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Article ; Online: H5Nx Viruses Emerged during the Suppression of H5N1 Virus Populations in Poultry.

Li, Yao-Tsun / Su, Yvonne C F / Smith, Gavin J D

2021 Volume 9, Issue 2, Page(s) e0130921

Abstract: Highly pathogenic avian influenza (HPAI) H5 viruses have posed a substantial pandemic threat through repeated human infection since their emergence in China in 1996. Nationwide control measures, including vaccination of poultry, were implemented in 2005, ...

Abstract	Highly pathogenic avian influenza (HPAI) H5 viruses have posed a substantial pandemic threat through repeated human infection since their emergence in China in 1996. Nationwide control measures, including vaccination of poultry, were implemented in 2005, leading to a sharp reduction in H5N1 virus outbreaks. In 2008, novel non-N1 subtype (H5Nx) viruses emerged, gradually replacing the dominant H5N1 subtype and causing global outbreaks. The cause of this major shift in the ecology of HPAI H5 viruses remains unknown. Here, we show that major H5N1 virus lineages underwent population bottlenecks in 2006, followed by a recovery in virus populations between 2007 and 2009. Our analyses indicate that control measures, not competition from H5Nx viruses, were responsible for the H5N1 decline, with an H5N1 lineage capable of infecting poultry and wild birds experiencing a less severe population bottleneck due to circulation in unaffected wild birds. We show that H5Nx viruses emerged during the successful suppression of H5N1 virus populations in poultry, providing an opportunity for antigenically distinct H5Nx viruses to propagate. Avian influenza vaccination programs would benefit from universal vaccines targeting a wider diversity of influenza viruses to prevent the emergence of novel subtypes.
MeSH term(s)	Animals ; Animals, Wild/virology ; Birds/virology ; Chickens/virology ; China ; Ducks/virology ; Geese/virology ; Influenza A Virus, H5N1 Subtype/genetics ; Influenza A Virus, H5N1 Subtype/physiology ; Influenza A virus/classification ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza A virus/physiology ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Phylogeny ; Poultry Diseases/epidemiology ; Poultry Diseases/virology
Language	English
Publishing date	2021-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/Spectrum.01309-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Optimization and Improvement of qPCR Detection Sensitivity of SARS-CoV-2 in Saliva.

Ko, Hui-Ying / Li, Yao-Tsun / Li, Ya-Yuan / Chiang, Ming-Tsai / Lee, Yi-Ling / Liu, Wen-Chun / Liao, Chun-Che / Chang, Chih-Shin / Lin, Yi-Ling

Microbiology spectrum

2023 Volume 11, Issue 3, Page(s) e0464022

Abstract: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a major public health threat globally, especially during the beginning of the pandemic in 2020. Reverse transcription-quantitative PCR ( ... ...

Abstract	Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a major public health threat globally, especially during the beginning of the pandemic in 2020. Reverse transcription-quantitative PCR (RT-qPCR) is utilized for viral RNA detection as part of control measures to limit the spread of COVID-19. Collecting nasopharyngeal swabs for RT-qPCR is a routine diagnostic method for COVID-19 in clinical settings, but its large-scale implementation is hindered by a shortage of trained health professionals. Despite concerns over its sensitivity, saliva has been suggested as a practical alternative sampling approach to the nasopharyngeal swab for viral RNA detection. In this study, we spiked saliva from healthy donors with inactivated SARS-CoV-2 from an international standard to evaluate the effect of saliva on viral RNA detection. On average, the saliva increased the cycle threshold (
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19 Testing ; Saliva ; Clinical Laboratory Techniques/methods ; RNA, Viral/genetics ; RNA, Viral/analysis ; Endoribonucleases
Chemical Substances	RNA, Viral ; Endoribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.04640-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Co-circulation of both low and highly pathogenic avian influenza H5 viruses in current poultry epidemics in Taiwan.

Li, Yao-Tsun / Chen, Chen-Chih / Chang, Ai-Mei / Chao, Day-Yu / Smith, Gavin J D

Virus evolution

2020 Volume 6, Issue 1, Page(s) veaa037

Abstract: Highly pathogenic avian influenza (HPAI) A(H5) viruses belonging to clade 2.3.4.4c of the A/goose/Guangdong/1/96-like (Gs/GD) lineage caused severe global outbreaks in domestic birds from 2014 to 2015, that also represented the first incursions of Gs/GD ... ...

Abstract	Highly pathogenic avian influenza (HPAI) A(H5) viruses belonging to clade 2.3.4.4c of the A/goose/Guangdong/1/96-like (Gs/GD) lineage caused severe global outbreaks in domestic birds from 2014 to 2015, that also represented the first incursions of Gs/GD viruses into Taiwan and the USA. However, few studies have investigated the circulation of clade 2.3.4.4c viruses after 2015. Here, we describe Gs/GD clade 2.3.4.4c and Mexican-like H5N2 viruses that were isolated in Taiwan during active surveillance conducted in chicken farms from February to March 2019. Phylogenetic analysis demonstrated two distinct genome constellations of the clade 2.3.4.4c H5 viruses, with the internal genes of one of the new genotypes closely related to a virus isolated from a pintail (
Keywords	covid19
Language	English
Publishing date	2020-06-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa037
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Emerging lethal infectious bronchitis coronavirus variants with multiorgan tropism

Li, Yao‐Tsun / Chen, Ting‐Chih / Lin, Shu‐Yi / Mase, Masaji / Murakami, Shin / Horimoto, Taisuke / Chen, Hui‐Wen

Transboundary and emerging diseases. 2020 Mar., v. 67, no. 2

2020

Abstract: Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide. Despite vaccine use, there have been field outbreaks of IBV in Taiwan. This study aimed to characterize the emerging ...

Abstract	Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide. Despite vaccine use, there have been field outbreaks of IBV in Taiwan. This study aimed to characterize the emerging IBV variants circulating in Taiwan. The analysis of the structural protein genes showed that these variants emerged through frequent recombination events among Taiwan strains, China strains, Japan strains and vaccine strains. Cross‐neutralization tests revealed that two of the variants exhibited novel serotypes. Clinicopathological assessment showed that two of the variants caused high fatality rates of 67% and 20% in one‐day‐old SPF chicks, and all the variants possessed multiorgan tropisms, including trachea, proventriculus and urogenital tissues. Furthermore, the commercial live‐attenuated Mass‐type vaccine conferred poor protection against these variants. This study identified novel genotypes, serotypes and pathotypes of emerging IBV variants circulating in Taiwan. There is an urgent need for effective countermeasures against these variant strains.
Keywords	Infectious bronchitis virus ; chickens ; chicks ; emerging diseases ; genes ; infectious bronchitis ; live vaccines ; mortality ; pathotypes ; poultry industry ; proventriculus ; respiratory tract diseases ; serotypes ; structural proteins ; tissues ; tropisms ; China ; Japan ; Taiwan ; covid19
Language	English
Dates of publication	2020-03
Size	p. 884-893.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.13412
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Avian influenza viruses in humans: lessons from past outbreaks.

Li, Yao-Tsun / Linster, Martin / Mendenhall, Ian H / Su, Yvonne C F / Smith, Gavin J D

British medical bulletin

2019 Volume 132, Issue 1, Page(s) 81–95

Abstract: Background: Human infections with avian influenza viruses (AIV) represent a persistent public health threat. The principal risk factor governing human infection with AIV is from direct contact with infected poultry and is primarily observed in Asia and ... ...

Abstract	Background: Human infections with avian influenza viruses (AIV) represent a persistent public health threat. The principal risk factor governing human infection with AIV is from direct contact with infected poultry and is primarily observed in Asia and Egypt where live-bird markets are common. Areas of agreement: Changing patterns of virus transmission and a lack of obvious disease manifestations in avian species hampers early detection and efficient control of potentially zoonotic AIV. Areas of controversy: Despite extensive studies on biological and environmental risk factors, the exact conditions required for cross-species transmission from avian species to humans remain largely unknown. Growing points: The development of a universal ('across-subtype') influenza vaccine and effective antiviral therapeutics are a priority. Areas timely for developing research: Sustained virus surveillance and collection of ecological and physiological parameters from birds in different environments is required to better understand influenza virus ecology and identify risk factors for human infection.
MeSH term(s)	Animals ; Antiviral Agents/therapeutic use ; Birds ; Disease Outbreaks ; Disease Susceptibility ; Humans ; Influenza A virus/classification ; Influenza Vaccines ; Influenza in Birds/epidemiology ; Influenza in Birds/therapy ; Influenza in Birds/transmission ; Influenza, Human/epidemiology ; Influenza, Human/therapy ; Influenza, Human/transmission ; Risk Factors ; Zoonoses/epidemiology ; Zoonoses/therapy ; Zoonoses/transmission
Chemical Substances	Antiviral Agents ; Influenza Vaccines
Language	English
Publishing date	2019-12-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	213294-1
ISSN	1471-8391 ; 0007-1420
ISSN (online)	1471-8391
ISSN	0007-1420
DOI	10.1093/bmb/ldz036
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ecological factors associated with persistent circulation of multiple highly pathogenic avian influenza viruses among poultry farms in Taiwan during 2015-17.

Liang, Wei-Shan / He, Yu-Chen / Wu, Hong-Dar / Li, Yao-Tsun / Shih, Tai-Hwa / Kao, Gour-Shenq / Guo, Horng-Yuh / Chao, Day-Yu

PloS one

2020 Volume 15, Issue 8, Page(s) e0236581

Abstract: Emergence and intercontinental spread of highly pathogenic avian influenza A (HPAI) H5Nx virus clade 2.3.4.4 has resulted in substantial economic losses to the poultry industry in Asia, Europe, and North America. The long-distance migratory birds have ... ...

Abstract	Emergence and intercontinental spread of highly pathogenic avian influenza A (HPAI) H5Nx virus clade 2.3.4.4 has resulted in substantial economic losses to the poultry industry in Asia, Europe, and North America. The long-distance migratory birds have been suggested to play a major role in the global spread of avian influenza viruses during this wave of panzootic outbreaks since 2013. Poultry farm epidemics caused by multiple introduction of different HPAI novel subtypes of clade 2.3.4.4 viruses also occurred in Taiwan between 2015 and 2017. The mandatory and active surveillance detected H5N3 and H5N6 circulation in 2015 and 2017, respectively, while H5N2 and H5N8 were persistently identified in poultry farms since their first arrival in 2015. This study intended to assess the importance of various ecological factors contributed to the persistence of HPAI during three consecutive years. We used satellite technology to identify the location of waterfowl flocks. Four risk factors consistently showed strong association with the spatial clustering of H5N2 and H5N8 circulations during 2015 and 2017, including high poultry farm density (aOR:17.46, 95%CI: 5.91-74.86 and 8.23, 95% CI: 2.12-54.86 in 2015 and 2017, respectively), poultry heterogeneity index (aOR of 12.28, 95%CI: 5.02-31.14 and 2.79, 95%CI: 1.00-7.69, in 2015 and 2017, respectively), non-registered waterfowl flock density (aOR: 6.8, 95%CI: 3.41-14.46 and 9.17, 95%CI: 3.73-26.20, in 2015 and 2017, respectively) and higher percentage of cropping land coverage (aOR of 1.36, 95%CI: 1.10-1.69 and 1.04, 95%CI: 1.02-1.07, in 2015 and 2017, respectively). Our study highlights the application of remote sensing and clustering analysis for the identification and characterization of environmental factors in facilitating and contributing to the persistent circulation of certain subtypes of H5Nx in poultry farms in Taiwan.
MeSH term(s)	Animals ; Environment ; Farms ; Influenza A Virus, H5N2 Subtype/isolation & purification ; Influenza A Virus, H5N8 Subtype/isolation & purification ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Poultry/virology ; Poultry Diseases/epidemiology ; Poultry Diseases/virology ; Risk Factors ; Taiwan/epidemiology ; Water Microbiology
Language	English
Publishing date	2020-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0236581
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genomic Evidence for Sequestration of Influenza A Virus Lineages in Sea Duck Host Species.

McBride, Dillon S / Lauterbach, Sarah E / Li, Yao-Tsun / Smith, Gavin J D / Killian, Mary Lea / Nolting, Jacqueline M / Su, Yvonne C F / Bowman, Andrew S

Viruses

2021 Volume 13, Issue 2

Abstract: Wild birds are considered the natural reservoir of influenza A viruses (IAVs) making them critical for IAV surveillance efforts. While sea ducks have played a role in novel IAV emergence events that threatened food security and public health, very few ... ...

Abstract	Wild birds are considered the natural reservoir of influenza A viruses (IAVs) making them critical for IAV surveillance efforts. While sea ducks have played a role in novel IAV emergence events that threatened food security and public health, very few surveillance samples have been collected from sea duck hosts. From 2014-2018, we conducted surveillance focused in the Mississippi flyway, USA at locations where sea duck harvest has been relatively successful compared to our other sampling locations. Our surveillance yielded 1662 samples from sea ducks, from which we recovered 77 IAV isolates. Our analyses identified persistence of sea duck specific IAV lineages across multiple years. We also recovered sea duck origin IAVs containing an H4 gene highly divergent from the majority of North American H4-HA with clade node age of over 65 years. Identification of IAVs with long branch lengths is indicative of substantial genomic change consistent with persistence without detection by surveillance efforts. Sea ducks play a role in the movement and long-term persistence of IAVs and are likely harboring more undetected IAV diversity. Sea ducks should be a point of emphasis for future North American wild bird IAV surveillance efforts.
MeSH term(s)	Animals ; Animals, Wild/virology ; Ducks/virology ; Genomics ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Host Specificity ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza in Birds/epidemiology ; Influenza in Birds/virology ; Phylogeny ; Poultry ; United States/epidemiology
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2021-01-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13020172
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Emerging lethal infectious bronchitis coronavirus variants with multiorgan tropism.

Li, Yao-Tsun / Chen, Ting-Chih / Lin, Shu-Yi / Mase, Masaji / Murakami, Shin / Horimoto, Taisuke / Chen, Hui-Wen

Transboundary and emerging diseases

2019 Volume 67, Issue 2, Page(s) 884–893

Abstract	Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide. Despite vaccine use, there have been field outbreaks of IBV in Taiwan. This study aimed to characterize the emerging IBV variants circulating in Taiwan. The analysis of the structural protein genes showed that these variants emerged through frequent recombination events among Taiwan strains, China strains, Japan strains and vaccine strains. Cross-neutralization tests revealed that two of the variants exhibited novel serotypes. Clinicopathological assessment showed that two of the variants caused high fatality rates of 67% and 20% in one-day-old SPF chicks, and all the variants possessed multiorgan tropisms, including trachea, proventriculus and urogenital tissues. Furthermore, the commercial live-attenuated Mass-type vaccine conferred poor protection against these variants. This study identified novel genotypes, serotypes and pathotypes of emerging IBV variants circulating in Taiwan. There is an urgent need for effective countermeasures against these variant strains.
MeSH term(s)	Animals ; Bronchitis/veterinary ; Bronchitis/virology ; Chickens/virology ; Coronavirus Infections/epidemiology ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Disease Outbreaks/veterinary ; Female ; Genetic Variation ; Infectious bronchitis virus/genetics ; Infectious bronchitis virus/immunology ; Infectious bronchitis virus/physiology ; Poultry Diseases/epidemiology ; Poultry Diseases/virology ; Proventriculus/virology ; Specific Pathogen-Free Organisms ; Taiwan/epidemiology ; Trachea/virology ; Viral Tropism
Keywords	covid19
Language	English
Publishing date	2019-11-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.13412
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ecological factors associated with persistent circulation of multiple highly pathogenic avian influenza viruses among poultry farms in Taiwan during 2015-17.

Wei-Shan Liang / Yu-Chen He / Hong-Dar Wu / Yao-Tsun Li / Tai-Hwa Shih / Gour-Shenq Kao / Horng-Yuh Guo / Day-Yu Chao

PLoS ONE, Vol 15, Iss 8, p e

2020 Volume 0236581

Abstract	Emergence and intercontinental spread of highly pathogenic avian influenza A (HPAI) H5Nx virus clade 2.3.4.4 has resulted in substantial economic losses to the poultry industry in Asia, Europe, and North America. The long-distance migratory birds have been suggested to play a major role in the global spread of avian influenza viruses during this wave of panzootic outbreaks since 2013. Poultry farm epidemics caused by multiple introduction of different HPAI novel subtypes of clade 2.3.4.4 viruses also occurred in Taiwan between 2015 and 2017. The mandatory and active surveillance detected H5N3 and H5N6 circulation in 2015 and 2017, respectively, while H5N2 and H5N8 were persistently identified in poultry farms since their first arrival in 2015. This study intended to assess the importance of various ecological factors contributed to the persistence of HPAI during three consecutive years. We used satellite technology to identify the location of waterfowl flocks. Four risk factors consistently showed strong association with the spatial clustering of H5N2 and H5N8 circulations during 2015 and 2017, including high poultry farm density (aOR:17.46, 95%CI: 5.91-74.86 and 8.23, 95% CI: 2.12-54.86 in 2015 and 2017, respectively), poultry heterogeneity index (aOR of 12.28, 95%CI: 5.02-31.14 and 2.79, 95%CI: 1.00-7.69, in 2015 and 2017, respectively), non-registered waterfowl flock density (aOR: 6.8, 95%CI: 3.41-14.46 and 9.17, 95%CI: 3.73-26.20, in 2015 and 2017, respectively) and higher percentage of cropping land coverage (aOR of 1.36, 95%CI: 1.10-1.69 and 1.04, 95%CI: 1.02-1.07, in 2015 and 2017, respectively). Our study highlights the application of remote sensing and clustering analysis for the identification and characterization of environmental factors in facilitating and contributing to the persistent circulation of certain subtypes of H5Nx in poultry farms in Taiwan.
Keywords	Medicine ; R ; Science ; Q
Subject code	333
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Emerging lethal infectious bronchitis coronavirus variants with multiorgan tropism

Li, Yao-Tsun / Chen, Ting-Chih / Lin, Shu-Yi / Mase, Masaji / Murakami, Shin / Horimoto, Taisuke / Chen, Hui-Wen

Transboundary and Emerging Diseases

Abstract: Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide Despite vaccine use, there have been field outbreaks of IBV in Taiwan This study aimed to characterize the emerging ... ...

Abstract	Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide Despite vaccine use, there have been field outbreaks of IBV in Taiwan This study aimed to characterize the emerging IBV variants circulating in Taiwan The analysis of the structural protein genes showed that these variants emerged through frequent recombination events among Taiwan strains, China strains, Japan strains and vaccine strains Cross-neutralization tests revealed that two of the variants exhibited novel serotypes Clinicopathological assessment showed that two of the variants caused high fatality rates of 67% and 20% in one-day-old SPF chicks, and all the variants possessed multiorgan tropisms, including trachea, proventriculus and urogenital tissues Furthermore, the commercial live-attenuated Mass-type vaccine conferred poor protection against these variants This study identified novel genotypes, serotypes and pathotypes of emerging IBV variants circulating in Taiwan There is an urgent need for effective countermeasures against these variant strains
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #797115
Database	COVID19

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