Tony Joannis - Academia.edu (original) (raw)

Papers by Tony Joannis

Emerging Infectious Diseases

Emerging Microbes & Infections

Genome announcements, Jan 15, 2018

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

Scientific reports, Jan 12, 2018

Avian influenza viruses (AIV) potentially transmit to swine as shown by experiments, where furthe... more Avian influenza viruses (AIV) potentially transmit to swine as shown by experiments, where further reassortment may contribute to the generation of pandemic strains. Associated risks of AIV inter-species transmission are greater in countries like Nigeria with recurrent epidemics of highly pathogenic AI (HPAI) in poultry and significant pig population. Analysis of 129 tracheal swab specimens collected from apparently healthy pigs at slaughterhouse during presence of HPAI virus H5N1 in poultry in Nigeria for influenza A by RT-qPCR yielded 43 positive samples. Twenty-two could be determined by clade specific RT-qPCR as belonging to the H5N1 clade 2.3.2.1c and confirmed by partial hemagglutinin (HA) sequence analysis. In addition, 500 swine sera were screened for antibodies against influenza A virus nucleoprotein and H5 HA using competition ELISAs and hemagglutination inhibition (HI) tests. Serologically, 222 (44.4%) and 42 (8.4%) sera were positive for influenza A virus NP and H5 antib...

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2018

Phylogenetic analyses of the complete genomes of the highly pathogenic avian influenza (HPAI) 2.3... more 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 N...

Virology journal, Apr 7, 2017

Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequen... more 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. 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...

Archives of Virology, 2016

Genetic analysis of the complete haemagglutinin (HA) gene of fourteen Nigerian avian influenza is... more Genetic analysis of the complete haemagglutinin (HA) gene of fourteen Nigerian avian influenza isolates showed multiple basic amino acids at the cleavage site ((321)PQRERRRK (del) R*GLF(333)), 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&amp;amp;amp;#39;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.

VirusDisease, 2016

Over the years, Newcastle disease (ND) has defied all available control measures. The disease has... more Over the years, Newcastle disease (ND) has defied all available control measures. The disease has remained at the forefront of infectious diseases afflicting poultry production after avian influenza. Despite the continuous global use of million doses of ND vaccine annually, the causative pathogen, avian paramyxovirus type 1 also known as Newcastle disease virus (NDV) has continued to evolve causing, even more, a threat not only to the unvaccinated but the vaccinated flocks inclusive. The disease has been well studied in the developed countries where the virus is found in circulation. However, limited information exists on the epizootiology and circulating genotypes of the virus in developing countries where the majority of the flocks are raised on the extensive management system. Identification of virulent NDV in apparently healthy free-range ducks in this system calls for concern and pragmatic approach to investigate factor(s) that favour the virus inhabiting the ducks without clinical manifestation of the disease. Recently, novel genotypes (XIV, XVII, and XVIII) with peculiarity to West and Central African countries have been discovered and due to lack or poor surveillance system possibility of hitherto unreported genotypes are likely. This review elucidates and discusses available literature on the diversity of the circulating NDV genotypes across the West Africa countries and the epizootiology (molecular) of the disease in Nigeria with the view of identifying gaps in knowledge that can assist in the development of effective vaccines and control strategies to combat the peril of the disease.

Journal of Immunoassay and Immunochemistry, 2016

Infectious laryngotracheitis (ILT) is a highly contagious acute respiratory disease of chickens w... more Infectious laryngotracheitis (ILT) is a highly contagious acute respiratory disease of chickens with outbreaks resulting in high economic losses due to increased mortality and drop in egg production. This study reports a survey of ILT virus antibody conducted in nine local government areas (LGAs) of Plateau State involving 67 randomly selected commercial poultry flocks. In all, 938 sera were tested using the Agar Gel Immuno-diffusion (AGID) technique. Overall prevalence of 1.2% (N = 11) was recorded. ILT virus antibody was found in 2.5% (n = 9) and 7.1% (n = 2) of the tested sera from Jos South and Langtang North LGAs, respectively. No detectable ILT virus antibody was found from the other seven LGAs. This is the first report of ILT infection in poultry from the North central part of Nigeria. It is therefore recommended that the economic implication of ILT infection in Nigerian poultry population be conducted in order to know if vaccination should be adopted for control.

Emerging Infectious Diseases, 2016

Global Initiative on Sharing All Influenza Data (GISAID) accession numbers, submitting laboratori... more Global Initiative on Sharing All Influenza Data (GISAID) accession numbers, submitting laboratories, and authors of the sequences used in study of genetically different highly pathogenic avian influenza A(H5N1) viruses in West Africa, 2015*

Genome announcements, Jan 4, 2016

The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII ... more The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the fusion protein gene and complete genome classified the isolate as a member of NDV class II, genotype XVII.

Genome Announcements, 2016

The first complete genome sequence of a strain of Newcastle disease virus (NDV) from genotype XIV... more The first complete genome sequence of a strain of Newcastle disease virus (NDV) from genotype XIV is reported here. Strain duck/Nigeria/NG-695/KG.LOM.11-16/2009 was isolated from an apparently healthy domestic duck from a live bird market in Kogi State, Nigeria, in 2009. This strain is classified as a member of subgenotype XIVb of class II.

Genetic characterization of a selection of infl uenza virus (H5N1) samples, circulating in 8 Nige... more Genetic characterization of a selection of infl uenza virus (H5N1) samples, circulating in 8 Nigerian states over a 39-day period in early 2007, indicates that a new reassortant strain is present in 7 of the 8 states. Our study reports an entirely different infl uenza virus (H5N1) reassortant becoming predominant and widespread in poultry. Since its emergence in 2006 in Africa, avian influenza viruses of the H5N1 subtype have spread rapidly to poultry farms in several African countries. In February 2006, Kaduna State in Nigeria was the first of 36 states to report infection of poultry with highly pathogenic avian influenza virus (H5N1). Currently, infection has spread to 22 of the 36 Nigerian states and to the Federal Capital Territory. In February 2007, 1 case of avian influenza was reported in a woman from the southern state of Lagos. Thus, the extensive circulation of influenza virus (H5N1) in Nigeria raises concerns about human and animal health issues. A previous study indicate...

Folia veterinaria

The effect of four commonly employed infectious bursal disease (IBD) vaccines on the immune respo... more The effect of four commonly employed infectious bursal disease (IBD) vaccines on the immune response of chickens vaccinated with Newcastle disease (ND) vaccine were assessed in pullets using a pre-existing vaccination regimen, depicting field situations. The antibodies to IBD was evaluated by the qualitative and quantitative agar gel immunodiffusion method while the haemagglution inhibition (HI) test was used for the detection of ND antibodies. The immunosuppressive effect was assessed by: the suppression of the ND titres; the bursa of Fabricius (BF) index; the BF diameter; and the BF histopathological lesions. The results showed that the IBD vaccines caused a transient immunosuppression in the ND vaccinated chicks. This immunosuppressive effect was non existent when a booster dose of Newcastle disease — Komarov vaccine (NDV-K) was administered. Both the BF index and diameter were significantly higher (P < 0.05) in the vaccinated groups when compared with the control unvaccinated...