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1.
Pan Afr Med J ; 39: 129, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34527145

RESUMO

Rabies is a deadly viral disease transmitted through bites of infected animals. Outbreaks continue to escalate in Africa, with fatalities in humans, especially in rural areas, but are rarely reported. About 40% casualties occur among children of < 15 years. A 5-year-old boy on referral from a Primary Health Care Centre to a tertiary hospital presented with anxiety, confusion, agitation, hydrophobia, photo-phobia and aero-phobia, seven weeks after he was bitten by a stray dog in a rural community in Nigeria. The patient did not receive post-exposure prophylaxis and died 48 hours post admission. Confirmatory diagnosis was rabies and the phylogenetic analysis of the partial N-gene sequence of the virus localized it to Africa 2 (genotype 1) Lyssaviruses. There was 95.7-100% and 94.9-99.5% identity between the isolate and other genotype 1 Lyssaviruses and 100% homology with rabies viruses from Mali, Burkina Faso, Senegal and Central African Republic.


Assuntos
Mordeduras e Picadas/complicações , Vírus da Raiva/genética , Raiva/diagnóstico , Animais , Mordeduras e Picadas/virologia , Pré-Escolar , Cães , Evolução Fatal , Genótipo , Humanos , Masculino , Nigéria , Raiva/transmissão , Raiva/virologia , Vírus da Raiva/isolamento & purificação , População Rural
2.
Viruses ; 13(8)2021 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-34452311

RESUMO

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats.

3.
medRxiv ; 2021 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-33880478

RESUMO

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is an open-access qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that open-access, direct RT-PCR assays are a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.

4.
Transbound Emerg Dis ; 2021 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-33480188

RESUMO

Among recurrent sanitary emergencies able to spread rapidly worldwide, avian influenza is one of the main constraints for animal health and food security. In West Africa, Nigeria has been experiencing repeated outbreaks of different strains of avian influenza virus (AIV) since 2006 and is also recognized as a hot spot in the region for the introduction of emerging strains by migratory wild birds. Here, we generated complete genomes of 20 highly pathogenic avian influenza (HPAI) H5N8 viruses collected during active surveillance in Nigerian live bird markets (LBM) and from outbreaks reported in the country between 2016 and 2019. Phylogenetic analysis reveals that the Nigerian viruses cluster into four separate genetic groups within HPAI H5 clade 2.3.4.4b. The first group includes 2016-2017 Nigerian viruses with high genetic similarity to H5N8 viruses detected in Central African countries, while the second includes Nigerian viruses collected both in LBM and poultry farms (2018-2019), as well as in Cameroon, Egypt and Siberia. A natural reassortant strain identified in 2019 represents the third group: H5N8 viruses with the same gene constellation were identified in 2018 in South Africa. Finally, the fourth introduction represents the first detection in the African continent of the H5N6 subtype, which is related to European viruses. Bayesian phylogeographic analyses confirmed that the four introductions originated from different sources and provide evidence of the virus spread within Nigeria, as well as diffusion beyond its borders. The multiple epidemiological links between Nigeria, Central and Southern African countries highlight the need for harmonized and coordinated surveillance system to control AIV impact. Improved surveillance at the Wetlands, LBMs and early warning of outbreaks are crucial for prevention and control of AIV, which can be potentially zoonotic and be a threat to human health.

5.
Transbound Emerg Dis ; 68(3): 1253-1262, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-32770642

RESUMO

Since November 2018, several countries in West and Central Africa have reported mortalities in donkeys and horses. Specifically, more than 66,000 horses and donkeys have succumbed to disease in Burkina Faso, Chad, Cameroon, The Gambia, Ghana, Mali, Niger, Nigeria, and Senegal. Strangles caused by Streptococcus equi subsp equi, African Horse Sickness (AHS) virus, and Equine influenza virus (EIV) were all suspected as potential causative agents. This study reports the identification of EIV in field samples collected in Niger and Senegal. Phylogenetic analysis of the hemagglutinin and neuraminidase genes revealed that the identified viruses belonged to clade 1 of the Florida sublineage and were very similar to viruses identified in Nigeria in 2019. Interestingly, they were also more similar to EIVs from recent outbreaks in South America than to those in Europe and the USA. This is one of the first reports providing detailed description and characterization of EIVs in West and Central Africa region.


Assuntos
Surtos de Doenças/veterinária , Doenças dos Cavalos/epidemiologia , Vírus da Influenza A Subtipo H3N8/genética , Infecções por Orthomyxoviridae/veterinária , Animais , Genes Virais , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Doenças dos Cavalos/transmissão , Doenças dos Cavalos/virologia , Cavalos , Vírus da Influenza A Subtipo H3N8/classificação , Neuraminidase/genética , Níger/epidemiologia , Infecções por Orthomyxoviridae/epidemiologia , Infecções por Orthomyxoviridae/transmissão , Infecções por Orthomyxoviridae/virologia , Filogenia , Senegal/epidemiologia
6.
Vet Microbiol ; 248: 108820, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32891950

RESUMO

In December 2018, suspected outbreaks of equine influenza (EI) were observed in donkeys in Sokoto State, in the extreme northwest of Nigeria bordering the Republic of the Niger. Equine influenza virus (EIV) subtype H3N8 was the etiologic agent identified in the outbreaks using real-time RT-qPCR and sequencing of both the partial haemagglutinin (HA) gene and the complete genome. Since then the H3N8 virus spread to 7 of the 19 northern states of Nigeria, where it affected both donkeys and horses. Phylogenetic analysis of the partial and complete HA gene revealed the closest nucleotide similarity (99.7%) with EIVs belonging to the Florida clade 1 (Fc-1) of the American lineage isolated in 2018 from Argentina and Chile. In total, 80 amino acid substitutions were observed in the viral proteins when compared to the OIE-recommended Fc-1 vaccine strains. The HA and neuraminidase proteins respectively had 13 and 16 amino acid substitutions. This study represents the first reported outbreak of EI caused by an Fc-1 virus in Nigeria and in the West Africa sub-region. Based on this report, extensive disease surveillance in equids is required to establish the circulating lineages and design an effective control strategy to protect the considerable population of horses and donkeys in the country.


Assuntos
Surtos de Doenças/veterinária , Doenças dos Cavalos/mortalidade , Vírus da Influenza A Subtipo H3N8/patogenicidade , Infecções por Orthomyxoviridae/mortalidade , Infecções por Orthomyxoviridae/veterinária , África Ocidental/epidemiologia , Animais , Genoma Viral , Doenças dos Cavalos/virologia , Cavalos , Nigéria/epidemiologia , Filogenia , Proteínas Virais/genética
8.
Emerg Infect Dis ; 26(7): 1557-1561, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32568059

RESUMO

We report detection of a highly pathogenic avian influenza A(H5N8) clade 2.3.4.4b virus in Europe. This virus was generated by reassortment between H5N8 subtype virus from sub-Saharan Africa and low pathogenicity avian influenza viruses from Eurasia.


Assuntos
Vírus da Influenza A Subtipo H5N8 , Influenza Aviária , África ao Sul do Saara/epidemiologia , Animais , Europa (Continente) , Vírus da Influenza A Subtipo H5N8/genética , Influenza Aviária/epidemiologia , Filogenia , Vírus Reordenados/genética
9.
Avian Pathol ; 49(4): 394-403, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32301622

RESUMO

ABSTRACT Newcastle disease (ND) is an infectious viral poultry disease with great economic consequences. In developing countries, outbreaks of ND caused by virulent Newcastle disease virus (NDV) have been identified as a limiting factor to the growth of the poultry industry. Limited reports exist on the pathology of natural field infection caused by NDV genotype XVII in chickens. Here, we present clinical, pathological and molecular investigation of confirmed ND in a 24-week-old layer-type, semi-intensive poultry flock with recorded mortality of over 50%. During PM examination, tissues were harvested for virus isolation, histopathology and immunohistochemistry. Virus isolation was performed in 10-day-old embryonated chicken eggs, and a haemagglutinating agent thereof identified by one-step reverse transcription-polymerase chain reaction (RT-PCR). For the genotyping of the isolate, the full fusion gene was sequenced. Clinical signs observed included general body lethargy, inappetence and greenish diarrhoeic faeces from the cloaca before death with daily mortality exceeding 100 chickens. The pathology was characteristic of a viral haemorrhagic infection, with serosal haemorrhages, mucosal surface erosion and ulceration. In most of the carcasses, the main lesions seen included airsacculitis, meningeal congestion, haemorrhagic oophoritis, pancreatic necrosis, enteritis and faecal matting of the vent. Virus isolation and RT-PCR made a confirmatory diagnosis of ND. Based on the cleavage site motif sequence (112RRQKR/F117), the isolate was identified as a virulent strain with phylogenetic analysis showing clustering in genotype XVII viruses. To the best of the authors' knowledge, this is the first report describing the pathological findings of a natural outbreak caused by NDV involving viruses of genotype XVII. RESEARCH HIGHLIGHTS First report of a natural outbreak of Newcastle disease in White Yarkon Leghorns. The outbreak was caused by virulent NDV belonging to genotype XVII. Pathology differed slightly from those in experimental studies using SPF and other unvaccinated chickens.


Assuntos
Galinhas/virologia , Surtos de Doenças/veterinária , Doença de Newcastle/epidemiologia , Vírus da Doença de Newcastle/genética , Doenças das Aves Domésticas/epidemiologia , Animais , Feminino , Genótipo , Doença de Newcastle/virologia , Vírus da Doença de Newcastle/patogenicidade , Filogenia , Doenças das Aves Domésticas/virologia
10.
Emerg Microbes Infect ; 9(1): 886-888, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32312185

RESUMO

Since 2013, highly pathogenic avian influenza (HPAI) subtype H5N6 (clade 2.3.4.4) has been reported in wild birds and poultry in Asia as well as in other parts of the globe. In Africa, information on the presence of this virus subtype is lacking. This study reports the first detection of a HPAI (H5N6) virus (clade 2.3.4.4b) in a duck from a live bird market in Nigeria, whose genome is closely related to the European 2017-2018 H5N6 viruses, indricating a recent virus introduction into the African continent.


Assuntos
Animais Selvagens/virologia , Vírus da Influenza A/isolamento & purificação , Influenza Aviária/epidemiologia , Filogenia , Doenças das Aves Domésticas/virologia , Aves Domésticas/virologia , Animais , Surtos de Doenças/veterinária , Patos/virologia , Genoma Viral , Vírus da Influenza A/classificação , Influenza Aviária/virologia , Nigéria/epidemiologia , Doenças das Aves Domésticas/epidemiologia
11.
Nat Commun ; 10(1): 5310, 2019 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-31757953

RESUMO

The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.


Assuntos
Influenza Aviária/transmissão , Influenza Humana/transmissão , Doenças das Aves Domésticas/transmissão , África , África Ocidental , Animais , Humanos , Virus da Influenza A Subtipo H5N1/genética , Vírus da Influenza A Subtipo H5N8/genética , Vírus da Influenza A/genética , Influenza Aviária/economia , Influenza Aviária/epidemiologia , Influenza Aviária/virologia , Influenza Humana/economia , Influenza Humana/epidemiologia , Influenza Humana/virologia , Filogenia , Aves Domésticas , Doenças das Aves Domésticas/economia , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/virologia
12.
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
13.
Open Vet J ; 9(1): 74-80, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31086770

RESUMO

A flock of 54 wk-old layer birds exhibiting signs of respiratory distress, greenish diarrhea, and drop in egg production was investigated. A marked drop in egg production (55%) was recorded with eggs appearing white and soft-shelled. Mortality was in the range of 1%-2% with post-mortem lesions revealing cloudy air sacs, frothy, and congested lungs. Viral RNA was extracted from pooled tissue samples (trachea, lungs, spleen, and liver) and tested for Avian influenza virus (AIV), Newcastle disease virus (NDV), and infectious bronchitis virus (IBV) by reverse transcriptase-polymerase chain reaction (RT-PCR). In addition, virus isolation was attempted in 9-11 day-old embryonating chicken eggs (ECE). In order to determine the prevalence of IBV serotype(s) in the flock, serum samples were screened by hemagglutination-inhibition (HI) test using IBV antigens and antisera (Arkansas, Connecticut, and Massachusetts). Neither AIV nor NDV but IBV was detected in the tissue samples by RT-PCR. In addition, virus isolate obtained after four serial passages in ECE produced dwarfed, stunted, and hemorrhagic embryos, and the isolate was confirmed by RT-PCR to be IBV. The serum samples were 100% seropositive for three serotypes with HI titres ranging from 5 to 12 Log2. In this study, IBV was confirmed as the causative agent of the observed respiratory distress and drop in egg production. Also, the evidence of co-circulation of multiple IBV serotypes was established, this to the best of our knowledge is the first of such report in Nigeria. We recommend extensive molecular and sero-epidemiology of circulating IBV genotypes and serotypes in Nigeria with the aim of developing better control strategies, including vaccination.


Assuntos
Bronquite/veterinária , Galinhas , Infecções por Coronavirus/veterinária , Vírus da Bronquite Infecciosa/fisiologia , Doenças das Aves Domésticas/epidemiologia , Animais , Bronquite/epidemiologia , Bronquite/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Feminino , Testes de Inibição da Hemaglutinação/veterinária , Vírus da Bronquite Infecciosa/classificação , Vírus da Bronquite Infecciosa/genética , Nigéria/epidemiologia , Doenças das Aves Domésticas/virologia , Prevalência , Sorogrupo
14.
Arch Virol ; 164(8): 2031-2047, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31123963

RESUMO

Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still largely incomplete. Next-generation and Sanger sequencing was performed to provide complete (n = 73) and partial genomic sequence data (n = 38) for NDV isolates collected from domestic and wild birds in Nigeria during 2002-2015, including the first complete genome sequences of genotype IV and subgenotype VIh from the African continent. Phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating high genetic diversity of NDV for a single country. In addition, a high degree of similarity between NDV isolates from domestic and wild birds was observed, suggesting that spillovers had occurred, including to three species that had not previously been shown to be susceptible to NDV infection. Furthermore, the first spillover of a mesogenic Komarov vaccine virus is documented, suggesting a previous spillover and evolution of this virus. The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently. This is especially significant when considering that some viruses were isolated from species of conservation concern. The high diversity of NDV observed in both domestic and wild birds in Nigeria emphasizes the need for active surveillance and epidemiology of NDV in all bird species.


Assuntos
Animais Selvagens/virologia , Aves/virologia , Doença de Newcastle/virologia , Vírus da Doença de Newcastle/genética , Animais , Variação Genética/genética , Genômica/métodos , Genótipo , Nigéria , Filogenia , Aves Domésticas/virologia , Sequenciamento Completo do Genoma/métodos
15.
Biologicals ; 57: 29-33, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30454953

RESUMO

Globally, vaccines are used to prevent and control the menace of infectious diseases in livestock with some reported to be inadvertently contaminated with extraneous agents (EAs). With the aim of screening and characterizing for some selected EAs, 44 live viral poultry vaccines were randomly selected based on availability. The vaccines comprised 14 manufacturers in 10 different countries including Nigeria were screened by Polymerase Chain Reaction. In 9% (4/44) of the vaccines, contamination with only avian leukosis virus (ALV) subgroup J (ALV-J) was recorded. Other exogenous ALV subgroups, chicken infectious anemia and infectious laryngotracheitis viruses were absent. The EAs was found in infectious bursal disease (n = 1), Fowlpox (n = 2) and Mareks disease (n = 1) vaccines. Phylogenetic analysis of the ALV-J env gene showed clustering with contemporary group I and II. The result underscores the importance of screening vaccines to avoid the introduction and spread of EAs that could pose a threat to poultry production.


Assuntos
Vírus da Leucose Aviária/imunologia , Leucose Aviária/imunologia , Contaminação de Medicamentos , Doenças das Aves Domésticas/imunologia , Vacinas Virais/imunologia , Animais , Leucose Aviária/virologia , Vírus da Leucose Aviária/classificação , Vírus da Leucose Aviária/genética , Produtos do Gene env/classificação , Produtos do Gene env/genética , Produtos do Gene env/imunologia , Nigéria , Filogenia , Reação em Cadeia da Polimerase/métodos , Aves Domésticas , Doenças das Aves Domésticas/virologia , Vacinas Atenuadas/imunologia
16.
Vet Pathol ; 55(5): 682-692, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29661124

RESUMO

Newcastle disease (ND), caused by virulent strains of Newcastle disease virus (NDV), is a devastating disease of poultry worldwide. The pathogenesis of ND in quail is poorly documented. To characterize the ability of virulent NDV strains to replicate and cause disease in quail, groups of 14 two-week-old Japanese quail ( Coturnix japonica) were experimentally inoculated with 108 EID50 (embryo infectious dose 50%) units of 1 of 4 virulent NDV strains: 2 isolated from quail ( N2, N23) and 2 from chickens ( Israel, Pakistan). At day 2 postinfection, noninfected quail (contact group) were added to each infection group to assess the efficacy of virus transmission. Tested NDV strains showed moderate pathogenicity, with highest mortality being 28% for the N2 strain and below 10% for the others. Two N2-inoculated birds showed neurological signs, such as head tremor and ataxia. Microscopic lesions were present in N2-, Israel-, and Pakistan-inoculated birds and consisted of nonsuppurative encephalitis. Contact birds showed no clinical signs or lesions. In both inoculated and contact birds, virus replication was moderate to minimal, respectively, as observed by immunohistochemistry in tissues and virus isolation from oropharyngeal and cloacal swabs. Strains originally isolated from quail resulted in higher numbers of birds shedding in the inoculation group; however, transmission appeared slightly more efficient with chicken-derived isolates. This study shows that virulent NDV strains have limited replicative potential and mild to moderate disease-inducing ability in Japanese quail.


Assuntos
Coturnix/virologia , Doença de Newcastle/patologia , Vírus da Doença de Newcastle , Animais , Encéfalo/patologia , Encéfalo/virologia , Doença de Newcastle/virologia , Eliminação de Partículas Virais
17.
Genome Announc ; 6(11)2018 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-29545289

RESUMO

Here, we present the draft genome sequences of five multidrug-resistant novel Ochrobactrum species strains isolated from a pigeon, a duck, and chickens from Nigeria in 2009.

18.
Infect Genet Evol ; 57: 98-105, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29104094

RESUMO

Phylogenetic analyses of the complete genomes of the highly pathogenic avian influenza (HPAI) 2.3.2.1c H5N1 virus strains causing outbreaks in Nigeria's poultry population from 2014 to 2016 showed evidence of distinct co-circulating genotypes and the emergence of reassortant viruses. One of these reassortants became the predominant strain by 2016, and the NA protein of this strain possessed the V96A substitution known to confer reduced susceptibility to neuraminidase inhibiting antiviral drugs. Our findings also demonstrated evolutionary relationships between Nigerian isolates and European and Middle Eastern strains of H5N1 which provides further evidence for the proposed role of migratory birds in spreading the virus, although the involvement of the live poultry trade cannot be excluded. Efforts must be directed towards improving biosecurity and gaining the cooperation of poultry farmers for more effective control of HPAI, in order to mitigate the emergence of HPAI strains in Nigeria with biological properties that are potentially even more dangerous to animals and humans.


Assuntos
Evolução Molecular , Variação Genética , Genótipo , Virus da Influenza A Subtipo H5N1/classificação , Virus da Influenza A Subtipo H5N1/genética , Influenza Humana/epidemiologia , Influenza Humana/virologia , Genoma Viral , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Humanos , Nigéria/epidemiologia , Filogenia , Vírus Reordenados/genética , Sequenciamento Completo do Genoma
19.
Virol J ; 14(1): 72, 2017 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-28388925

RESUMO

BACKGROUND: Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. METHODS: In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. RESULTS: Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25-30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2-3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. CONCLUSIONS: This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples.


Assuntos
Genômica/economia , Genômica/métodos , Vírus de RNA/genética , Virologia/economia , Virologia/métodos , Animais , Aves , Biologia Computacional/economia , Biologia Computacional/métodos , Análise Custo-Benefício , Sequenciamento de Nucleotídeos em Larga Escala/economia , Sequenciamento de Nucleotídeos em Larga Escala/métodos
20.
Arch Virol ; 162(3): 841-847, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27873070

RESUMO

Genetic analysis of the complete haemagglutinin (HA) gene of fourteen Nigerian avian influenza isolates showed multiple basic amino acids at the cleavage site (321PQRERRRK del R*GLF333), characteristic of highly pathogenic avian influenza (HPAI). Substitution of Gln to Lys at position 322 (H5-specific numbering) was identified in one isolate. In some isolates, amino acid substitutions were observed across the HA gene, however the receptor binding, antigenic and glycosylation sites were conserved in all. Phylogenetic analysis revealed two clusters of the HPAI H5N1 clade 2.3.2.1c. Cluster I has close genetic relatedness (97.8-99.8%) with viruses circulating in some West Africa countries. Cluster II shared close identity (98.9-100.0%) with isolates from Europe, Côte d'Ivoire and Niger and viruses from this cluster were detected in five of the eleven states investigated in Nigeria. In view of the continuous HPAI outbreaks being recorded in Nigerian poultry and the zoonotic potential of the virus, extensive and continued characterization of HPAI isolates is advocated.


Assuntos
Virus da Influenza A Subtipo H5N1/isolamento & purificação , Influenza Aviária/virologia , Doenças das Aves Domésticas/virologia , Substituição de Aminoácidos , Animais , Galinhas , Surtos de Doenças , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Virus da Influenza A Subtipo H5N1/classificação , Virus da Influenza A Subtipo H5N1/genética , Virus da Influenza A Subtipo H5N1/patogenicidade , Influenza Aviária/epidemiologia , Nigéria/epidemiologia , Filogenia , Doenças das Aves Domésticas/epidemiologia , Virulência
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