | | - Anne W Rimoin
- Department of Epidemiology, University of California, 71-254 Center for Health Sciences, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bradley S Schneider
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Mosaic, Yaoundé, Centre Region, BP 35353, Cameroon
| | | | - David J McIver
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
- One Health Institute, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Sanjit Roy
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- University of Victoria, 3800 Finnerty Road, Victoria BC V8P 5C2, Canada
| | | | - Karen E Saylors
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
| | - Damien O Joly
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | | | - Edward M Rubin
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | - Christian E Lange
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
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5
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Ip HS, Griffin KM, Messer JD, Winzeler ME, Shriner SA, Killian ML, K. Torchetti M, DeLiberto TJ, Amman BR, Cossaboom CM, Harvey RR, Wendling NM, Rettler H, Taylor D, Towner JS, Barton Behravesh C, Blehert DS. An Opportunistic Survey Reveals an Unexpected Coronavirus Diversity Hotspot in North America. Viruses 2021; 13:v13102016. [PMID: 34696445 PMCID: PMC8539472 DOI: 10.3390/v13102016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus. Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified. Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus. Our findings indicate an unexpectedly high prevalence of coronavirus among the domestic and wild free-roaming animals tested on mink farms. These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses.
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Affiliation(s)
- Hon S. Ip
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
- Correspondence: ; Tel.: +1-608-270-2464
| | - Kathryn M. Griffin
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Jeffrey D. Messer
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Megan E. Winzeler
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Susan A. Shriner
- Wildlife Services, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA; (S.A.S.); (T.J.D.)
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Diagnostic Virology Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.K.T.)
| | - Mia K. Torchetti
- National Veterinary Services Laboratories, Diagnostic Virology Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.K.T.)
| | - Thomas J. DeLiberto
- Wildlife Services, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA; (S.A.S.); (T.J.D.)
| | - Brian R. Amman
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Caitlin M. Cossaboom
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - R. Reid Harvey
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Natalie M. Wendling
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Hannah Rettler
- Utah Department of Health, Salt Lake City, UT 84114, USA;
| | - Dean Taylor
- Utah Department of Agriculture and Food, Salt Lake City, UT 84116, USA;
| | - Jonathan S. Towner
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Casey Barton Behravesh
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - David S. Blehert
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
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6
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Virachith S, Pommelet V, Calvez E, Khounvisith V, Sayasone S, Kounnavong S, Mayxay M, Xangsayarath P, Temmam S, Eloit M, Escriou N, Rose T, Vongphayloth K, Hübschen JM, Lacoste V, Somlor S, Phonekeo D, Brey PT, Black AP. Low seroprevalence of COVID-19 in Lao PDR, late 2020. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 13:100197. [PMID: 34278365 PMCID: PMC8277598 DOI: 10.1016/j.lanwpc.2021.100197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/24/2021] [Accepted: 06/06/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND In 2020 Lao PDR had low reported COVID-19 cases but it was unclear whether this masked silent transmission. A seroprevalence study was done August - September 2020 to determine SARS-CoV-2 exposure. METHODS Participants were from the general community (n=2433) or healthcare workers (n=666) in five provinces and bat/wildlife contacts (n=74) were from Vientiane province. ELISAs detected anti- SARS-CoV-2 Nucleoprotein (N; n=3173 tested) and Spike (S; n=1417 tested) antibodies. Double-positive samples were checked by IgM/IgG rapid tests. Controls were confirmed COVID-19 cases (n=15) and pre-COVID-19 samples (n=265). Seroprevalence for the general community was weighted to account for complex survey sample design, age and sex. FINDINGS In pre-COVID-19 samples, 5·3%, [95% CI=3·1-8·7%] were anti-N antibody single-positive and 1·1% [0·3-3·5%] were anti-S antibody single positive. None were double positive. Anti-N and anti-S antibodies were detected in 5·2% [4·2-6·5%] and 2·1% [1·1-3·9%] of the general community, 2·0% [1·1-3·3%] and 1·4% [0·5-3·7%] of healthcare workers and 20·3% [12·6-31·0%] and 6·8% [2·8-15·3%] of bat/wildlife contacts. 0·1% [0·02-0·3%] were double positive for anti-N and anti-S antibodies (rapid test negative). INTERPRETATION We find no evidence for significant SARS-CoV-2 circulation in Lao PDR before September 2020. This likely results from early decisive measures taken by the government, social behavior, and low population density. High anti-N /low anti-S seroprevalence in bat/wildlife contacts may indicate exposure to cross-reactive animal coronaviruses with threat of emerging novel viruses. FUNDING Agence Française de Développement. Additional; Institut Pasteur du Laos, Institute Pasteur, Paris and Luxembourg Ministry of Foreign and European Affairs ("PaReCIDS II").
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Affiliation(s)
| | | | - Elodie Calvez
- Institut Pasteur du Laos, Vientiane Capital, Lao PDR
| | | | - Somphou Sayasone
- Lao Tropical Public Health Institute, Vientiane Capital, Lao PDR
| | | | - Mayfong Mayxay
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, University of Oxford, UK
| | | | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France
| | | | - Thierry Rose
- Lymphocyte Cell Biology Unit, INSERM 1221, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Paul T. Brey
- Institut Pasteur du Laos, Vientiane Capital, Lao PDR
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7
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Flower B, Marks M. Did Laos really control the transmission of SARS-CoV-2 in 2020? LANCET REGIONAL HEALTH-WESTERN PACIFIC 2021; 13:100202. [PMID: 34308399 PMCID: PMC8290237 DOI: 10.1016/j.lanwpc.2021.100202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Barnaby Flower
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London.,Hospital for Tropical Diseases, London, United Kingdom
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8
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Mu Y, Shao M, Zhong B, Zhao Y, Leung KMY, Giesy JP, Ma J, Wu F, Zeng F. Transmission of SARS-CoV-2 virus and ambient temperature: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:37051-37059. [PMID: 34053039 PMCID: PMC8164483 DOI: 10.1007/s11356-021-14625-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has brought unprecedented public health, and social and economic challenges. It remains unclear whether seasonal changes in ambient temperature will alter spreading trajectory of the COVID-19 epidemic. The probable mechanism on this is still lacking. This review summarizes the most recent research data on the effect of ambient temperature on the COVID-19 epidemic characteristic. The available data suggest that (i) mesophilic traits of viruses are different due to their molecular composition; (ii) increasing ambient temperature decreases the persistence of some viruses in aquatic media; (iii) a 1°C increase in the average monthly minimum ambient temperatures (AMMAT) was related to a 0.72% fewer mammalian individuals that would be infected by coronavirus; (iv) proportion of zoonotic viruses of mammals including humans is probably related to their body temperature difference; (v) seasonal divergence between the northern and southern hemispheres may be a significant driver in determining a waved trajectory in the next 2 years. Further research is needed to understand its effects and mechanisms of global temperature change so that effective strategies can be adopted to curb its natural effects. This paper mainly explores possible scientific hypothesis and evidences that local communities and authorities should consider to find optimal solutions that can limit the transmission of SARS-CoV-2 virus.
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Affiliation(s)
- Yunsong Mu
- School of Environment & Natural Resources, Renmin University of China, No.59, Zhongguancun Street, Haidian District, Beijing, 100872, China.
| | - Meichen Shao
- School of Environment & Natural Resources, Renmin University of China, No.59, Zhongguancun Street, Haidian District, Beijing, 100872, China
| | - Buqing Zhong
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yiqun Zhao
- School of Environment & Natural Resources, Renmin University of China, No.59, Zhongguancun Street, Haidian District, Beijing, 100872, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Science, Baylor University, Waco, TX, USA
| | - Jin Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fangang Zeng
- School of Environment & Natural Resources, Renmin University of China, No.59, Zhongguancun Street, Haidian District, Beijing, 100872, China.
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9
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Li Z, Jiang J, Ruan X, Tong Y, Xu S, Han L, Xu J. The zoonotic and natural foci characteristics of SARS-CoV-2. JOURNAL OF BIOSAFETY AND BIOSECURITY 2021; 3:51-55. [PMID: 34189426 PMCID: PMC8221912 DOI: 10.1016/j.jobb.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
The origin of SARS-CoV-2 is still an unresolved mystery. In this study, we systematically reviewed the main research progress of wild animals carrying virus highly homologous to SARS-CoV-2 and analyzed the natural foci characteristics of SARS-CoV-2. The complexity of SARS-CoV-2 origin in wild animals and the possibility of SARS-CoV-2 long-term existence in human populations are also discussed. The joint investigation of corona virus carried by wildlife, as well as the ecology and patho-ecology of bats and other wildlife, are key measures to further clarify the characteristics of natural foci of SARS-CoV-2 and actively defend against future outbreaks of emerging zoonotic diseases.
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Affiliation(s)
- Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jiafu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Xiangdong Ruan
- Academy of Forest Inventory and Planning, State Forestry and Grassland Administration, Beijing 100714, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Shuai Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Lichao Han
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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10
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Stout AE, Millet JK, Stanhope MJ, Whittaker GR. Furin cleavage sites in the spike proteins of bat and rodent coronaviruses: Implications for virus evolution and zoonotic transfer from rodent species. One Health 2021; 13:100282. [PMID: 34179330 PMCID: PMC8216856 DOI: 10.1016/j.onehlt.2021.100282] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/02/2022] Open
Abstract
Bats and rodents comprise two of the world's largest orders of mammals and the order Chiroptera (bats) has been implicated as a major reservoir of coronaviruses in nature and a source of zoonotic transfer to humans. However, the order Rodentia (rodents) also harbors coronaviruses, with two human coronaviruses (HCoV-OC43 and HCoV-HKU1) considered to have rodent origins. The coronavirus spike protein mediates viral entry and is a major determinant of viral tropism; importantly, the spike protein is activated by host cell proteases at two distinct sites, designated as S1/S2 and S2’. SARS-CoV-2, which is considered to be of bat origin, contains a cleavage site for the protease furin at S1/S2, absent from the rest of the currently known betacoronavirus lineage 2b coronaviruses (Sarbecoviruses). This cleavage site is thought to be critical to its replication and pathogenesis, with a notable link to virus transmission. Here, we examine the spike protein across coronaviruses identified in both bat and rodent species and address the role of furin as an activating protease. Utilizing two publicly available furin prediction algorithms (ProP and PiTou) and based on spike sequences reported in GenBank, we show that the S1/S2 furin cleavage site is typically not present in bat virus spike proteins but is common in rodent-associated sequences, and suggest this may have implications for zoonotic transfer. We provide a phylogenetic history of the Embecoviruses (betacoronavirus lineage 2a), including context for the use of furin as an activating protease for the viral spike protein. From a One Health perspective, continued rodent surveillance should be an important consideration in uncovering novel circulating coronaviruses.
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Affiliation(s)
- Alison E Stout
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352, Jouy-en-Josas, France
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.,Master of Public Health Program, Cornell University, Ithaca, NY, USA
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11
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Johansen MD, Irving A, Montagutelli X, Tate MD, Rudloff I, Nold MF, Hansbro NG, Kim RY, Donovan C, Liu G, Faiz A, Short KR, Lyons JG, McCaughan GW, Gorrell MD, Cole A, Moreno C, Couteur D, Hesselson D, Triccas J, Neely GG, Gamble JR, Simpson SJ, Saunders BM, Oliver BG, Britton WJ, Wark PA, Nold-Petry CA, Hansbro PM. Animal and translational models of SARS-CoV-2 infection and COVID-19. Mucosal Immunol 2020; 13:877-891. [PMID: 32820248 PMCID: PMC7439637 DOI: 10.1038/s41385-020-00340-z] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
COVID-19 is causing a major once-in-a-century global pandemic. The scientific and clinical community is in a race to define and develop effective preventions and treatments. The major features of disease are described but clinical trials have been hampered by competing interests, small scale, lack of defined patient cohorts and defined readouts. What is needed now is head-to-head comparison of existing drugs, testing of safety including in the background of predisposing chronic diseases, and the development of new and targeted preventions and treatments. This is most efficiently achieved using representative animal models of primary infection including in the background of chronic disease with validation of findings in primary human cells and tissues. We explore and discuss the diverse animal, cell and tissue models that are being used and developed and collectively recapitulate many critical aspects of disease manifestation in humans to develop and test new preventions and treatments.
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Affiliation(s)
- M D Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - A Irving
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, ZJU International Campus, Haining, China
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - X Montagutelli
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - M D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - I Rudloff
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia
| | - M F Nold
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Monash Newborn, Monash Children's Hospital, Clayton, VIC, Australia
| | - N G Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - R Y Kim
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - C Donovan
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - G Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - A Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - K R Short
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - J G Lyons
- Centenary Institute and Dermatology, The University of Sydney and Cancer Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - G W McCaughan
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - M D Gorrell
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - A Cole
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - C Moreno
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - D Couteur
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, and Faculty of Medicine and Health, Concord Clinical School, ANZAC Research Institute and Centre for Education and Research on Ageing, Sydney, Australia
| | - D Hesselson
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - J Triccas
- Discipline of Infectious Diseases and Immunology, Central Clinical School, Faculty of Medicine and Health and the Charles Perkins Centre, The University of Sydney, Camperdown, Sydney, Australia
| | - G G Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - J R Gamble
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - S J Simpson
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, and Faculty of Medicine and Health, Concord Clinical School, ANZAC Research Institute and Centre for Education and Research on Ageing, Sydney, Australia
| | - B M Saunders
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - B G Oliver
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Woolcock Institute of Medical Research, Sydney, Australia
| | - W J Britton
- Centenary Institute, The University of Sydney and Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - P A Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - C A Nold-Petry
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - P M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia.
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia.
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