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1.
Artigo em Inglês | MEDLINE | ID: mdl-34894077

RESUMO

BACKGROUND: Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS: We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS: In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS: This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.

3.
Viruses ; 13(10)2021 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-34696495

RESUMO

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.


Assuntos
COVID-19/epidemiologia , Genoma Viral/genética , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/transmissão , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Limite de Detecção , Filogenia , SARS-CoV-2/isolamento & purificação , Glicoproteína da Espícula de Coronavírus/genética
4.
Arch Virol ; 166(12): 3513-3566, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34463877

RESUMO

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

5.
Vaccines (Basel) ; 9(5)2021 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-34066605

RESUMO

When swine flu vaccines and circulating influenza A virus (IAV) strains are poorly matched, vaccine-induced antibodies may not protect from infection. Highly conserved T cell epitopes may, however, have a disease-mitigating effect. The degree of T cell epitope conservation among circulating strains and vaccine strains can vary, which may also explain differences in vaccine efficacy. Here, we evaluate a previously developed conserved T cell epitope-based vaccine and determine the persistence of T cell epitope conservation over time. We used a pair-wise homology score to define the conservation between the vaccine's swine leukocyte antigen (SLA) class I and II-restricted epitopes and T cell epitopes found in 1272 swine IAV strains sequenced between 2013 and 2017. Twenty-four of the 48 total T cell epitopes included in the epitope-based vaccine were highly conserved and found in >1000 circulating swine IAV strains over the 5-year period. In contrast, commercial swine IAV vaccines developed in 2013 exhibited a declining conservation with the circulating IAV strains over the same 5-year period. Conserved T cell epitope vaccines may be a useful adjunct for commercial swine flu vaccines and to improve protection against influenza when antibodies are not cross-reactive.

7.
Emerg Infect Dis ; 27(6): 1-9, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34013862

RESUMO

Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus.


Assuntos
Infecções por Vírus Respiratório Sincicial , Vírus Sincicial Respiratório Humano , Criança , Variação Genética , Genótipo , Humanos , Epidemiologia Molecular , Filogenia , Vírus Sincicial Respiratório Humano/genética
8.
Front Immunol ; 12: 642791, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33746985

RESUMO

Background: The overall performance of a multiple component vaccine assessed by the vaccine-elicited immune responses across various strains in a repeated vaccination setting has not been well-studied, and the comparison between adults and teenagers is yet to be made. Methods: A human cohort study was conducted at the University of Georgia, with 140 subjects (86 adults and 54 teenagers) repeatedly vaccinated in the 2017/2018 and 2018/2019 influenza seasons. Host information was prospectively collected, and serum samples were collected before and after vaccination in each season. The association between host factors and repeated measures of hemagglutination inhibition (HAI) composite scores was assessed by generalized linear models with generalized estimating equations. Results: The mean HAI composite scores for the entire sample (t = 4.26, df = 139, p < 0.001) and the teenager group (t = 6.44, df = 53, p < 0.001) declined in the second season, while the changes in the adults were not statistically significant (t = -1.14, df = 85, p = 0.26). A mixture pattern of changes in both directions was observed in the adults when stratified by prior vaccination. In addition, the regression analysis suggested an interactive effect of age and BMI on the HAI composite scores in the overall population (beta = 0.005; 95% CI, 0.0008-0.01) and the adults (beta = 0.005; 95% CI, 0.0005-0.01). Conclusions: Our study found distinct vaccine-elicited immune responses between adults and teenagers when both were repeatedly vaccinated in consecutive years. An interactive effect of age and BMI on the HAI composite scores were identified in the overall population and the adults.


Assuntos
Anticorpos Antivirais/sangue , Vacinas contra Influenza/imunologia , Vacinação , Adolescente , Adulto , Fatores Etários , Índice de Massa Corporal , Estudos de Coortes , Feminino , Testes de Inibição da Hemaglutinação , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Adulto Jovem
9.
Sci Rep ; 11(1): 3325, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33558579

RESUMO

This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010-2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.


Assuntos
Infecções por HIV , HIV-1 , Adulto , Infecções por HIV/epidemiologia , Infecções por HIV/etnologia , Infecções por HIV/transmissão , Humanos , Masculino , Texas/epidemiologia , Texas/etnologia
10.
Arch Virol ; 165(12): 3023-3072, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32888050

RESUMO

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.


Assuntos
Mononegavirais/classificação , Terminologia como Assunto
11.
Infect Genet Evol ; 84: 104376, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32454244

RESUMO

The HIV-1 epidemic is a remarkable public health concern in China, especially in developed trade areas. We aimed to investigate the interaction of migration with the local transmission network in a typical trade area, Yiwu City, the world's largest commodity distribution center. Based on 390 pol sequences from 413 participants diagnosed between 2014 and 2016, putative transmission clusters and the underlying demographic and behavioral characteristics were analyzed. Recent infection status was determined by HIV-1 limiting antigen avidity enzyme immunoassay to identify active clusters. Multiple subtypes were identified, with a predominance of CRF01_AE (47.4%) and CRF07_BC (40.8%), followed by 9 other subtypes and 8 URFs. Multivariable analyses revealed that individuals in clusters were more likely to be local residents, infected through heterosexual behaviors, and infected with CRF01_AE (P < .05). Of men who have sex with men (MSM), 81% were linked to other MSM, and only 3% were linked to heterosexual women. Of heterosexual women, 67% were linked to heterosexual men, and 11% to MSM. Yiwu residents were more likely to link to locals than that of migrants (43% vs 20%, P < .001). By contrast, local MSM and migrant MSM all had high percentages of linkage to migrant MSM (57% vs 69%, P = .069). Our findings reveal that migration promotes the dissemination and dynamic change of HIV, which are interwoven between locals and migrants. The results highlight the far-reaching influence of migrant MSM on the local HIV transmission network.


Assuntos
Infecções por HIV/transmissão , HIV-1 , Adulto , China/epidemiologia , Busca de Comunicante , Demografia , Feminino , Infecções por HIV/epidemiologia , Infecções por HIV/virologia , Humanos , Masculino , Epidemiologia Molecular , Estudos Retrospectivos , Adulto Jovem
12.
PLoS One ; 15(1): e0227558, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31923213

RESUMO

Respiratory syncytial virus (RSV) is a nonsegmented negative-strand RNA virus (NSV) and a leading cause of severe lower respiratory tract illness in infants and the elderly. Transcription of the ten RSV genes proceeds sequentially from the 3' promoter and requires conserved gene start (GS) and gene end (GE) signals. Previous studies using the prototypical GA1 genotype Long and A2 strains have indicated a gradient of gene transcription extending across the genome, with the highest level of mRNA coming from the most promoter-proximal gene, the first nonstructural (NS1) gene, and mRNA levels from subsequent genes dropping until reaching a minimum at the most promoter-distal gene, the polymerase (L) gene. However, recent reports show non-gradient levels of mRNA, with higher than expected levels from the attachment (G) gene. It is unknown to what extent different transcript stabilities might shape measured mRNA levels. It is also unclear whether patterns of RSV gene expression vary, or show strain- or genotype-dependence. To address this, mRNA abundances from five RSV genes were measured by quantitative real-time PCR (qPCR) in three cell lines and in cotton rats infected with RSV isolates belonging to four genotypes (GA1, ON, GB1, BA). Relative mRNA levels reached steady-state between four and 24 hours post-infection. Steady-state patterns were non-gradient and genotype-specific, where mRNA levels from the G gene exceeded those from the more promoter-proximal nucleocapsid (N) gene across isolates. Transcript stabilities could not account for the non-gradient patterns observed, indicating that relative mRNA levels more strongly reflect transcription than decay. Our results indicate that gene expression from a small but diverse set of RSV genotypes is non-gradient and genotype-dependent. We propose novel models of RSV transcription that can account for non-gradient transcription.


Assuntos
RNA Viral/metabolismo , Vírus Sincicial Respiratório Humano/genética , Transcrição Genética , Monofosfato de Adenosina/análogos & derivados , Monofosfato de Adenosina/farmacologia , Alanina/análogos & derivados , Alanina/farmacologia , Animais , Linhagem Celular , Feminino , Genótipo , Meia-Vida , Humanos , Masculino , Estabilidade de RNA , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Viral/genética , Infecções por Vírus Respiratório Sincicial/patologia , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/isolamento & purificação , Sigmodontinae , Transcrição Genética/efeitos dos fármacos , Replicação Viral
13.
PLoS Pathog ; 16(1): e1007857, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31961906

RESUMO

The 2014-2015 highly pathogenic avian influenza (HPAI) H5NX outbreak represents the largest and most expensive HPAI outbreak in the United States to date. Despite extensive traditional and molecular epidemiological studies, factors associated with the spread of HPAI among midwestern poultry premises remain unclear. To better understand the dynamics of this outbreak, 182 full genome HPAI H5N2 sequences isolated from commercial layer chicken and turkey production premises were analyzed using evolutionary models able to accommodate epidemiological and geographic information. Epidemiological compartmental models embedded in a phylogenetic framework provided evidence that poultry type acted as a barrier to the transmission of virus among midwestern poultry farms. Furthermore, after initial introduction, the propagation of HPAI cases was self-sustainable within the commercial poultry industries. Discrete trait diffusion models indicated that within state viral transitions occurred more frequently than inter-state transitions. Distance and sample size were very strongly supported as associated with viral transition between county groups (Bayes Factor > 30.0). Together these findings indicate that the different types of midwestern poultry industries were not a single homogenous population, but rather, the outbreak was shaped by poultry industries and geographic factors.


Assuntos
Vírus da Influenza A Subtipo H5N2/isolamento & purificação , Influenza Aviária/epidemiologia , Doenças das Aves Domésticas/epidemiologia , Agricultura , Animais , Surtos de Doenças , Evolução Molecular , Geografia , Vírus da Influenza A Subtipo H5N2/classificação , Vírus da Influenza A Subtipo H5N2/genética , Influenza Aviária/transmissão , Influenza Aviária/virologia , Filogenia , Aves Domésticas , Doenças das Aves Domésticas/transmissão , Doenças das Aves Domésticas/virologia , Estados Unidos/epidemiologia
14.
Transbound Emerg Dis ; 67(2): 844-851, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31675474

RESUMO

The H5N8 highly pathogenic avian influenza viruses (HPAIVs) belonging to clade 2.3.4.4 spread from Eastern China to Korea in 2014 and caused outbreaks in domestic poultry until 2016. To understand how H5N8 HPAIVs spread at host species level in Korea during 2014-2016, a Bayesian phylogenetic analysis was used for ancestral state reconstruction and estimation of the host transition dynamics between wild waterfowl, domestic ducks and chickens. Our data support that H5N8 HPAIV most likely transmitted from wild waterfowl to domestic ducks, and then maintained in domestic ducks followed by dispersal of HPAIV from domestic ducks to chickens, suggesting domestic duck population plays a central role in the maintenance, amplification and spread of wild HPAIV to terrestrial poultry in Korea.


Assuntos
Anseriformes/virologia , Galinhas/virologia , Surtos de Doenças/veterinária , Vírus da Influenza A Subtipo H5N8/fisiologia , Influenza Aviária/transmissão , Doenças das Aves Domésticas/transmissão , Aves Domésticas/virologia , Animais , Teorema de Bayes , Patos/virologia , Vírus da Influenza A Subtipo H5N8/genética , Vírus da Influenza A Subtipo H5N8/patogenicidade , Influenza Aviária/epidemiologia , Influenza Aviária/virologia , Filogenia , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/virologia , República da Coreia/epidemiologia
15.
Emerg Microbes Infect ; 8(1): 1370-1382, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31526249

RESUMO

Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016-2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.


Assuntos
Coinfecção/veterinária , Monitoramento Epidemiológico/veterinária , Evolução Molecular , Virus da Influenza A Subtipo H5N1/genética , Vírus da Influenza A Subtipo H9N2/genética , Vírus Reordenados , Animais , Galinhas , Coinfecção/epidemiologia , Coinfecção/virologia , Patos , Egito/epidemiologia , Virus da Influenza A Subtipo H5N1/isolamento & purificação , Vírus da Influenza A Subtipo H9N2/isolamento & purificação , Influenza Aviária/epidemiologia , Influenza Aviária/transmissão , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/virologia , Homologia de Sequência , Proteínas Virais/genética
16.
Infect Genet Evol ; 74: 103917, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31200111

RESUMO

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.


Assuntos
Vírus da Doença de Newcastle/classificação , RNA Viral/genética , Análise de Sequência de RNA/métodos , Teorema de Bayes , Consenso , Curadoria de Dados , Bases de Dados Genéticas , Genótipo , Guias como Assunto , Cooperação Internacional , Funções Verossimilhança , Vírus da Doença de Newcastle/genética , Filogenia
17.
Vaccines (Basel) ; 7(2)2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31141933

RESUMO

The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.

18.
BMC Evol Biol ; 19(1): 108, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31126244

RESUMO

BACKGROUND: Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was employed to estimate the evolutionary history of 1602 complete fusion gene APMV-1 sequences collected from 1970 to 2016 in order to infer viral transmission between avian host orders and diffusion among geographic regions. Ancestral states were estimated with a non-reversible continuous-time Markov chain model, allowing transition rates between discrete states to be calculated. The evolutionary analyses were stratified by APMV-1 classes I (n = 198) and II (n = 1404), and only those sequences collected between 2006 and 2016 were allowed to contribute host and location information to the viral migration networks. RESULTS: While the current data was unable to assess impact of host domestication status on APMV-1 diffusion, these analyses supported the sharing of APMV-1 among divergent host taxa. The highest supported transition rate for both classes existed from domestic chickens to Anseriformes (class I:6.18 transitions/year, 95% highest posterior density (HPD) 0.31-20.02, Bayes factor (BF) = 367.2; class II:2.88 transitions/year, 95%HPD 1.9-4.06, BF = 34,582.9). Further, among class II viruses, domestic chickens also acted as a source for Columbiformes (BF = 34,582.9), other Galliformes (BF = 34,582.9), and Psittaciformes (BF = 34,582.9). Columbiformes was also a highly supported source to Anseriformes (BF = 322.0) and domestic chickens (BF = 402.6). Additionally, our results provide support for the diffusion of viruses among continents and regions, but no interhemispheric viral exchange between 2006 and 2016. Among class II viruses, the highest transition rates were estimated from South Asia to the Middle East (1.21 transitions/year; 95%HPD 0.36-2.45; BF = 67,107.8), from Europe to East Asia (1.17 transitions/year; 95%HPD 0.12-2.61; BF = 436.2) and from Europe to Africa (1.06 transitions/year, 95%HPD 0.07-2.51; BF = 169.3). CONCLUSIONS: While migration appears to occur infrequently, geographic movement may be important in determining viral diversification and population structure. In contrast, inter-order transmission of APMV-1 may occur readily, but most events are transient with few lineages persisting in novel hosts.


Assuntos
Interações Hospedeiro-Patógeno , Internacionalidade , Doença de Newcastle/transmissão , Doença de Newcastle/virologia , Vírus da Doença de Newcastle/classificação , Filogenia , África , Animais , Ásia , Viés , Galinhas/virologia , Europa (Continente) , Genótipo , Geografia , Vírus da Doença de Newcastle/genética , Estados Unidos
19.
J Virol ; 93(2)2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30381492

RESUMO

Recently, two genetically distinct influenza viruses were detected in bats in Guatemala and Peru. We conducted influenza A virus surveillance among four bat species in Egypt. Out of 1,202 swab specimens, 105 were positive by real-time PCR. A virus was successfully isolated in eggs and propagated in MDCK cells in the presence of N-tosyl-l-phenylalanine chloromethyl ketone-treated trypsin. Genomic analysis revealed that the virus was phylogenetically distinct from all other influenza A viruses. Analysis of the hemagglutinin gene suggested a common ancestry with other H9 viruses, and the virus showed a low level of cross-reactivity with serum raised against H9N2 viruses. Bats were seropositive for the isolated viruses. The virus replicated in the lungs of experimentally infected mice. While it is genetically distinct, this virus shares several avian influenza virus characteristics suggesting a more recent avian host origin.IMPORTANCE Through surveillance, we isolated and characterized an influenza A virus from Egyptian fruit bats. This virus had an affinity to avian-like receptors but was also able to infect mice. Our findings indicate that bats may harbor a diversity of influenza A viruses. Such viruses may have the potential to cross the species barrier to infect other species, including domestic birds, mammals, and, possibly, humans.


Assuntos
Quirópteros/virologia , Vírus da Influenza A/classificação , Infecções por Orthomyxoviridae/imunologia , RNA Viral/genética , Análise de Sequência de RNA/métodos , Animais , Anticorpos Antivirais/metabolismo , Galinhas , Cães , Egito , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Pulmão/virologia , Células Madin Darby de Rim Canino , Infecções por Orthomyxoviridae/virologia , Filogenia
20.
Emerg Infect Dis ; 24(10): 1840-1848, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30226167

RESUMO

Eurasia highly pathogenic avian influenza virus (HPAIV) H5 clade 2.3.4.4 emerged in North America at the end of 2014 and caused outbreaks affecting >50 million poultry in the United States before eradication in June 2015. We investigated the underlying ecologic and epidemiologic processes associated with this viral spread by performing a comparative genomic study using 268 full-length genome sequences and data from outbreak investigations. Reassortant HPAIV H5N2 circulated in wild birds along the Pacific flyway before several spillover events transmitting the virus to poultry farms. Our analysis suggests that >3 separate introductions of HPAIV H5N2 into Midwest states occurred during March-June 2015; transmission to Midwest poultry farms from Pacific wild birds occurred ≈1.7-2.4 months before detection. Once established in poultry, the virus rapidly spread between turkey and chicken farms in neighboring states. Enhanced biosecurity is required to prevent the introduction and dissemination of HPAIV across the poultry industry.


Assuntos
Vírus da Influenza A/classificação , Vírus da Influenza A/genética , Influenza Aviária/transmissão , Influenza Aviária/virologia , Doenças das Aves Domésticas/transmissão , Doenças das Aves Domésticas/virologia , Animais , Teorema de Bayes , Surtos de Doenças , Genoma Viral , História do Século XXI , Vírus da Influenza A/patogenicidade , Influenza Aviária/epidemiologia , Influenza Aviária/história , América do Norte/epidemiologia , Filogenia , Aves Domésticas , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/história , RNA Viral , Vírus Reordenados
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