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Article ; Online: Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States.

Feng, Aijing / Bevins, Sarah / Chandler, Jeff / DeLiberto, Thomas J / Ghai, Ria / Lantz, Kristina / Lenoch, Julianna / Retchless, Adam / Shriner, Susan / Tang, Cynthia Y / Tong, Suxiang Sue / Torchetti, Mia / Uehara, Anna / Wan, Xiu-Feng

Nature communications

2023 Volume 14, Issue 1, Page(s) 4078

Abstract: SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the ... ...

Abstract	SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.
MeSH term(s)	Animals ; Humans ; Deer ; SARS-CoV-2/genetics ; COVID-19/veterinary ; Washington
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39782-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2.

Paden, Clinton R / Tao, Ying / Queen, Krista / Zhang, Jing / Li, Yan / Uehara, Anna / Tong, Suxiang

Emerging infectious diseases

2020 Volume 26, Issue 10, Page(s) 2401–2405

Abstract: We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the ... ...

Abstract	We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Multiplex Polymerase Chain Reaction ; Pandemics ; Pneumonia, Viral/virology ; RNA, Viral/analysis ; SARS-CoV-2 ; Sequence Analysis, RNA/methods ; Whole Genome Sequencing/methods
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2610.201800
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Article ; Online: GPS Tracking of Free-Roaming Cats (

Amman, Brian R / Cossaboom, Caitlin M / Wendling, Natalie M / Harvey, R Reid / Rettler, Hannah / Taylor, Dean / Kainulainen, Markus H / Ahmad, Ausaf / Bunkley, Paige / Godino, Claire / Tong, Suxiang / Li, Yan / Uehara, Anna / Kelleher, Anna / Zhang, Jing / Lynch, Brian / Behravesh, Casey Barton / Towner, Jonathan S

Viruses

2022 Volume 14, Issue 10

Abstract: Zoonotic transmission of SARS-CoV-2 from infected humans to other animals has been documented around the world, most notably in mink farming operations in Europe and the United States. Outbreaks of SARS-CoV-2 on Utah mink farms began in late July 2020 ... ...

Abstract	Zoonotic transmission of SARS-CoV-2 from infected humans to other animals has been documented around the world, most notably in mink farming operations in Europe and the United States. Outbreaks of SARS-CoV-2 on Utah mink farms began in late July 2020 and resulted in high mink mortality. An investigation of these outbreaks revealed active and past SARS-CoV-2 infections in free-roaming and in feral cats living on or near several mink farms. Cats were captured using live traps, were sampled, fitted with GPS collars, and released on the farms. GPS tracking of these cats show they made frequent visits to mink sheds, moved freely around the affected farms, and visited surrounding residential properties and neighborhoods on multiple occasions, making them potential low risk vectors of additional SARS-CoV-2 spread in local communities.
MeSH term(s)	Cats ; Animals ; Humans ; SARS-CoV-2 ; Mink ; COVID-19/epidemiology ; COVID-19/veterinary ; Farms ; Utah/epidemiology
Language	English
Publishing date	2022-09-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14102131
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Article ; Online: SARS-CoV-2 Outbreak among Malayan Tigers and Humans, Tennessee, USA, 2020.

Grome, Heather N / Meyer, Becky / Read, Erin / Buchanan, Martha / Cushing, Andrew / Sawatzki, Kaitlin / Levinson, Kara J / Thomas, Linda S / Perry, Zachary / Uehara, Anna / Tao, Ying / Queen, Krista / Tong, Suxiang / Ghai, Ria / Fill, Mary-Margaret / Jones, Timothy F / Schaffner, William / Dunn, John

Emerging infectious diseases

2022 Volume 28, Issue 4, Page(s) 833–836

Abstract: We report an outbreak of severe acute respiratory syndrome coronavirus 2 involving 3 Malayan tigers (Panthera tigris jacksoni) at a zoo in Tennessee, USA. Investigation identified naturally occurring tiger-to-tiger transmission; genetic sequence change ... ...

Abstract	We report an outbreak of severe acute respiratory syndrome coronavirus 2 involving 3 Malayan tigers (Panthera tigris jacksoni) at a zoo in Tennessee, USA. Investigation identified naturally occurring tiger-to-tiger transmission; genetic sequence change occurred with viral passage. We provide epidemiologic, environmental, and genomic sequencing data for animal and human infections.
MeSH term(s)	Animals ; COVID-19/epidemiology ; Disease Outbreaks ; Humans ; SARS-CoV-2 ; Tennessee/epidemiology ; Tigers/genetics
Language	English
Publishing date	2022-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2804.212219
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Article ; Online: COVID-19 on the Nile: a cross-sectional investigation of COVID-19 among Nile River cruise travellers returning to the United States, February-March 2020.

Guagliardo, Sarah Anne J / Quilter, Laura A S / Uehara, Anna / White, Stefanie B / Talarico, Sarah / Tong, Suxiang / Paden, Clinton R / Zhang, Jing / Li, Yan / Pray, Ian / Novak, Ryan T / Fukunaga, Rena / Rodriguez, Andrea / Medley, Alexandra M / Wagner, Riley / Weinberg, Michelle / Brown, Clive M / Friedman, Cindy R

Journal of travel medicine

2022 Volume 30, Issue 4

Abstract: Background: Early in the pandemic, cruise travel exacerbated the global spread of SARS-CoV-2. We report epidemiologic and molecular findings from an investigation of a cluster of travellers with confirmed COVID-19 returning to the USA from Nile River ... ...

Abstract	Background: Early in the pandemic, cruise travel exacerbated the global spread of SARS-CoV-2. We report epidemiologic and molecular findings from an investigation of a cluster of travellers with confirmed COVID-19 returning to the USA from Nile River cruises in Egypt. Methods: State health departments reported data on real-time reverse transcription-polymerase chain reaction-confirmed COVID-19 cases with a history of Nile River cruise travel during February-March 2020 to the Centers for Disease Control and Prevention (CDC). Demographic and epidemiologic data were collected through routine surveillance channels. Sequences were obtained either from state health departments or from the Global Initiative on Sharing Avian Flu Data (GISAID). We conducted descriptive analyses of epidemiologic data and explored phylogenetic relationships between sequences. Results: We identified 149 Nile River cruise travellers with confirmed COVID-19 who returned to 67 different US counties in 27 states: among those with complete data, 4.7% (6/128) died and 28.1% (38/135) were hospitalized. These individuals travelled on 20 different Nile River cruise voyages (12 unique vessels). Fifteen community transmission events were identified in four states, with 73.3% (11/15) of these occurring in Wisconsin (as the result of a more detailed contact investigation in that state). Phylogenetic analyses supported the hypothesis that travellers were most likely infected in Egypt, with most sequences in Nextstrain clade 20A 93% (87/94). We observed genetic clustering by Nile River cruise voyage and vessel. Conclusions: Nile River cruise travellers with COVID-19 introduced SARS-CoV-2 over a very large geographic range, facilitating transmission across the USA early in the pandemic. Travellers who participate in cruises, even on small river vessels as investigated in this study, are at increased risk of SARS-CoV-2 exposure. Therefore, history of river cruise travel should be considered in contact tracing and outbreak investigations.
MeSH term(s)	Humans ; United States/epidemiology ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Phylogeny ; Cross-Sectional Studies ; Rivers
Language	English
Publishing date	2022-12-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taac153
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Article ; Online: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans.

Tan, Chee Wah / Wittwer, Kevin / Lim, Xiao Fang / Uehara, Anna / Mani, Shailendra / Wang, Lin-Fa / Anderson, Danielle E

Emerging microbes & infections

2019 Volume 8, Issue 1, Page(s) 787–795

Abstract: Pteropine orthoreoviruses (PRV) are emerging bat-borne viruses with proven zoonotic transmission. We recently demonstrated human exposure to PRV in Singapore, which together with previous reports from Malaysia and Vietnam suggest that human infection of ... ...

Abstract	Pteropine orthoreoviruses (PRV) are emerging bat-borne viruses with proven zoonotic transmission. We recently demonstrated human exposure to PRV in Singapore, which together with previous reports from Malaysia and Vietnam suggest that human infection of PRV may occur periodically in the region. This raises the question whether bats are the only sources of human infection. In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We found that 67 serum samples were PRV3M positive by ELISA and 34 were also positive by virus neutralization assay. To investigate whether monkeys could act as hosts for PRV transmission, we experimentally infected cynomolgus macaques with PRV3M and housed these animals with uninfected monkeys. Although no clinical signs of infection were observed in infected animals, viral RNA was detected in nasal and rectal swabs and all infected macaques seroconverted. Additionally, one of the uninfected animals seroconverted, implying active shedding and transmission of PRV3M. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs.
MeSH term(s)	Animals ; Antibodies, Viral/blood ; Antibodies, Viral/immunology ; Female ; Humans ; Macaca fascicularis/blood ; Macaca fascicularis/virology ; Monkey Diseases/blood ; Monkey Diseases/transmission ; Monkey Diseases/virology ; Neutralization Tests ; Orthoreovirus/genetics ; Orthoreovirus/physiology ; Reoviridae Infections/blood ; Reoviridae Infections/transmission ; Reoviridae Infections/veterinary ; Reoviridae Infections/virology ; Singapore ; Zoonoses/blood ; Zoonoses/transmission ; Zoonoses/virology
Chemical Substances	Antibodies, Viral
Keywords	covid19
Language	English
Publishing date	2019-05-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2019.1621668
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Article ; Online: Serological evidence of human infection by bat orthoreovirus in Singapore.

Uehara, Anna / Tan, Chee Wah / Mani, Shailendra / Chua, Kaw Bing / Leo, Yee Sin / Anderson, Danielle E / Wang, Lin-Fa

Journal of medical virology

2018 Volume 91, Issue 4, Page(s) 707–710

Abstract: To determine whether Pteropine orthoreovirus (PRV) exposure has occurred in Singapore, we tested 856 individuals from an existing serum panel collected from 2005-2013. After an initial screen with luciferase immunoprecipitation system and secondary ... ...

Abstract	To determine whether Pteropine orthoreovirus (PRV) exposure has occurred in Singapore, we tested 856 individuals from an existing serum panel collected from 2005-2013. After an initial screen with luciferase immunoprecipitation system and secondary confirmation with virus neutralization test, we identified at least seven individuals with specific antibodies against PRV in both assays. Our findings confirm that PRV spillover into human populations is relatively common in this region of the world.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Animals ; Antibodies, Viral/blood ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Orthoreovirus/immunology ; Reoviridae Infections/epidemiology ; Reoviridae Infections/virology ; Seroepidemiologic Studies ; Serologic Tests/methods ; Singapore/epidemiology ; Young Adult ; Zoonoses/epidemiology ; Zoonoses/virology
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2018-11-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25355
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Article ; Online: Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)

Paden, Clinton R / Tao, Ying / Queen, Krista / Zhang, Jing / Li, Yan / Uehara, Anna / Tong, Suxiang

bioRxiv

Abstract: SARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating high-quality full-length genomes from primary samples. ... ...

Abstract	SARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating high-quality full-length genomes from primary samples. The first employs multiplex RT-PCR followed by MinION or MiSeq sequencing. The second uses singleplex, nested RT-PCR and Sanger sequencing.
Keywords	covid19
Language	English
Publishing date	2020-04-24
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.04.22.055897
Database	COVID19

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Article: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2

Paden, Clinton R. / Tao, Ying / Queen, Krista / Zhang, Jing / Yan, Li / Uehara, Anna / Tong, Suxiang

Emerg Infect Dis

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #712837
Database	COVID19

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Article: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2

Paden, Clinton R / Tao, Ying / Queen, Krista / Zhang, Jing / Li, Yan / Uehara, Anna / Tong, Suxiang

Emerg Infect Dis

Abstract	We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #627407
Database	COVID19

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