Frederick Kibenge - Academia.edu (original) (raw)

Papers by Frederick Kibenge

Pathogens

Infectious pancreatic necrosis (IPN), caused by IPNV, affects several species of farmed fish, par... more Infectious pancreatic necrosis (IPN), caused by IPNV, affects several species of farmed fish, particularly Atlantic salmon, and is responsible for significant economic losses in salmon aquaculture globally. Despite the introduction of genetically resistant farmed Atlantic salmon and vaccination strategies in the Chilean salmon industry since 2019, the number of IPN outbreaks has been increasing in farmed Atlantic salmon in the freshwater phase. This study examined gross and histopathological lesions of IPNV-affected fish, as well as the IPNV nucleotide sequence encoding the VP2 protein in clinical cases. The mortality reached 0.4% per day, and the cumulative mortality was from 0.4 to 3.5%. IPNV was isolated in the CHSE-214 cell line and was confirmed by RT-PCR, and VP2 sequence analysis. The analyzed viruses belong to IPNV genotype 5 and have 11 mutations in their VP2 protein. This is the first report of IPN outbreaks in farmed Atlantic salmon genetically resistant to IPNV in Chile....

Journal of Virology, 2009

As nonenveloped viruses, the aquareoviruses and orthoreoviruses are unusual in their ability to i... more As nonenveloped viruses, the aquareoviruses and orthoreoviruses are unusual in their ability to induce cell-cell fusion and syncytium formation. While an extraordinary family of fusion-associated small transmembrane (FAST) proteins is responsible for orthoreovirus syncytiogenesis, the basis for aquareovirus-induced syncytiogenesis is unknown. We now report that the S7 genome segment of an Atlantic salmon reovirus is polycistronic and uses a noncanonical CUG translation start codon to produce a 22-kDa integral membrane protein responsible for syncytiogenesis. The aquareovirus p22 protein represents a fourth distinct member of the FAST family with a unique repertoire and arrangement of structural motifs.

Aquaculture, 2021

Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and ... more Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.

PLOS ONE

The supplementary datafiles for this paper did not include Ct values for the PRV tests. We now pr... more The supplementary datafiles for this paper did not include Ct values for the PRV tests. We now provide these values in S1 File and S2 File of this Correction. The performance of the real-time RT-PCR assay for PRV was based on published protocols (the assay used primers and probe by Haugland et al.

Canadian journal of veterinary research = Revue canadienne de recherche vétérinaire, 2001

It is generally known that the pathogenicity of infectious bursal disease virus (IBDV) strains de... more It is generally known that the pathogenicity of infectious bursal disease virus (IBDV) strains decreases following passage in cell culture. However, there is no information about the effect of passage under immune pressure on the phenotypic and molecular properties of IBDV. In the present study, a small plaque mutant virus with poor neutralization capability, but showing similar growth characteristics as the parental virus strain, QC2, was isolated after serial passage in Vero cells in presence of IBDV serotype 1 chicken polyclonal antiserum. This mutant virus showed reduced pathogenicity but enhanced immunogenicity compared to the parental virus. Sequence analysis of the non-coding regions of the genome revealed 4 and 3 nucleotide changes in the 3' non-coding regions of segments A and B, respectively, and none in the 5' non-coding regions. Restriction enzyme analysis of selected coding regions of the IBDV genome in both viruses revealed a loss of the PstI site in the VP2 re...

Journal of Wildlife Diseases, 2012

In 2007, we assessed whether trapping method influenced apparent prevalence of low pathogenic avi... more In 2007, we assessed whether trapping method influenced apparent prevalence of low pathogenic avian influenza viruses (AIV) in wild ducks sampled during Canada's Inter-agency Wild Bird Influenza Survey. Combined cloacal and oropharyngeal swabs were collected from 514 ducks captured by bait trapping (356) and netting from airboats (158), and tested by real-time reverse transcriptase polymerase chain reaction for influenza type A viruses. When controlling for species and capture site, ducks caught in bait traps were 2.6 times more likely to test positive for AIV compared with those netted from airboats (95% CI51.2-6.0). If bait trapping increases AIV transmission among artificially aggregated ducks, this could have important implications for interpretation of disease surveillance results and waterfowl management programs.

Journal of Wildlife Diseases, 2011

Journal of Virological Methods, 1999

Infection with bovine herpesvirus 1 (BHV 1) occurs worldwide and causes serious economic losses d... more Infection with bovine herpesvirus 1 (BHV 1) occurs worldwide and causes serious economic losses due to loss of animals, abortions, decreased milk production, and loss of body weight. There is a real need for sensitive diagnostic procedures for detection of the presence of virus in order to achieve effective control of BHV 1-induced diseases. BHV 1 is frequently found in bovine semen and can be widely transmitted through artificial insemination. Thus the detection of BHV 1 in artificial insemination centers and semen banks is of crucial importance in the control of its dissemination to the cattle industry, worldwide. In the present study, a protein amplification assay following polymerase chain reaction (PCR) of the highly conserved BHV 1 glycoprotein D gene was used in order to improve the sensitivity of direct virus detection in bovine semen. This method of BHV 1 detection is at least 200 orders of magnitude more sensitive than traditional PCR and would have direct clinical applications in antigen-based detection tests. In this method, amplification of the BHV 1 gD gene by PCR is followed by a coupled in vitro transcription translation of a small aliquot from the reaction. When the transcription translation was carried out in the presence of [35S]methionine and the products analyzed by SDS PAGE and autoradiography, 0.0014 TCID50 of virus could be detected in raw bovine semen in contrast to 0.28 TCID50 of virus detected using traditional PCR. Given the limitations in the method used for protein detection, this 'in vitro protein amplification' has the potential of attaining superior sensitivity for direct virus detection in clinical samples.

Journal of General Virology, 1990

The nucleotide sequence of genome segment A cDNA of the STC strain of infectious bursal disease v... more The nucleotide sequence of genome segment A cDNA of the STC strain of infectious bursal disease virus (IBDV) was determined and compared with sequences of the homologous genome segment of the 002-73 strain of IBDV and the Jasper strain of infectious pancreatic necrosis virus (IPNV). The STC-IBDV genome segment A was determined to be 3262 base pairs (bp), which is close to the estimated total length of 3300 bp for genome segment A in IBDV, although there is no proof that it is the real length of this genome segment. The STC-IBDV genome segment A contains two major overlapping open reading frames (ORFs). The large ORF of 3036 bp predicts a polyprotein of Mr 109 358, whereas the small ORF is 435 bp and predicts a protein of Mr 16550 in STC-IBDV. STC-IBDV and 002-73-IBDV polyproteins are closely related (97.4% amino acid homology). Most of the amino acid mismatches are in VP2 sequences, mainly within the area of the conformation-dependent epitope. Comparison with the Jasper-IPNV polyprotein reveals levels of amino acid sequence homology of about 40 % in VP2, 32% in VP3 and 21% in VP4. Within the VP2 molecule the conformation-dependent epitope area is again the least homologous, but the heterogeneity is more conspicuous than between the two IBDV strains, which is not surprising since IBDV and IPNV are serologically unrelated. The small ORF proteins have about 88% amino acid sequence homology between STC-IBDV and 002-73-IBDV, and 30 % between each IBDV strain and Jasper-IPNV. There is no homology at all in the non-coding regions of IBDV and IPNV. These comparative sequence data will be useful for subgrouping the Birnaviridae family.

Journal of Clinical Microbiology, 2002

Infection with bovine herpesvirus type 1 (BHV-1) occurs worldwide and causes serious economic los... more Infection with bovine herpesvirus type 1 (BHV-1) occurs worldwide and causes serious economic losses due to the deaths of animals, abortions, decreased milk production, and loss of body weight. BHV-1 is frequently found in bovine semen and is transmitted through natural service and artificial insemination. The detection of BHV-1 in bovine semen is a long-standing problem in veterinary virology which is important in disease control schemes. In the present study, ordered deletions of the full-length BHV-1 glycoprotein open reading frame were used to identify an epitope recognized by a specific monoclonal antibody (MAb). A glycoprotein D fragment containing this epitope was then amplified using an in vitro protein amplification assay developed previously (J. Zhou, J. Lyaku, R. A. Fredrickson, and F. S. Kibenge, J. Virol. Methods 79:181-189, 1999), and the resulting peptide was detected by indirect enzyme-linked immunosorbent assay (ELISA) with the specific MAb. This method detected 0.0...

Avian Diseases, 1997

Bursa samples from the United States, Mexico, and Puerto Rico were tested for the presence of inf... more Bursa samples from the United States, Mexico, and Puerto Rico were tested for the presence of infectious bursal disease virus (IBDV) using the reverse transcriptase/polymerase chain reaction-restriction endonuclease (RT/PCR-RE) assay. This assay amplifies a 394-bp fragment of the IBDV VP2 gene. A total of 151 samples were tested. Each was from a different physical location or farm. Forty-eight of the samples were determined to contain IBDV using RT/PCR. The RE profiles on 44 of these positive samples were determined using the enzymes BstNI or EcoRII, StyI, DraI, SacI, Sau3AI or MboI, and TaqI. A majority of the samples (34) had RE profiles typical of variant IBDV strains. One of six samples from Mexico was positive for IBDV. This virus had an RE profile typical of variant strains of IBDV. Three of seven samples from Puerto Rico had RE profiles characteristic of variant viruses. Two samples from the United States had RE profiles characteristic of classic vaccine IBDV strains and nine samples had new RE profiles. Five of these new profiles were BstNI- and StyI-negative, indicating that these viruses may be antigenically related to variant types. Although the new RE pattern observed in the other four samples was BstNI- and StyI-positive, it was not typical of classic vaccine IBDV strains. One flock from the United States had a mixture of two RE profiles, a typical variant type profile and an unknown variant RE profile. Two-thirds of the positive samples from flocks where the age of the birds was reported were observed between 21 and 28 days of age. The results of these studies demonstrate that the RT/PCR-RE assay can be used to diagnose IBDV in chickens and that IBDV strains exist in commercially reared chickens that have RE patterns different than known IBDV strains. The molecular differences observed using the RT/PCR-RE test were in a region of the VP2 gene, which is known to code for important neutralizing epitopes and to be highly variable among IBDV strains. Although the results demonstrate RE patterns different than those observed in known classic and variant IBDV strains, the influence of these molecular differences on biological properties of the viruses requires further investigation.

Virology, 2002

Virus protein VP4 of infectious bursal disease virus (IBDV) is a protease which separates VPX and... more Virus protein VP4 of infectious bursal disease virus (IBDV) is a protease which separates VPX and VP3 from the polyprotein. We studied the importance of serine and aspartic acid on cleavage at the VPX/VP4 junction and analysed the role of the proposed H547, D590, and S653 catalytic site using five different mutations on VP4. Our results suggest that the replacement of serine by lysine in AXAAS motifs in serotype II IBDV influences polyprotein (PP) processing by VP4 and also indicate the presence of an alternative cleavage site. Mutation on D (510 TLAADK 515) prevented the cleavage at the VPX/VP4 junction, but we have found that independently of the importance of those alanines in LAA, D has an important role as part of the cleavage site. Replacement of histidine by proline H547P completely abolished PP processing. Mutation on D590 induced a partial PP processing when it was replaced by proline and the replacement of serine by proline at S653P induced a prominent change in PP processing. These results permit us to conclude that IBDV VP4 has the ability to act according to structural and topographical changes during translational and posttranslational processes and allow multiple hit sites, which serve to increase effectiveness.

Archives of Virology, 1997

The regions of the infectious bursal disease virus (IBDV) genome with regulatory function are not... more The regions of the infectious bursal disease virus (IBDV) genome with regulatory function are not known. In the present study, progressively deleted lengths of the 5 H noncoding region of segment A were constructed in pGL3 vectors having SV40 enhancer or promoter, and a luciferase (LUC) reporter gene. Transient transfections of the constructs made in a promoter-less pGL3-Enhancer vector when transfected in Vero cells and the lysates assayed for LUC expression, allowed the localization of maximal activity to the 32nucleotide stretch (precursor polyprotein ORF positions À131 to À100), which is highly conserved at the 5 H end of both genome segments. This fragment, when evaluated in parallel in an enhancer-less pGL3-Promoter vector demonstrated no activity. To determine if this region is recognized by IBDV replicative proteins, we engineered modi®cations in an enhancer-less pGL3-Promoter vector where the terminal 32-bp fragment, the full-length noncoding region, or the noncodig region with the 32-bp fragment deleted was positioned in either the plus-sense or the minus-sense orientation immediately downstream of the SV40 promoter and upstream of the LUC gene. Transfections of these constructs in IBDV-infected and uninfected Vero cells resulted in the endogenous generation of recombinant viral-LUC RNAs containing the 5 H terminal viral RNA sequences in either the plus-sense or the minus-sense orientation. LUC assays of the infected cell lysates showed up-regulated expression of LUC only with constructs containing the 32-bp fragment in the minus-sense orientation. Deletion of this 32-bp fragment abolished such LUC expression. We therefore conclude that the 5 H-terminal 32 base pairs of genomic segment A contain a major promoter element in IBDV. In addition, our results show that IBDV replicative proteins recognize and transcribe single-stranded RNA in vivo.

Journal of General Virology, 1988

Microbiology Research, 2021

Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading fram... more Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein is strikingly similar to the coronavirus E protein in structure. This is the first report to identify a putative E protein ORF in the genome of members of the Oncotshavirus genus (subfamily Piscavirinae, family Tobaniviridae, order Nidovirales) and, if expressed would be the third family (after Coronaviridae and Arteriviridae) within the order to have the E protein as a major structural protein.

Pathogens, 2021

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in ass... more Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which...

PloS one, 2017

The disease Heart and Skeletal Muscle Inflammation (HSMI) is causing substantial economic losses ... more The disease Heart and Skeletal Muscle Inflammation (HSMI) is causing substantial economic losses to the Norwegian salmon farming industry where the causative agent, piscine orthoreovirus (PRV), is reportedly spreading from farmed to wild Atlantic salmon (Salmo salar) with as yet undetermined impacts. To assess if PRV infection is epidemiologically linked between wild and farmed salmon in the eastern Pacific, wild Pacific salmon (Oncorhynchus sp.) from regions designated as high or low exposure to salmon farms and farmed Atlantic salmon reared in British Columbia (BC) were tested for PRV. The proportion of PRV infection in wild fish was related to exposure to salmon farms (p = 0.0097). PRV was detected in: 95% of farmed Atlantic salmon, 37-45% of wild salmon from regions highly exposed to salmon farms and 5% of wild salmon from the regions furthest from salmon farms. The proportion of PRV infection was also significantly lower (p = 0.0008) where wild salmon had been challenged by an ...