Last data update: Jun 24, 2024. (Total: 47078 publications since 2009)
Records 1-11 (of 11 Records) |
Query Trace: Balish Amanda [original query] |
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Avian influenza surveillance in domestic waterfowl and environment of live bird markets in Bangladesh, 2007-2012.
Khan SU , Gurley ES , Gerloff N , Rahman MZ , Simpson N , Rahman M , Haider N , Chowdhury S , Balish A , Zaman RU , Nasreen S , Chandra Das B , Azziz-Baumgartner E , Sturm-Ramirez K , Davis CT , Donis RO , Luby SP . Sci Rep 2018 8 (1) 9396 Avian influenza viruses, including highly pathogenic strains, pose severe economic, animal and public health concerns. We implemented live bird market surveillance in Bangladesh to identify the subtypes of avian influenza A viruses in domestic waterfowl and market environments. We collected waterfowl samples monthly from 4 rural sites from 2007 to 2012 and environmental samples from 4 rural and 16 urban sites from 2009 to 2012. Samples were tested through real-time RT-PCR, virus culture, and sequencing to detect and characterize avian influenza A viruses. Among 4,308 waterfowl tested, 191 (4.4%) were positive for avian influenza A virus, including 74 (1.9%) avian influenza A/H5 subtype. The majority (99%, n = 73) of the influenza A/H5-positive samples were from healthy appearing waterfowl. Multiple subtypes, including H1N1, H1N3, H3N2, H3N6, H3N8, H4N1, H4N2, H4N6, H5N1 (clades 2.2.2, 2.3.2.1a, 2.3.4.2), H5N2, H6N1, H7N9, H9N2, H11N2 and H11N3, H11N6 were detected in waterfowl and environmental samples. Environmental samples tested positive for influenza A viruses throughout the year. Avian influenza viruses, including H5N1 and H9N2 subtypes were also identified in backyard and small-scale raised poultry. Live bird markets could be high-risk sites for harboring the viruses and have the potential to infect naive birds and humans exposed to them. |
Highly Pathogenic Avian Influenza A(H5N1) Viruses at the Animal-Human Interface in Vietnam, 2003-2010.
Creanga A , Hang NLK , Cuong VD , Nguyen HT , Phuong HVM , Thanh LT , Thach NC , Hien PT , Tung N , Jang Y , Balish A , Dang NH , Duong MT , Huong NT , Hoa DN , Tho ND , Klimov A , Kapella BK , Gubareva L , Kile JC , Hien NT , Mai LQ , Davis CT . J Infect Dis 2017 216 S529-s538 Mutation and reassortment of highly pathogenic avian influenza A(H5N1) viruses at the animal-human interface remain a major concern for emergence of viruses with pandemic potential. To understand the relationship of H5N1 viruses circulating in poultry and those isolated from humans, comprehensive phylogenetic and molecular analyses of viruses collected from both hosts in Vietnam between 2003 and 2010 were performed. We examined the temporal and spatial distribution of human cases relative to H5N1 poultry outbreaks and characterized the genetic lineages and amino acid substitutions in each gene segment identified in humans relative to closely related viruses from avian hosts. Six hemagglutinin clades and 8 genotypes were identified in humans, all of which were initially identified in poultry. Several amino acid mutations throughout the genomes of viruses isolated from humans were identified, indicating the potential for poultry viruses infecting humans to rapidly acquire molecular markers associated with mammalian adaptation and antiviral resistance. |
Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh.
Gerloff NA , Khan SU , Zanders N , Balish A , Haider N , Islam A , Chowdhury S , Rahman MZ , Haque A , Hosseini P , Gurley ES , Luby SP , Wentworth DE , Donis RO , Sturm-Ramirez K , Davis CT . PLoS One 2016 11 (3) e0152131 Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. These findings, combined with the seven year timeframe of sampling, indicate a continuous circulation of these viruses in the country. |
Generation and Characterization of Live Attenuated Influenza A(H7N9) Candidate Vaccine Virus Based on Russian Donor of Attenuation.
Shcherbik S , Pearce N , Balish A , Jones J , Thor S , Davis CT , Pearce M , Tumpey T , Cureton D , Chen LM , Villanueva J , Bousse TL . PLoS One 2015 10 (9) e0138951 BACKGROUND: Avian influenza A (H7N9) virus has emerged recently and continues to cause severe disease with a high mortality rate in humans prompting the development of candidate vaccine viruses. Live attenuated influenza vaccines (LAIV) are 6:2 reassortant viruses containing the HA and NA gene segments from wild type influenza viruses to induce protective immune responses and the six internal genes from Master Donor Viruses (MDV) to provide temperature sensitive, cold-adapted and attenuated phenotypes. METHODOLOGY/PRINCIPAL FINDINGS: LAIV candidate A/Anhui/1/2013(H7N9)-CDC-LV7A (abbreviated as CDC-LV7A), based on the Russian MDV, A/Leningrad/134/17/57 (H2N2), was generated by classical reassortment in eggs and retained MDV temperature-sensitive and cold-adapted phenotypes. CDC-LV7A had two amino acid substitutions N123D and N149D (H7 numbering) in HA and one substitution T10I in NA. To evaluate the role of these mutations on the replication capacity of the reassortants in eggs, the recombinant viruses A(H7N9)RG-LV1 and A(H7N9)RG-LV2 were generated by reverse genetics. These changes did not alter virus antigenicity as ferret antiserum to CDC-LV7A vaccine candidate inhibited hemagglutination by homologous A(H7N9) virus efficiently. Safety studies in ferrets confirmed that CDC-LV7A was attenuated compared to wild-type A/Anhui/1/2013. In addition, the genetic stability of this vaccine candidate was examined in eggs and ferrets by monitoring sequence changes acquired during virus replication in the two host models. No changes in the viral genome were detected after five passages in eggs. However, after ten passages additional mutations were detected in the HA gene. The vaccine candidate was shown to be stable in the ferret model; post-vaccination sequence data analysis showed no changes in viruses collected in nasal washes present at day 5 or day 7. CONCLUSIONS/SIGNIFICANCE: Our data indicate that the A/Anhui/1/2013(H7N9)-CDC-LV7A reassortant virus is a safe and genetically stable candidate vaccine virus that is now available for distribution by WHO to vaccine manufacturers. |
Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013.
Thor SW , Nguyen H , Balish A , Hoang AN , Gustin KM , Nhung PT , Jones J , Thu NN , Davis W , Ngoc TN , Jang Y , Sleeman K , Villanueva J , Kile J , Gubareva LV , Lindstrom S , Tumpey TM , Davis CT , Long NT . PLoS One 2015 10 (8) e0133867 Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses. |
Identification of molecular markers associated with alteration of receptor-binding specificity in a novel genotype of highly pathogenic avian influenza A(H5N1) viruses detected in Cambodia in 2013.
Rith S , Davis CT , Duong V , Sar B , Horm SV , Chin S , Ly S , Laurent D , Richner B , Oboho I , Jang Y , Davis W , Thor S , Balish A , Iuliano AD , Sorn S , Holl D , Sok T , Seng H , Tarantola A , Tsuyuoka R , Parry A , Chea N , Allal L , Kitsutani P , Warren D , Prouty M , Horwood P , Widdowson MA , Lindstrom S , Villanueva J , Donis R , Cox N , Buchy P . J Virol 2014 88 (23) 13897-909 Human infections with influenza A(H5N1) virus in Cambodia increased sharply during 2013. Molecular characterization of viruses detected in clinical specimens from human cases revealed the presence of mutations associated with alteration of receptor-binding specificity (K189R, Q222L) and respiratory droplet transmission in ferrets (N220K with Q222L). Discovery of quasispecies at position 222 (Q/L), in addition to absence of the mutations in poultry/environmental samples, suggested the mutations occurred during human infection and did not transmit further. |
Genetic characterization of clade 2.3.2.1 avian influenza A(H5N1) viruses, Indonesia, 2012.
Dharmayanti NL , Hartawan R , Wibawa H , Balish A , Donis R , Davis CT , Samaan G . Emerg Infect Dis 2014 20 (4) 677-80 After reports of unusually high mortality rates among ducks on farms in Java Island, Indonesia, in September 2012, influenza A(H5N1) viruses were detected and characterized. Sequence analyses revealed all genes clustered with contemporary clade 2.3.2.1 viruses, rather than enzootic clade 2.1.3 viruses, indicating the introduction of an exotic H5N1 clade into Indonesia. |
Multiple reassortment events among highly pathogenic avian influenza A(H5N1) viruses detected in Bangladesh.
Gerloff NA , Khan SU , Balish A , Shanta IS , Simpson N , Berman L , Haider N , Poh MK , Islam A , Gurley E , Hasnat MA , Dey T , Shu B , Emery S , Lindstrom S , Haque A , Klimov A , Villanueva J , Rahman M , Azziz-Baumgartner E , Ziaur Rahman M , Luby SP , Zeidner N , Donis RO , Sturm-Ramirez K , Davis CT . Virology 2014 450-451 297-307 In Bangladesh, little is known about the genomic composition and antigenicity of highly pathogenic avian influenza A(H5N1) viruses, their geographic distribution, temporal patterns, or gene flow within the avian host population. Forty highly pathogenic avian influenza A(H5N1) viruses isolated from humans and poultry in Bangladesh between 2008 and 2012 were analyzed by full genome sequencing and antigenic characterization. The analysis included viruses collected from avian hosts and environmental sampling in live bird markets, backyard poultry flocks, outbreak investigations in wild birds or poultry and from three human cases. Phylogenetic analysis indicated that the ancestors of these viruses reassorted (1) with other gene lineages of the same clade, (2) between different clades and (3) with low pathogenicity avian influenza A virus subtypes. Bayesian estimates of the time of most recent common ancestry, combined with geographic information, provided evidence of probable routes and timelines of virus spread into and out of Bangladesh. |
Evolution of highly pathogenic avian influenza (H5N1) virus populations in Vietnam between 2007 and 2010.
Nguyen T , Rivailler P , Davis CT , Thi Hoa D , Balish A , Hoang Dang N , Jones J , Thi Vui D , Simpson N , Thu Huong N , Shu B , Loughlin R , Ferdinand K , Lindstrom SE , York IA , Klimov A , Donis RO . Virology 2012 432 (2) 405-16 We report on the genetic analysis of 213 highly pathogenic avian influenza (HPAI) H5N1 viruses isolated from poultry in Vietnam between 2007 and 2010. Phylogenetic analyses of the viral genomes revealed 38 distinct viral genotypes, 29 were novel and 9 were reported in Vietnam or neighboring countries in recent years. Viruses from only six genotypes persisted beyond one season or year. Thus, most reassortant viruses were transient, suggesting that such genotypes lacked significant fitness advantages. Viruses with clade 2.3.2.1 HA were re-introduced into Vietnam in 2009 and their prevalence rose steeply towards the end of 2010. Clade 2.3.4-like viruses (genotype V) were predominant in northern Vietnam and caused the majority of zoonotic infections, whereas clade 1.1 (genotype Z) viruses were only detected in the Mekong delta region, in southern Vietnam. Antigenic analysis of representative viruses from the four clades indicated substantial drift. |
Epidemiological and virological characteristics of influenza in the Western Pacific Region of the World Health Organization, 2006-2010
Western Pacific Region Global Influenza Surveillance and Response System , Balish Amanda , Corwin Andrew , Kapella Bryan K , Kitsutani Paul , McFarland Jeffrey , Moen Ann , Xu Xiyan . PLoS One 2012 7 (5) e37568 BACKGROUND: Influenza causes yearly seasonal epidemics and periodic pandemics. Global systems have been established to monitor the evolution and impact of influenza viruses, yet regional analysis of surveillance findings has been limited. This study describes epidemiological and virological characteristics of influenza during 2006-2010 in the World Health Organization's Western Pacific Region. METHODOLOGY/PRINCIPAL FINDINGS: Influenza-like illness (ILI) and influenza virus data were obtained from the 14 countries with National Influenza Centres. Data were obtained directly from countries and from FluNet, the web-based tool of the Global Influenza Surveillance and Response System. National influenza surveillance and participation in the global system increased over the five years. Peaks in ILI reporting appeared to be coincident with the proportion of influenza positive specimens. Temporal patterns of ILI activity and the proportion of influenza positive specimens were clearly observed in temperate countries: Mongolia, Japan and the Republic of Korea in the northern hemisphere, and Australia, New Zealand, Fiji and New Caledonia (France) in the southern hemisphere. Two annual peaks in activity were observed in China from 2006 through the first quarter of 2009. A temporal pattern was less evident in tropical countries, where influenza activity was observed year-round. Influenza A viruses accounted for the majority of viruses reported between 2006 and 2009, but an equal proportion of influenza A and influenza B viruses was detected in 2010. CONCLUSIONS/SIGNIFICANCE: Despite differences in surveillance methods and intensity, commonalities in ILI and influenza virus circulation patterns were identified. Patterns suggest that influenza circulation may be dependent on a multitude of factors including seasonality and population movement. Dominant strains in Southeast Asian countries were later detected in other countries. Thus, timely reporting and regional sharing of information about influenza may serve as an early warning, and may assist countries to anticipate the potential severity and burden associated with incoming strains. |
Genetic analysis and antigenic characterization of swine origin influenza viruses isolated from humans in the United States, 1990-2010.
Shu B , Garten R , Emery S , Balish A , Cooper L , Sessions W , Deyde V , Smith C , Berman L , Klimov A , Lindstrom S , Xu X . Virology 2011 422 (1) 151-60 Swine influenza viruses (SIV) have been recognized as important pathogens for pigs and occasional human infections with swine origin influenza viruses (SOIV) have been reported. Between1990 and 2010, a total of twenty seven human cases of SOIV infections have been identified in the United States. Six viruses isolated from1990 to 1995 were recognized as classical SOIV (cSOIV) A(H1N1). After 1998, twenty-one SOIV recovered from human cases were characterized as triple reassortant (tr_SOIV) inheriting genes from classical swine, avian and human influenza viruses. Of those twenty-one tr_SOIV, thirteen were of A(H1N1), one of A(H1N2), and seven of A(H3N2) subtype. SOIV characterized were antigenically and genetically closely related to the subtypes of influenza viruses circulating in pigs but distinct from contemporary influenza viruses circulating in humans. The diversity of subtypes and genetic lineages in SOIV cases highlights the importance of continued surveillance at the animal-human interface. |
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