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Since the first 2006 Avian Influenza (AI) outbreak in Nigeria, it has continued to circulate and ravage the poultry industry with huge economic losses above 130 billion naira. Local poultry are important sources of AI transmission and maintenance of the highly pathogenic avian influenza H5N1. Live bird markets (LBMs) are "breeding grounds" and major risk factors for human infection of AI. The seroprevalence of AI in local chickens in LBMs in Kaduna Metropolis, Nigeria was determined. Sera were obtained from the local chickens (n=300) in 5 daily LBMs and subjected to competitive enzyme-linked immunosorbent assay (c-ELISA) to detect the nucleoprotein antibodies. The c-ELISA positive samples were further screened by haemagglutination inhibition (HI) test for AI using H5, H7 and H9 antigens. The overall AI seroprevalence was 1.7 % with the highest individual seroprevalence of 3.3% in Kawo and Railway LBMs. There was no statistically significant association between the location of LBMs and AI presence, and between the sex and presence of AI antibodies (p = 0.427). One sample was HI positive for antibodies against H5, H7 and H9 with mean titers of 4, 2.5 and 3.5 log2, respectively. This implies the potential danger of the spread of AI among humans and animals. There should be sustained surveillance and biosecurity in the live bird market. [ABSTRACT FROM AUTHOR]

Influenza A virus presents a significant public health burden worldwide, with the 1918 Spanish flu pandemic being the most dramatic example. Swine influenza viruses can be transmitted to humans through occupational exposures and in live pig markets. Novel variants can emerge in pigs because they can be infected by human, avian and swine strains. This study was carried out to determine the seroprevalence and serotypes of swine influenza in pigs from a major slaughter slab in southern Kaduna. Using competitive ELISA and haemagglutination-inhibition (HI) assays, 305 swine sera were analysed. The result showed an overall seroprevalence of 28.20% (n=86), with H3N2 7.87% (n=24) emerging as the most dominant subtype in circulation. Concurrent antibody detection of H1N1 in 5.26% (n=16) was also detected in boar 2.62% (n=8) and sows 2.62% (n=8). This study revealed swine Influenza H1N1 and H3N2 serotypes are in circulation in pigs in Kaduna State, and that reassortment in the instance of co-infection of swine host is possible. [ABSTRACT FROM AUTHOR]

Avian influenza has impacted negatively on poultry production in Nigeria. The aim of this study was to determine the status of avian influenza virus (AIV) antibodies in wild birds to provide early warning of an outbreak. One hundred and forty-six sera from five different species of wild birds were tested for antibodies to avian influenza A viruses (H5 and H9) using enzyme linked immunosorbent assay and haemagglutination inhibition (HI) tests. An overall seroprevalence of 3.4% (5/146) was recorded in the study area. Seroprevalence of 6.67% (2/30) was recorded in speckled pigeons (Columba guinea) and Village weavers (Ploceus cucullatus) respectively and 3.33% (1/30) in Cattle egrets (Bubulcus ibis). No antibodies were detected in laughing doves (Spilolepia senegalensis) and African silver bill (Euodice cantans). The serological detection of AIV subtypes H5 and H9 by HI showed the exposure of these birds to the two subtypes. The result from this study indicates evidence of the presence of H5 and H9 AI viruses in wild birds in Zaria, Kaduna State. Therefore, comprehensive surveillance of influenza A involving wild birds' population and H5 as well as H9 subtype is recommended. This is necessary in order to know the actual status of these strains in the poultry population in Nigeria in view of their zoonotic and economic importance. [ABSTRACT FROM AUTHOR]

Infectious bronchitis (IB) is one of the most common highly infectious viral respiratory diseases of poultry having wide geographical distribution. Yet, little is known about the infection in the northwestern states of Nigeria. In this study, a total of 263 pooled cloacal and tracheal swab samples were collected from apparently healthy avian species (duck, dove, geese, guinea fowl, local chicken, ostrich, parrot, pigeon, peacock, and turkey). The samples were from nine live bird markets in three states (Kaduna, Kano and Jigawa) of northwestern, Nigeria collected from September through November 2017. Total RNAs were extracted directly from the swab samples and screened for infectious bronchitis virus (IBV) using real-time reverse transcription-polymerase chain reaction. An overall prevalence of 38.0% (100/263) was recorded. IB was detected in 70 % (7/10) of the avian species with prevalence of 100 % in dove, local chicken 45.9 %, duck 42.3 %, geese 26.6 %, pigeon 23.5 %, turkey 20.0 % and guinea fowl 6.2 %. Conversely, no detection was made from ostrich, parrot, and peacock. Widespread distribution of IBV was observed and evidence of subclinical infection in seven out of ten (70 %) of the avian species sampled. These avian species harbouring IBV may act as reservoirs with an influence on the ecology and epidemiology of the disease. Continuous surveillance and characterization of the different serotypes in avian species are recommended to inform the adoption of suitable vaccination strategy and control measures for the disease in Nigeria. [ABSTRACT FROM AUTHOR]

Globally, infectious bronchitis (IB) is an important respiratory viral disease responsible for enormous economic losses to poultry farmers. In Nigeria, limited reports on the prevalence and serotypes of the IB virus are available. Here, we investigated the prevalence and serotypes of infectious bronchitis virus (IBV) in chicken in Plateau State. A descriptive cross-sectional study was carried out involving 440 apparently healthy free-range local chickens sampled from eleven villages in four Local Government Areas (LGA) of Plateau State. Sera collected from the birds were screened for the presence of four IBV serotypes namely; Massachusetts (Mass), Arkansas (Ark), Connecticut (Con) and Delaware (De-072) using haemagglutinationinhibition (HI) test. In all, a prevalence of 82.95% (n = 365) was recorded. At LGA level, prevalence of 79.50%, 47.37%, 95.45% and 100% were recorded in Kanam, Mangu, Qua'an pan and Bassa LGAs, respectively. Based on serotype prevalence, Mass had 89.30% (n = 326); Ark 79.70% (n = 291); Con 88.20% (n = 322) while De-072 was 42.70% (n = 156). There were statistically significant associations between dominant serotype and the LGAs (p=0.001). This study shows high prevalence of IB with at least four strains of IBV present in free-range chicken flocks in Plateau State requiring attention for control measures. [ABSTRACT FROM AUTHOR]

Newcastle disease is one of the major economic threats to poultry population because of its high morbidity and mortality varying from 90-100%. It is caused by Avian Paramyxovirus-1 (APMV-1). This research work was carried out to identify Newcastle disease virus (NDV) by using reverse transcription-polymerase chain reaction (RT-PCR) assay and further isolate the virus in embryonated chicken eggs. A total of 127 cloacal swabs were collected from local chickens in live bird market and exotic chickens in commercial poultry farms in Zaria and environs, Nigeria between November, 2014 and January, 2015. Five commercial poultry farms and four live bird markets were purposively sampled. Molecular screening of NDV Matrix-gene (M-gene) was performed on all the samples using Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). Newcastle disease positive samples were further inoculated into embryonated chicken eggs for isolation of Newcastle disease virus. Isolates were confirmed as Newcastle disease virus by haemaggulitination inhibition (HI) test. Newcastle disease virus Matrix-gene was detected in 16 (12.5%) out of 127 cloacal swabs; 13 (10.2%) from live bird markets and 3 (2.3%) from commercial poultry farms. However, only 10 Newcastle disease viruses were isolated in embryonated chicken eggs as confirmed by Haemagglutination inhibition (HI) test. Due to the higher detection rate recorded by reverse transcriptase-polymerase chain reaction (RT-PCR), it is therefore important that molecular technique be made easily accessible so that samples from each suspected outbreaks of NDV be screened so that rapid and confirmatory diagnosis can be achieved. [ABSTRACT FROM AUTHOR]

Over the years the federal government of Nigeria's budget has been in deficit and this has been receiving attention as regards its effect on the economy and other macroeconomic variables in Nigeria. The study, therefore, examines the impact of government budget deficits on macroeconomic variables (interest rate, exchange rate, inflation rate, money supply, and gross domestic product) in Nigeria. The study employed a time series data between 1981 and 2019 which was subjected to unit root test adopting Augmented Dickey-Fuller to test the stationary of the variable. The result revealed that the variables are stationary at level and 1st difference at intercept. VAR lag order selection criteria test was conducted and most of the criteria suggested lag 2 which was used for the analysis. ARDL bounds test affirmed the existence of a long-run relationship among the variables, hence subjected to ARDL cointegration and long-run form test. The interest rate model indicated a positive and significant relationship between government budget deficits and interest rate while the exchange rate model specified a negative but insignificant relationship between government budget deficits and exchange rate. The study, therefore, recommended that government should minimize budget deficits by minimizing its recurrent expenditure and ensure strict government expenditure control to avoid possible corruption. Government support for local production should be improved to encourage export and minimize importation which will thereby appreciate Naira, and government should ensure a way of improving revenue generation to minimize deficits through tax collection and other levies.

The COVID-19 pandemic has caused the death of 7.1 million people worldwide as of 7 July 2024. In Nigeria, the first confirmed case was reported on 27 February 2020, subsequently followed by a nationwide spread of SARS-CoV-2 with morbidity and mortality reaching 267 173 and 3155, respectively, as of 7 July 2024. At the beginning of the pandemic, only a few public health laboratories in Nigeria had the capacity for SARS-CoV-2 molecular diagnosis. The National Veterinary Research Institute (NVRI), already experienced in influenza diagnosis, responded to the public health challenge for the diagnosis of COVID-19 samples from humans. The feat was possible through the collective utilisation of NVRI human and material resources, including biosafety facilities, equipment, reagents and consumables donated by international partners and collaborators. Within 6 months of the reported COVID-19 outbreak in Nigeria, over 33 000 samples were processed in NVRI facilities covering five states. Thereafter, many field and laboratory projects were jointly implemented between NVRI and collaborating sectors including the Nigerian Centre for Disease Control (NCDC) and the National Institute for Medical Research (NIMR), which brought together professionals in the health, veterinary, education and socio-sciences. In addition, One Health grants were secured to enhance surveillance for coronavirus and other zoonoses and build capacity in genomics. Bio-surveillance for coronaviruses and other emerging zoonotic pathogens at the human-animal interface was activated and continued with sample collection and analysis in the laboratory for coronaviruses, Lassa fever virus and Mpox. One Health approach has shown that inter-sectoral and multinational collaboration for diagnosis, research and development in animals, and the environment to better understand pathogen spillover events at the human-animal interface is an important global health priority and pandemic preparedness.

During March and April 2024, we studied dairy cattle specimens from a single farm in Texas, USA, using multiple molecular, cell culture, and next-generation sequencing pathogen detection techniques. Here, we report evidence that highly pathogenic avian influenza A(H5N1) virus strains of clade 2.3.4.4b were the sole cause of this epizootic.

Anthropogenic exposure of domestic animals, as well as wildlife, can result in zoonotic transmission events with known and unknown pathogens including sarbecoviruses. During the COVID-19 pandemic, SARS-CoV-2 infections in animals, most likely resulting from spill-over from humans, have been documented worldwide. However, only limited information is available for Africa. The anthropozoonotic transmission from humans to animals, followed by further inter- and intraspecies propagation may contribute to viral evolution, and thereby subsequently alter the epidemiological patterns of transmission. To shed light on the possible role of domestic animals and wildlife in the ecology and epidemiology of sarbecoviruses in Nigeria, and to analyze the possible circulation of other, undiscovered, but potentially zoonotic sarbecoviruses in animals, we tested 504 serum samples from dogs, rabbits, bats, and pangolins collected between December 2020 and April 2022. The samples were analyzed using an indirect multi-species enzyme-linked immunosorbent assay (ELISA) based on the receptor binding domain (RBD) of SARS-CoV and SARS-CoV -2, respectively. ELISA reactive sera were further analyzed by highly specific virus neutralization test and indirect immunofluorescence assay for confirmation of the presence of antibodies. In this study, we found SARS-CoV reactive antibodies in 16 (11.5%) dogs, 7 (2.97%) rabbits, 2 (7.7%) pangolins and SARS-CoV-2 reactive antibodies in 20 (13.4%) dogs, 6 (2.5%) rabbits and 2 (7.7%) pangolins, respectively. Interestingly, 2 (2.3%) bat samples were positive only for SARS-CoV RBD reactive antibodies. These serological findings of SARS-CoV and/or SARS-CoV-2 infections in both domestic animals and wildlife indicates exposure to sarbecoviruses and requires further One Health-oriented research on the potential reservoir role that different species might play in the ecology and epidemiology of coronaviruses at the human-animal interface., Competing Interests: The authors declare no competing interest., (© 2024 The Authors.)

Marek's disease (MD) and chicken infectious anaemia (CIA) are viral immunosuppressive diseases of poultry caused by the MD virus (MDV) and CIA virus (CIAV) respectively. Despite vaccination against MD, the incidence of the disease in vaccinated poultry flocks in Nigeria persists. However, underlying factors like co-infection with CIAV have not been investigated in the country. This study was designed to investigate possible co-infections of MDV and CIAV in poultry flocks in Nigeria. In 2016, tumorous tissue samples were collected from suspected cases of MD at necropsy in Jos, Plateau State, Nigeria. The samples collected were fixed in formalin for histopathological examination, genomic DNA was extracted from a second part and analysed by polymerase chain reaction (PCR), targeting the meq and VP1 genes of the MDV and CIAV, respectively. The histology results revealed that the cutaneous and proventricular lymphomas were characterized by large numbers of mononuclear cellular infiltrates admixed with heterophils. The PCR results revealed that MDV was detected in 66.7% (16/24), CIAV in 45.8% (11/24), and co-infections of MDV and CIAV were detected in 45.8% (11/24) of the samples analysed. In addition, co-infections of MD and CIA were recorded in 100% (6/6) and 27.7% (5/18) of broilers and layer/pullet' samples respectively. Phylogenetic analysis of the meq gene sequences revealed that the Nigerian MDV clusters with very virulent MDV from Egypt and Italy. While, CIAV sequences were genotype II and genotype III and clustered with CIAVs from Cameroon and China. This is the first report of co-infections of MD and CIA in Nigeria., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Background: The introduction of multiple avian influenza virus (AIV) subtypes into Nigeria has resulted in several poultry outbreaks purportedly linked to trade and wild birds. The role of wild birds in perpetuating AIV in Nigeria was, therefore, elucidated., Methods: A cross-sectional study was conducted among wild aquatic bird species at the Hadejia-Nguru wetlands in Northeastern Nigeria between March and April 2022. A total of 452 swabs (226 cloacae and 226 oropharyngeal) were collected using a mist net to capture the birds. These samples were tested by RT-qPCR, followed by sequencing., Results: Highly pathogenic AIV of the H5N1 subtype was identified in clinically healthy wild bird species, namely, African jacana, ruff, spur-winged goose, squared-tailed nightjar, white-faced whistling ducks, and white stork. A prevalence of 11.1% (25/226) was recorded. Phylogenetic analysis of the complete HA gene segment indicated the presence of clade 2.3.4.4b. However, these H5N1 viruses characterized from these wild birds cluster separately from the H5N1 viruses characterized in Nigerian poultry since early 2021. Specifically, the viruses form two distinct genetic groups both linked with the Eurasian H5N1 gene pool but likely resulting from two distinct introductions of the virus in the region. Whole-genome characterization of the viruses reveals the presence of mammalian adaptive marker E627K in two Afro-tropical resident aquatic ducks. This has zoonotic potential., Conclusion: Our findings highlight the key role of surveillance in wild birds to monitor the diversity of viruses in this area, provide the foundations of epidemiological understanding, and facilitate risk assessment., Competing Interests: The authors declare no conflict of interest., (© 2024 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)

In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative regions in Nigeria. In this study, we characterized the genomes of 97 influenza A viruses of the subtypes H5N1, H5N2, and H5N8, which were identified in different agro-ecological zones and farms during the 2021-2022 epidemic. The phylogenetic analysis of the HA genes showed a widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses that have been detected in Europe since late 2020. The topology of the phylogenetic trees indicated the occurrence of several independent introductions of the virus into the country, followed by a regional evolution of the virus that was most probably linked to its persistent circulation in West African territories. Additional evidence of the evolutionary potential of the HPAI viruses circulating in this region is the identification in this study of a putative H5N1/H9N2 reassortant virus in a mixed-species commercial poultry farm. Our data confirm Nigeria as a crucial hotspot for HPAI virus introduction from the Eurasian territories and reveal a dynamic pattern of avian influenza virus evolution within the Nigerian poultry population.

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.

Arthropods, especially ixodid ticks, have been incriminated in the epidemiology of Spotted Fever Group rickettsioses globally leading to an increasing spectrum of emerging and re-emerging zoonoses with attendant consequences on trade and tourism. The objective of this study was to determine the role of ixodid ticks infesting small ruminants in Plateau State, Nigeria, in the epidemiology of Spotted Fever Group Rickettsiae (SFGR) in the study area. DNA from 130 out of 323 ixodid ticks collected from 179 goats and 121 sheep owned by agro-pastoralists in Plateau State were screened for the evidence of SFGR by molecular methods. Six tick species from four genera were identified: Amblyomma, Hyalomma, Rhipicephalus (Boophilus) and Rhipicephalus. Rhipicephalus sanguineus sensu lato (s.l.) was the predominant (54.5%) species among collected ticks. Tick infestation was significantly associated with the species of small ruminants, the sex of the animals and the sampling locations except for Jos South. Conventional PCR targeting the 381 bp of the citrate synthase (gltA) and 820 bp of the outer membrane protein B (ompB) genes detected DNA of SFGR in nine and eight samples, respectively. Sequence analysis revealed that five sequences obtained from Amblyomma variegatum were 99-100% identical to Rickettsia africae and three sequences from Rh. sanguineus (s.l.) were 100% identical to Rickettsia massiliae reported from Spain. To our knowledge, this is the first report of the detection of R. africae DNA in Am. variegatum collected from small ruminants in Plateau State. Ixodid ticks infesting small ruminants in Plateau state harbor DNA of SFGR with potential veterinary and public health implications., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

The coronavirus disease 2019 (COVID-19) pandemic has become the most far-reaching public health crisis of modern times. Several efforts are underway to unravel its root cause as well as to proffer adequate preventive or inhibitive measures. Zoonotic spillover of the causative virus from an animal reservoir to the human population is being studied as the most likely event leading to the pandemic. Consequently, it is important to consider viral evolution and the process of spread within zoonotic anthropogenic transmission cycles as a global public health impact. The diverse routes of interspecies transmission of SARS-CoV-2 offer great potential for a future reservoir of pandemic viruses evolving from the current SARS-CoV-2 pandemic circulation. To mitigate possible future infectious disease outbreaks in Africa and elsewhere, there is an urgent need for adequate global surveillance, prevention, and control measures that must include a focus on known and novel emerging zoonotic pathogens through a one health approach. Human immunization efforts should be approached equally through the transfer of cutting-edge technology for vaccine manufacturing throughout the world to ensure global public health and one health.

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., Competing Interests: The authors have no conflicts of interest to declare that are relevant to the content of this article., (Copyright © 2022 Olubukola O. Funsho-Sanni et al.)

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.

Avian metaavulavirus 2 (AMAV-2) previously known as the avian paramyxovirus-2 causes mild to severe respiratory disease, reduced hatchability and infertility of eggs, including increase in white-shelled eggs in chickens and Turkey breeders. When exacerbated by secondary pathogens and environmental stresses, infection is more severe leading to significant economic losses. This study was conducted to determine, if any, the presence of antibodies to Avian metaavulavirus 2 (AMAV-2) in peri-domestic birds in Bauchi State, Nigeria. In all, one hundred sera samples from pigeons (n = 10) and doves (n = 90 were collected in Bauchi, Nigeria. Based on hemagglutination-inhibition (HI) test, overall seroprevalence of 27.0% (27/100) was recorded. In pigeon, the seroprevalence was 80.0% while 21.1% was recorded for dove with HI antibody titers ranging from 3log 2 to 8log 2 . There was statistical significance obtained between dove and pigeon sera tested (p < .05). Until now and to the best of our knowledge, there are no reports on AMAV-2 in poultry or wild birds in Nigeria. This study, thus, provides preliminary information on AMAV-2 seroprevalence in Nigerian peri-domestic birds. The need to conduct further studies in other avian species and wild birds in Nigeria is highlighted.

Avian influenza viruses of the H9 subtype cause significant losses to poultry production in endemic regions of Asia, Africa and the Middle East and pose a risk to human health. The availability of reliable and updated diagnostic tools for H9 surveillance is thus paramount to ensure the prompt identification of this subtype. The genetic variability of H9 represents a challenge for molecular-based diagnostic methods and was the cause for suboptimal detection and false negatives during routine diagnostic monitoring. Starting from a dataset of sequences related to viruses of different origins and clades (Y439, Y280, G1), a bioinformatics workflow was optimized to extract relevant sequence data preparatory for oligonucleotides design. Analytical and diagnostic performances were assessed according to the OIE standards. To facilitate assay deployment, amplification conditions were optimized with different nucleic extraction systems and amplification kits. Performance of the new real-time RT-PCR was also evaluated in comparison to existing H9-detection methods, highlighting a significant improvement of sensitivity and inclusivity, in particular for G1 viruses. Data obtained suggest that the new assay has the potential to be employed under different settings and geographic areas for a sensitive detection of H9 viruses.

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., (© 2021 Wiley-VCH GmbH.)

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 a transparent and accessible 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 direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic., Competing Interests: The authors have declared that no competing interests exist.

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.

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., Competing Interests: The authors declare no competing interests., (Copyright: Ishaya Sini Tekki et al.)

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., (© 2020 Wiley-VCH GmbH.)

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., (Copyright © 2020 Elsevier B.V. All rights reserved.)