Human Respiratory Infections in Nigeria: Influenza and the Emergence of SARS-CoV-2 Pandemic

The increasing outbreak of zoonotic diseases presents challenging times for nations and calls for a renewed effort to disrupt the chain of events that precede it. Nigeria’s response to the 2006 bird flu provided a platform for outbreak response, yet it was not its first experience with Influenza. This study describes the impact of SARS-CoV-2 on Influenza surveillance and, conversely, while the 1918 Influenza pandemic remains the most devastating (500,000 deaths in 18 million population) in Nigeria, the emergence of SARS CoV-2 presented renewed opportunities for the development of vaccines with novel technology, co-infection studies outcome, and challenges globally. Although the public health Intervention and strategies left some positive outcomes for other viruses, Nigeria and Africa’s preparation against the next pandemic may involve prioritizing a combination of technology, socioeconomic growth, and active surveillance in the spirit of One Health

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

The role of Africa in the dynamics of the global spread of a zoonotic and economicallyimportant 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.USAID under the OSRO/GLO/501/USA and OSRO/GLO/507/USA projects and by European Union’s Horizon 2020 research and innovation programme under grant agreement No 727922 (DELTAFLU). The European Research Council under the European Unionʼs Horizon 2020 research and innovation programme (grant agreement no. 725422-ReservoirDOCS). P.L. acknowledges support by the Research Foundation – Flanders FWO, G066215N, G0D5117N and G0B9317N). B.V. is a postdoctoral research fellow supported by the FWO.http://www.nature.com/naturecommunicationsam2020Microbiology and Plant Patholog

Response of cyclophosphamide-treated broiler chickens to challenge with velogenic Newcastle disease virus

This study investigated whether prior cyclophosphamide (CY) treatment influenced the susceptibility of young broiler chickens to velogenic Newcastle disease (vND) virus (vNDV) challenge. Broiler chickens treated with CY at 4 weeks of age showed a loss of weight, severe atrophy of the bursa and thymus and severe lymphocytic depletion in the bursa, spleen and thymus and lymphopaenia. On challenge at 6 weeks of age with vNDV, there were significant (p < .05) weight loss, severe depression, diarrhoea, coughing and sero-mucous nasal discharges and torticollis. Lesions included severe atrophy of the lymphoid organs and congested lungs. Proventricular, intestinal and caecal tonsil haemorrhages and ulcers were more severe in the CY-untreated than the treated broilers. Histopathology showed severe necrosis and depletion of the lymphocytes in the lymphoid organs, perivascular cuffin and endotheliosis in the brain. Total mortalities in the CY-treated and untreated broilers were 100% and 94.44%, respectively, by day 6 post-challenge. There was no statistical difference (p < .05) between the mortalities. These results show that CY treatment may not have an effect on the susceptibility of broilers to an acute disease like vND

Analysis of Amino Acid Changes in the Fusion Protein of Virulent Newcastle Disease Virus from Vaccinated Poultry in Nigerian Isolates

The roles of fusion gene in the virulence of Newcastle disease virus are well established, but the extent of its variation among the XIV, XVII, and XVIII genotypes reported in Central Africa and West Africa has until recently been understudied. In this study, virulent Newcastle disease virus (vNDV) was isolated from dead chickens among vaccinated flocks between March and April 2020. Fusion (F) gene was sequenced and analysed for characterization and information about genetic changes. Many substitutions were observed along the region and some of their functions are yet to be determined. Results showed that all study isolates have virulent cleavage site sequence 112-RRRKR-116/F117 and clustered within genotype XIVb. Sequence analysis showed K78R mutation in the A2 antigenic epitope in all isolates and more along the F-gene which varied in some instances within the isolates. Mutation in this A2 antigenic epitope has been reported to induce escape mutation to monoclonal antibodies generated using the NDV LaSota strain. The range of percentage nucleotide and amino acid homology between the study isolates and commercially available vaccine strains is 81.14%–84.39% and 0.175–0.211, respectively. This report provides evidence of vNDV among vaccinated chicken flock and molecular information about circulating vNDV strains in Kano State, Nigeria, which is useful for the development of virus matched vaccines. Newcastle disease (ND) surveillance and molecular analysis of circulating strains in this region should be encouraged and reported. Furthermore, ND outbreaks or cases among vaccinated poultry presented to veterinary clinics should be reported to the state epidemiologist. Nucleotide sequences were assigned accession numbers OK491971–OK491977

Molecular characterization of field infectious bursal disease virus isolates from Nigeria

Aim: To characterize field isolates of infectious bursal disease virus (IBDV) from outbreaks in nine states in Nigeria through reverse transcription polymerase chain reaction (RT-PCR) and sequence analysis of portions of the VP2 and VP1 genes and to determine the presence or absence of reassortant viruses. Materials and Methods: A total of 377 bursa samples were collected from 201 suspected IBD outbreaks during 2009 to 2014 from nine states in Nigeria. Samples were subjected to RT-PCR using VP2 and VP1 gene specific primers, and the resulting PCR products were sequenced. Results: A total of 143 samples were positive for IBDV by RT-PCR. These assays amplified a 743 bp fragment from nt 701 to 1444 in the IBDV VP2 hypervariable region (hvVP2) of segment A and a 722 bp fragment from nt 168 to 889 in the VP1 gene of segment B. RT-PCR products were sequenced, aligned and compared with reference IBDV sequences obtained from GenBank. All but one hvVP2 sequence showed similarity to very virulent IBDV (vvIBDV) reference strains, yet only 3 of the VP1 67 VP1 sequences showed similarity to the VP1 gene of vvIBDV. Phylogenetic analysis revealed a new lineage of Nigerian reassortant IBDV strains. Conclusion: Phylogenetic analysis of partial sequences of genome segment A and B of IBDV in Nigeria confirmed the existence of vvIBDV in Nigeria. In addition, we noted the existence of reassortant IBDV strains with novel triplet amino acid motifs at positions 145, 146 and 147 in the reassorted Nigerian IBDV

A two-year monitoring period of the genetic properties of clade 2.3.2.1c H5N1 viruses in Nigeria reveals the emergence and co-circulation of distinct genotypes

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.This work was supported by the Food and Agriculture Organization of the United Nations (UN-FAO) with funding from the United States Agency for International Development (USAID) under the OSRO/GLO/501/USA project entitled “Emergency Assistance for prevention and control of H5N1 HPAI in West and Central Africa”.http://www.elsevier.com/locate/meegid2019-01-01hj2018Production Animal Studie

Occurrence of infectious bronchitis in layer birds in Plateau state, north central Nigeria

A flock of 54 week-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 prevalence of IBV serotype(s) in the flock, serum samples were screened by haemagglutination-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 haemorrhagic 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, 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

Occurrence of infectious bronchitis in layer birds in Plateau state, north central Nigeria

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 transcriptasepolymerase 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.Keywords: Drop in egg production, Infectious bronchitis, Respiratory distress, Serotypes, Virus isolation