Genomic Analysis of Infectious Bursal Disease Virus in Nigeria: Identification of Unique Mutations of Yet Unknown Biological Functions in Both Segments A and B.

Infectious bursal disease (IBD) is a viral poultry disease known worldwide for impacting the economy and food security. The disease is endemic in Nigeria, with reported outbreaks in vaccinated poultry flocks. To gain insight into the dynamics of infectious bursal disease virus (IBDV) evolution in Nigeria, near-complete genomes of four IBDVs were evaluated. Amino acid sequences in the hypervariable region of the VP2 revealed conserved markers (222A, 242I, 256I, 294I and 299S) associated with very virulent (vv) IBDV, including the serine-rich heptapeptide motif (SWSASGS). Based on the newly proposed classification for segments A and B, the IBDVs clustered in the A3B5 group (where A3 are IBDVs with vvIBDV-like segment A, and where B5 are from non-vvIBDV-like segment B) form a monophyletic subcluster. Unique amino acid mutations with yet-to-be-determined biological functions have been observed in both segments. Amino acid sequences of the Nigerian IBDVs showed that they are reassortant viruses. Circulation of reassortant IBDVs may be responsible for the vaccination failures observed in the Nigerian poultry population. Close monitoring of changes in the IBDV genome is recommended to nip deleterious changes in the bud through the identification and introduction of the most appropriate vaccine candidates and advocacy/extension programs for properly implementing disease control.

Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria.

African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760-18,295 of the genome, and an apparent reverse complement duplication of the 5' end of the genome at the 3' end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.

A survey of contagious ecthyma and molecular characterization of Orf virus in sheep and goats in Nigeria (2014-2016).

Background: Outbreaks of contagious ecthyma (CE) are frequently reported in sheep and goat flocks in Nigeria with severe clinical outcomes. CE is a debilitating and economically important disease primarily affecting sheep and goats caused by the Orf virus (ORFV). Despite field reports of CE in the country, there is no concise country-wide epidemiological data on the disease and limited genetic data of circulating Nigerian ORFV are available in the public domain. Aim: An epidemiological survey of CE and molecular characterization of ORFV circulating in Nigeria from 2014 to 2016. Method: Data were collected using designed questionnaires, administered to veterinarians and farmers in selected States of Nigeria. Samples were collected during passive surveillance for CE from 2014 to 2016 which were analyzed by polymerase chain reaction (PCR). The A32L and B2L genes of circulating ORFV were also characterized. Results: Analysis of the questionnaire showed that 69.54% (n = 82/118) of the farmers claimed to have experienced CE in their flocks with average morbidity and mortality rates of 25% and 15%, respectively. A total of 113 veterinarians participated in the study, with 69.9% (n = 79) familiar with CE and claimed CE causes morbidity rates of 25%-37% and mortality rates of 10%-15% in sheep and goats. Laboratory results revealed that ORFV was detected in 72% (18/25) of outbreak samples analyzed by real-time PCR. Phylogenetic analysis of A32L and B2L genes revealed that Nigerian ORFV sequences belong to clusters I and II and are similar to viruses from India, Ethiopia, and China. Conclusions: This study is the first nationwide epidemiological data on the status of CE in sheep and goats in Nigeria. It is also the first report of molecular characterization of two genes of ORFV circulating and causing outbreaks in small ruminants in the country. This study showed that CE is under-reported, widespread and of economic importance to sheep and goat farmers in Nigeria.

A Retrospective Study of the Seroprevalence of Dengue Virus and Chikungunya Virus Exposures in Nigeria, 2010-2018.

Arboviruses are important public health threats in many regions of the world. Nigeria has experienced outbreaks of arboviruses over the past decades, leading to concerns of widespread endemicity, which are frequently misdiagnosed. This study aimed to determine the seroprevalence of dengue virus (DENV) (a flavivirus) and chikungunya virus (CHIKV) (an alphavirus) infections in three major population centers of Nigeria. A convenience sample of 701 sera was collected from both healthy and febrile participants between August 2010 and March 2018. Sera were tested for prior exposure to CHIKV virus and DENV using indirect IgG ELISA. Results showed that 54.1% (379/701) of participants were seropositive for anti-DENV antibodies, 41.3% (290/701) were seropositive for anti-CHIKV antibodies, and 20.1% (141/701) had previous exposure to both. The seropositivity for prior CHIKV exposure and prior exposure to DENV and CHIKV was significantly associated with age (CHIKV: OR = 2.7 (95% CI: 1.7-4.3); DENV and CHIKV: OR = 2.2 (95% CI: 1.2-4.0) for adults compared to participants under 18 years old). Overall, the high seropositivity across all age groups suggests that arboviral infections are prevalent in Nigeria and indicates that surveillance and further epidemiological studies are required to determine the true burden of these infections and the spectrum of diseases associated with these exposures.

Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms.

Resistance to last resort drugs such as carbapenem and colistin is a serious global health threat. This study investigated carbapenem and colistin resistance in 583 non-duplicate Enterobacteriaceae isolates utilizing phenotypic methods and whole genome sequencing (WGS). Of the 583 isolates recovered from humans, animals and the environment in Nigeria, 18.9% (110/583) were resistant to at least one carbapenem (meropenem, ertapenem, and imipenem) and 9.1% (53/583) exhibited concurrent carbapenem-colistin resistance. The minimum inhibitory concentrations of carbapenem and colistin were 2-32 µg/mL and 8 to >64 µg/mL, respectively. No carbapenem resistant isolates produced carbapenemase nor harbored any known carbapenemase producing genes. WGS supported that concurrent carbapenem-colistin resistance was mediated by novel and previously described alterations in chromosomal efflux regulatory genes, particularly mgrB (M1V) ompC (M1_V24del) ompK37 (I70M, I128M) ramR (M1V), and marR (M1V). In addition, alterations/mutations were detected in the etpA, arnT, ccrB, pmrB in colistin resistant bacteria and ompK36 in carbapenem resistant bacteria. The bacterial isolates were distributed into 37 sequence types and characterized by the presence of internationally recognized high-risk clones. The results indicate that humans and animals in Nigeria may serve as reservoirs and vehicles for the global spread of the isolates. Further studies on antimicrobial resistance in African countries are warranted.

Household and animal factors associated with sheeppox and goatpox sero-prevalence and identification of high-risk areas in selected States of northern Nigeria.

Sheeppox and goatpox (SGP) are transboundary, highly contagious diseases affecting sheep and goats with characteristic clinical signs. SGP affect populations of small ruminants in Africa, Asia and the Middle East and, as a result, threaten farmers' livelihoods. Despite their importance, studies looking at factors that increase the risk of sheeppox-virus (SPPV) and goatpox-virus (GTPV) exposure and infection are limited. A cross-sectional study was conducted in three states of Northern Nigeria (Bauchi, Kaduna and Plateau) to determine the sero-prevalence and spatial patterns of SGP, and identify risk factors for SPPV/GTPV exposure at animal and household level. Sera samples were collected from 1,800 small ruminants from 300 households. Data on putative risk factors were collected using a standardised questionnaire. Twenty-nine small ruminants were sero-positive to SGP - apparent weighted sero-prevalence 2.0 %; 95 % C.I. 1.1-.3.0 %. Sero-positive animals came from 19 (6.3 %) households. Analysis of the questionnaire showed that a fifth (20.3 %) of farmers claimed to have experienced SGP outbreaks previously in their flocks, with 33 (1.8 %) of the individual animals sampled in this study reported to have had clinical signs. At animal level, the odds of being sero-positive were higher in older animals (>24months; OR = 8.0, p = 0.008 vs ≤24 months) and small ruminants with a history of clinical SGP (OR = 16.9, p = 0.01). Bringing new small ruminants into the household and having a history of SGP in the flock were the main factors identified at household level. Households were less likely to be sero-positive if the time between bringing animals into the household and sampling was over a year (PR = 0.31, p = 0.05), while households with a history of SGP were more likely to be sero-positive regardless of the timeframe. Important spatial heterogeneity was found. The Bayes smooth rate ranged from 0.06 to 4.10 % across local government areas (LGA), with LGA in the north-east or north-west of the study area identified as hot-spots for SGP exposure. Results from this study shed new light on the understanding of SGP epidemiology and provide key inputs to design risk-based surveillance and intervention programmes in the area.

Knowledge, attitude, and practice among healthcare workers towards COVID-19 outbreak in Nigeria.

BACKGROUND: Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection is a global pandemic. Healthcare workers' (HCWs) role in patient management is predisposing and can serve as means of hospitals and community transmission. This study evaluated HCWs' knowledge, attitude, and practice towards COVID-19 in Nigeria. METHODS: we carried out a cross-sectional survey among HCWs during the COVID-19 outbreak in Nigeria from March to June 2020. The study assessed 346 HCWs for Knowledge, attitude, and practice by using an online (Google form) self-administered questionnaire, based on a convinience sampling technique Data were retrieved and analyzed using descriptive statistics. Chi-Square and one-way ANOVA were used to measure association and difference among demographic variables. The relationship between knowledge, attitude, and practice was measured using Spearman's rho correlation test. RESULTS: the mean knowledge score of the HCWs was 7.1 on a scale of 0-8. The correct overall rate of the knowledge questionnaire was 88.75%. Knowledge was gained mainly from television (35.0%) and social media (35.0%). The mean attitude score on a scale of 0-6 was 5.31 ± 0.39. Most (92.5%) participants were confident that Nigerian medical scientists would win the war against COVID-19. The majority (92.2%) of the respondents thought that SARS-CoV-2 was not a biological weapon. About 1 out of 5 respondents held that faith healing or prayer is the only cure for COVID-19. A vast majority of the HCWs were taking precautionary measures such as avoiding crowded places (94.2%), washing of hands (96.0%), and the use of personal protective equipment (91.6%) against SARS-CoV-2 infection. Nevertheless, only 3 out of 5 HCWs used a face mask when leaving home. There was a significant (p = 0.046) positive correlation (0.584) between knowledge and attitude. CONCLUSION: our results showed that HCWs in Nigeria had excellent knowledge and possessed a positive attitude and good practice towards COVID-19. However; there were areas where poor knowledge, negative attitudes and unacceptable practices were observed. We recommend continuous public health education of HCWs on SARS-COV-2 infection control and prevention.

RABIES IN A SET OF EIGHT-WEEK OLD PUPPIES IN NIGERIA: THE NEED FOR REVIEW OF CURRENT DOG ANTIRABIES VACCINATION SCHEDULE.

BACKGROUND: Rabies is endemic in Nigeria with clinical cases reported mainly in dogs and occasionally in livestock from all the geo-ecological zones of the country. Detection of rabies virus antigen in puppies at the age of five to ten weeks and in apparently healthy dogs shedding the virus in their saliva have been reported in some parts of Nigeria. MATERIAL AND METHOD: This report describes a clinical rabies in a set of eight weeks old puppies confirmed by antigen detection using the direct fluorescent antibody test (DFAT), the direct rapid immunohistochemical test (DRIT), and RT-PCR. RESULTS: it was positive for all test used including the RT-PCR which amplified at 750 bp from the gel electrophoresis. CONCLUSION: Occurrence of rabies in puppies of this age, within which they are acquired and owned by other unsuspecting members of the public, is of grave public health consequences. People that love puppies, especially children, who are fond of carrying and playing with them, are also faced with the risk of exposure to rabies. Consequently, review of the existing dog antirabies vaccination schedule at twelve weeks of age in Nigeria, is recommended to ensure effective immunization of this age group of dogs and for the overall safety of the vulnerable members of the public.

DIAGNOSIS OF ORF IN WEST AFRICAN DWARF GOATS IN UYO, AKWA IBOM STATE, NIGERIA.

BACKGROUND: Sixty (60) male West African Dwarf goats were reported with clinical signs of enlarged lymph nodes, scabs on the mouth, nose and ears. Two of the goats died and post mortem examination reveals enlarged submandibular lymph nodes and vesicular lesions on the tongue. Clinical diagnosis of Orf has been reported in Nigeria but this report is the confirmatory diagnosis of Orf in a suspected outbreak in an experimental farm in Uyo, Akwa Ibom State, Nigeria using molecular techniques. MATERIALS AND METHODS: Scabs, spleen and lymph node samples from goats suspected to have died from Orf were collected, transported on ice to the laboratory and homogenized. The DNA was extracted using QIAmp DNA minikit (Qiagen) according to the manufacturer's instructions. Orf virus (ORFV) was amplified using published ORFVspecific primers by PCR. RESULTS: Morbidity and mortality were 100% and 3.3% respectively, while ORFV was detected by PCR. Diagnosis of Orf was confirmed based on clinical signs of enlarged lymph nodes, scabs on the mouth, nose and ears, necropsy findings of enlarged submandibular lymph nodes and vesicular lesions on the tongue and PCR results. CONCLUSION: This may be the first report of molecular diagnosis of Orf in Nigeria. The 100% morbidity and 3.3% mortality rate is higher than previously reported thus Orf is becoming of greater economic importance than previously thought. It is therefore recommended that routine laboratory diagnosis of Orf be carried nationwide to determine the prevalence of Orf in Nigeria.

Characterization of high level ampicillin- and aminoglycoside-resistant enterococci isolated from non-hospital sources.

PURPOSE: High level ampicillin- and aminoglycoside-resistant enterococci are being increasingly reported from non-hospital sources. This study was carried out to characterize these strains from non-hospital sources in Nigeria. METHODOLOGY: A collection of Enterococcus faecium isolated from vegetables, soil, farm animals and manure and observed to be resistant to ampicillin (n=63) and gentamicin (n=37) discs, were screened for resistance to high levels of ampicillin and aminoglycoside using E-test strips. Putative high level ampicillin- and aminoglycoside-resistant strains were screened for pbp5 and aminoglycoside modifying enzyme genes, respectively, by PCR. The C-terminal region of the amplified pbp5 gene was also sequenced. RESULTS: Five (5/63) and thirty-five (35/37) of the ampicillin- and aminoglycoside-resistant strains were identified as high level ampicillin- and aminoglycoside-resistant E. faecium strains, respectively, based on the MIC results. The amplified pbp5 gene from the high level ampicillin-resistant isolates displayed 96-99 % nucleotide sequence similarity with the reference strains and three novel insertions (500Glu→Leu, 502Asp→Arg and 614Ile→Phe) in the amino acid sequence. Aminoglycoside modifying enzyme genes aac(6')-Ie-aph(2″) (100 %), aph(2')-Ic (88.8 %), aph(3')-IIIa (90 %) and ant(4')-Ia (40 %) were detected among the high level aminoglycoside-resistant isolates. CONCLUSION: This is the first report on the characterization of high level ampicillin- and aminoglycoside-resistant Enterococcus faecium among animals and vegetables in Nigeria. The results show that non-hospital sources can constitute a reservoir for potential dissemination of these strains and genes to humans via the food chain or by direct contact.

Equine Dermatophytosis: A Survey of Its Occurrence and Species Distribution among Horses in Kaduna State, Nigeria.

This study was designed to determine the occurrence and species distribution of dermatophyte from cutaneous skin lesions of horses in Kaduna State, Nigeria. A total of 102 skin scrapings were collected from 102 horses with skin lesions. Mycological studies were carried out using conventional techniques. Dermatophytes were isolated from 18 (17.6%) of the 102 samples collected. The 18 dermatophytes were distributed into 10 different species belonging to Microsporum (n = 5) and Trichophyton (n = 5) genera. T. verrucosum (n = 4) was the most predominant species isolated followed by M. equinum (n = 3), T. vanbreuseghemii (n = 2), M. gypseum (n = 2), and M. canis (n = 2). Others include M. fulvum (n = 2), T. mentagrophytes (n = 1), T. equinum (n = 1), T. soudanense (n = 1), and M. gallinae (n = 1). The present study reveals the occurrence of dermatophytes in cutaneous skin lesions of horses in Kaduna State, Nigeria. In addition for the first time in this environment the anthropophilic dermatophyte T. soudanense was isolated from horses. These findings have great economic, veterinary, and public health significance as they relate to the cost of treatment and dissemination of zoonotic dermatophytes.