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Emergence and spread of novel H5N8, H5N5 and H5N1 clade 2.3.4.4 highly pathogenic avian influenza in 2020.

Nicola S Lewis, Ashley C Banyard, Elliot Whittard, Talgat Karibayev, Thamer Al Kafagi, Ilya Chvala, Alex Byrne, Saduakassova Meruyert Akberovna, Jacqueline King, Timm Harder, Christian Grund, Steve Essen, Scott M Reid, Adam Brouwer, Nikolay G Zinyakov, Azimkhan Tegzhanov, Victor Irza, Anne Pohlmann, Martin Beer, Ron A M Fouchier, Sultanov Akhmetzhan Akievich, Ian H Brown,

Analyses of HPAI H5 viruses from poultry outbreaks across a wide Eurasian region since July 2020 including the Russian Federation, Republics of Iraq and Kazakhstan, and recent detections in migratory waterfowl in the Netherlands, revealed undetected maintenance of H5N8, likely in galliform poultry since 2017/18 and both H5N5 and H5N1. ... Read more >>

Emerg Microbes Infect (Emerging microbes & infections)
[2021, 10(1):148-151]

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Isolation and characterization of novel reassortant mammalian orthoreovirus from pigs in the United States.

Liping Wang, Yan Li, Timothy Walsh, Zhenyu Shen, Yonghai Li, Nirmalendu Deb Nath, Jinhwa Lee, Baoliang Zheng, Ying Tao, Clinton R Paden, Krista Queen, Shuping Zhang, Suxiang Tong, Wenjun Ma,

Mammalian orthoreovirus (MRV) infects multiple mammalian species including humans. A United States Midwest swine farm with approximately one thousand 3-month-old pigs experienced an event, in which more than 300 pigs showed neurological signs, like "down and peddling", with approximately 40% mortality. A novel MRV was isolated from the diseased pigs. ... Read more >>

Emerg Microbes Infect (Emerging microbes & infections)
[2021, 10(1):1137-1147]

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Mink is a highly susceptible host species to circulating human and avian influenza viruses.

Honglei Sun, Fangtao Li, Qingzhi Liu, Jianyong Du, Litao Liu, Haoran Sun, Chong Li, Jiyu Liu, Xin Zhang, Jizhe Yang, Yuhong Duan, Yuhai Bi, Juan Pu, Yipeng Sun, Qi Tong, Yongqiang Wang, Xiangjun Du, Yuelong Shu, Kin-Chow Chang, Jinhua Liu,

Pandemic influenza, typically caused by the reassortment of human and avian influenza viruses, can result in severe or fatal infections in humans. Timely identification of potential pandemic viruses must be a priority in influenza virus surveillance. However, the range of host species responsible for the generation of novel pandemic influenza ... Read more >>

Emerg Microbes Infect (Emerging microbes & infections)
[2021, 10(1):472-480]

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Progress and Challenge in Computational Identification of Influenza Virus Reassortment.

Xiao Ding, Luyao Qin, Jing Meng, Yousong Peng, Aiping Wu, Taijiao Jiang,

Genomic reassortment is an important evolutionary mechanism for influenza viruses. In this process, the novel viruses acquire new characteristics by the exchange of the intact gene segments among multiple influenza virus genomes, which may cause flu endemics and epidemics within or even across hosts. Due to the safety and ethical ... Read more >>

Virol Sin (Virologica Sinica)
[2021, :]

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Joint inference of migration and reassortment patterns for viruses with segment genomes

Ugnė Stolz, Tanja Stadler, Nicola Müller, Timothy Vaughan,

The structured coalescent allows inferring migration patterns between viral sub-populations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different ... Read more >>

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Phylogenetic Analysis of Massilia phlebovirus in Portugal

Fátima Amaro, Líbia Zé-Zé, José Lourenço, Marta Giovanetti, Stefanie Christine Becker, Maria João Alves,

In the last two decades, molecular surveys of arboviruses have enabled the identification of several new viruses, contributing to the knowledge of viral diversity and providing important epidemiological data regarding possible new emerging viruses. A combination of diagnostic assays, Illumina sequencing and phylogenetic inference are here used to characterize two ... Read more >>

Viruses (Viruses)
[2021, 13(7):]

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RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks

Alexey Markin, Sanket Wagle, Tavis Anderson, Oliver Eulenstein,

<h4>Motivation</h4> A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g., hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we ... Read more >>

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Diversity and Reassortment Rate of Influenza a Viruses in Wild Ducks and Gulls

Yulia Postnikova, Anastasia Treshchalina, Elizaveta Boravleva, Alexandra Gambaryan, Aydar Ishmukhametov, Mikhail Matrosovich, Ron A.M. Fouchier, Galina Sadykova, Alexei Prilipov, Natalia Lomakina,

Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of ... Read more >>

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Pathogenic assessment of avian influenza viruses in migratory birds.

Eun-Ha Kim, Young-Ll Kim, Se Mi Kim, Kwang-Min Yu, Mark Anthony B Casel, Seung-Gyu Jang, Philippe Noriel Q Pascua, Richard J Webby, Young Ki Choi,

<b>ABSTRACT</b>Several subtypes of avian influenza (AI) viruses have caused human infections in recent years; however, there is a severe knowledge gap regarding the capacity of wild bird viruses to infect mammals. To assess the risk of mammalian infection by AI viruses from their natural reservoirs, a panel of isolates from ... Read more >>

Emerg Microbes Infect (Emerging microbes & infections)
[2021, 10(1):565-577]

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Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals.

Ketaki Ganti, Anish Bagga, Juliana DaSilva, Samuel S Shepard, John R Barnes, Susan Shriner, Katia Koelle, Anice C Lowen,

Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped ... Read more >>

Viruses (Viruses)
[2021, 13(3):]

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Innate Antiviral Cytokine Response to Swine Influenza Virus by Swine Respiratory Epithelial Cells.

Abhijeet A Bakre, Les P Jones, Jackelyn Murray, Z Beau Reneer, Victoria A Meliopoulos, Sean Cherry, Stacey Schultz-Cherry, Ralph A Tripp,

Swine influenza virus (SIV) can cause respiratory illness in swine. Swine contribute to influenza virus reassortment, as avian, human, and/or swine influenza viruses can infect swine and reassort, and new viruses can emerge. Thus, it is important to determine the host antiviral responses that affect SIV replication. In this study, ... Read more >>

J Virol (Journal of virology)
[2021, 95(15):e0069221]

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Influenza D virus in respiratory disease in Canadian, province of Québec, cattle: Relative importance and evidence of new reassortment between different clades.

Claude Saegerman, Maria Gaudino, Christian Savard, André Broes, Olivier Ariel, Gilles Meyer, Mariette F Ducatez,

<h4>Background</h4>Influenza D virus (IDV), a segmented single-stranded negative-sense ribonucleic acid (RNA) virus, belongs to the new Delta influenza virus genus of the Orthomyxoviridae family. Cattle were proposed as the natural reservoir of IDV in which infection was associated with mild-to-moderate respiratory clinical signs (i.e. cough, nasal discharge and dyspnoea).<h4>Methods and ... Read more >>

Transbound Emerg Dis (Transboundary and emerging diseases)
[2021, :]

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Avian influenza A viruses reassort and diversify differently in mallards and mammals

Ketaki Ganti, Anish Bagga, Juliana DaSilva, Samuel Shepard, John Barnes, Susan Shriner, Katia Koelle, Anice Lowen,

Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped ... Read more >>

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Reassortment and Persistence of Influenza A Viruses from Diverse Geographic Origins within Australian Wild Birds: Evidence from a Small, Isolated Population of Ruddy Turnstones.

Bethany J Hoye, Celeste M Donato, Simeon Lisovski, Yi-Mo Deng, Simone Warner, Aeron C Hurt, Marcel Klaassen, Dhanasekaran Vijaykrishna,

Australian lineages of avian influenza A viruses (AIVs) are thought to be phylogenetically distinct from those circulating in Eurasia and the Americas, suggesting the circulation of endemic viruses seeded by occasional introductions from other regions. However, processes underlying the introduction, evolution and maintenance of AIVs in Australia remain poorly understood. ... Read more >>

J Virol (Journal of virology)
[2021, 95(9):]

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Reassortment with dominant chicken H9N2 influenza virus contributed to the fifth H7N9 virus human epidemic.

Juan Pu, Yanbo Yin, Jiyu Liu, Xinyu Wang, Yong Zhou, Zejiang Wang, Yipeng Sun, Honglei Sun, Fangtao Li, Jingwei Song, Runkang Qu, Weihua Gao, Dongdong Wang, Zhen Wang, Shijie Yan, Mingyue Chen, Jinfeng Zeng, Zhimin Jiang, Haoran Sun, Yanan Zong, Chenxi Wang, Qi Tong, Yuhai Bi, Yinhua Huang, Xiangjun Du, Kin-Chow Chang, Jinhua Liu,

H9N2 Avian influenza virus (AIV) is regarded as a principal donor of viral genes through reassortment to co-circulating influenza viruses that can result in zoonotic reassortants. Whether H9N2 virus can maintain sustained evolutionary impact on such reassortants is unclear. Since 2013, avian H7N9 virus had caused five sequential human epidemics ... Read more >>

J Virol (Journal of virology)
[2021, :]

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Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia.

Marlen Martinez-Gutierrez, Estiven Hernandez-Mira, Santiago Rendon-Marin, Julian Ruiz-Saenz,

Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the <i>Reoviridae</i> family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and ... Read more >>

Viruses (Viruses)
[2021, 13(6):]

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Resistance-breaking tomato spotted wilt virus variant that recently occurred in pepper in South Korea is a genetic reassortant.

Sun-Jung Kwon, Young-Eun Cho, Oh-Hun Kwon, Hyung-Gon Kang, Jang-Kyun Seo,

Tomato spotted wilt virus (TSWV) is a destructive viral pathogen in various crops, including pepper. While the single dominant gene Tsw has been utilized in pepper breeding to confer resistance to TSWV, the occurrence of TSWV variants that overcome Tsw-mediated resistance has been reported in various countries after several years ... Read more >>

Plant Dis (Plant disease)
[2021, :]

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Biological Properties and Genetic Characterization of Novel Low Pathogenic H7N3 Avian Influenza Viruses Isolated from Mallard Ducks in the Caspian Region, Dagestan, Russia.

Marina Gulyaeva, Maria Alessandra De Marco, Ganna Kovalenko, Eric Bortz, Tatiana Murashkina, Kseniya Yurchenko, Marzia Facchini, Mauro Delogu, Ivan Sobolev, Alimurad Gadzhiev, Kirill Sharshov, Alexander Shestopalov,

Avian influenza viruses (AIVs) are maintained in wild bird reservoirs, particularly in mallard ducks and other waterfowl. Novel evolutionary lineages of AIV that arise through genetic drift or reassortment can spread with wild bird migrations to new regions, infect a wide variety of resident bird species, and spillover to domestic ... Read more >>

Microorganisms (Microorganisms)
[2021, 9(4):]

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Genetic Characterization and Pathogenesis of Avian Influenza Virus H7N3 Isolated from Spot-Billed Ducks in South Korea, Early 2019.

Thuy-Tien Thi Trinh, Indira Tiwari, Kaliannan Durairaj, Bao Tuan Duong, Anh Thi Viet Nguyen, Hien Thi Tuong, Vui Thi Hoang, Duong Duc Than, SunJeong Nam, Seon-Ju Yeo, Hyun Park,

Low-pathogenicity avian influenza viruses (LPAIV) introduced by migratory birds circulate in wild birds and can be transmitted to poultry. These viruses can mutate to become highly pathogenic avian influenza viruses causing severe disease and death in poultry. In March 2019, an H7N3 avian influenza virus-A/Spot-billed duck/South Korea/WKU2019-1/2019 (H7N3)-was isolated from ... Read more >>

Viruses (Viruses)
[2021, 13(5):]

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Taxonomy of Phleboviruses, Emphasizing Those That Are Sandfly-Borne.

Charles H Calisher, Mattia Calzolari,

Sandfly-borne phleboviruses (phylum <i>Negarnavaricota</i>, realm <i>Riboviria</i>, kingdom <i>Orthornavirae</i>, genus <i>Phlebovirus</i>) comprise three genome segments of ribonucleic acid (RNA) and which encode an RNA-dependent RNA polymerase, which they use to transcribe the viral RNA genome into messenger RNA and to replicate the genome. At least some of these viruses cause mild ... Read more >>

Viruses (Viruses)
[2021, 13(5):]

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FluReassort: a database for the study of genomic reassortments among influenza viruses.

Xiao Ding, Xuye Yuan, Longfei Mao, Aiping Wu, Taijiao Jiang,

Genomic reassortment is an important genetic event in the generation of emerging influenza viruses, which can cause numerous serious flu endemics and epidemics within hosts or even across different hosts. However, there is no dedicated and comprehensive repository for reassortment events among influenza viruses. Here, we present FluReassort, a database ... Read more >>

Brief Bioinform (Briefings in bioinformatics)
[2020, 21(6):2126-2132]

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Antibodies to Highly Pathogenic A/H5Nx (Clade 2.3.4.4) Influenza Viruses in the Sera of Vietnamese Residents.

Tatyana Ilyicheva, Vasily Marchenko, Olga Pyankova, Anastasia Moiseeva, Tran Thi Nhai, Bui Thi Lan Anh, Trinh Khac Sau, Andrey Kuznetsov, Alexander Ryzhikov, Rinat Maksyutov,

To cause a pandemic, an influenza virus has to overcome two main barriers. First, the virus has to be antigenically new to humans. Second, the virus has to be directly transmitted from humans to humans. Thus, if the avian influenza virus is able to pass the second barrier, it could ... Read more >>

Pathogens (Pathogens (Basel, Switzerland))
[2021, 10(4):]

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Highly Pathogenic Avian Influenza A(H5N8) Virus Clade 2.3.4.4b, Western Siberia, Russia, 2020.

Ivan Sobolev, Kirill Sharshov, Nikita Dubovitskiy, Olga Kurskaya, Alexander Alekseev, Sergey Leonov, Yuriy Yushkov, Victor Irza, Andrey Komissarov, Artem Fadeev, Daria Danilenko, Junki Mine, Ryota Tsunekuni, Yuko Uchida, Takehiko Saito, Alexander Shestopalov,

Two variants of highly pathogenic avian influenza A(H5N8) virus were detected in dead poultry in Western Siberia, Russia, during August and September 2020. One variant was represented by viruses of clade 2.3.4.4b and the other by a novel reassortant between clade 2.3.4.4b and Eurasian low pathogenicity avian influenza viruses circulating ... Read more >>

Emerg Infect Dis (Emerging infectious diseases)
[2021, 27(8):2224-2227]

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Two Different Strains of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in North and South Osaka by Phylogenetic Analysis of Evolutionary Lineage: Evidence for Independent SFTSV Transmission.

Ryo Ikemori, Ikuko Aoyama, Tadahiro Sasaki, Hirono Takabayashi, Kazutoshi Morisada, Masaru Kinoshita, Kazuyoshi Ikuta, Takahiro Yumisashi, Kazushi Motomura,

Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne infectious disease, therefore, the information on the whole genome of the SFTS virus (SFTSV) is still limited. This study demonstrates a nearly whole genome of the SFTSV identified in Osaka in 2017 and 2018 by next-generation sequencing (NGS). The evolutionary ... Read more >>

Viruses (Viruses)
[2021, 13(2):]

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Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic.

Virginie Banga-Mingo, Mathew D Esona, Naga S Betrapally, Rashi Gautam, Jose Jaimes, Eric Katz, Diane Waku-Kouomou, Michael D Bowen, Ionela Gouandjika-Vasilache,

<h4>Objective</h4>Rotavirus A (RVA) remains the main causative agent of gastroenteritis in young children and the young of many mammalian and avian species. In this study we describe a RVA strain detected from a 6-month-old child from Central African Republic (CAR).<h4>Results</h4>We report the 11 open reading frame sequences of a G29-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 ... Read more >>

BMC Res Notes (BMC research notes)
[2021, 14(1):218]

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