In August 2025, Mozambique's Central Veterinary Laboratory, part of the Agricultural Research Institute, received broiler chicken carcasses for investigation after reports of elevated flock mortality. Pooled samples from the carcasses (i.e. trachea and lung) tested positive for influenza A. Subsequent subtyping ruled out hemagglutinin subtypes H5 and H7. Further analysis including tests for Newcastle disease virus, infectious bronchitis virus, infectious laryngotracheitis, and avian influenza subtype H9 confirmed the presence of H9. Whole-genome sequencing using Nanopore technology identified the virus as H9N2. Phylogenetic analysis of the hemagglutinin gene classified the virus within lineage G5.5, showing closer genetic similarity to strains circulating in the Middle East (e.g., Saudi Arabia, Jordan, and Israel) than to those in East or West Africa. This report is the first documented detection of H9N2 avian influenza in Mozambique, with significant implications for regional food security and disease management.

BACKGROUND:Streptococcus suis (S. suis) is a zoonotic pathogen causing economic losses in the swine industry and severe human infections. High serotype variability and genomic diversity of S. suis hinder cross-protective vaccine development. Although advances in in silico prediction-driven antigen discovery have accelerated protein vaccine development, discrepancies between predicted immunogenicity and experimentally verified protection in animal models emphasize the need to integrate computational design with empirical validation. METHODS:Using an in silico design strategy, predicted T- and B-cell epitope-rich domains from S. suis antigens (HP0197, Fnbp, Sao, ScpB, and SLY) were assembled into a multimeric vaccine, ATOMSSUISpenta, optimized for predicted immunogenicity, solubility, and allergenicity. Vaccine efficacy was evaluated in mice through antibody profiling, cellular immunity analysis, and assessment of cross-serotype immunity. RESULTS:ATOMSSUISpenta elicited strong humoral responses against all component antigens. The vaccine also induced Th1- and Th17-type cellular responses, critical for opsonic and mucosal defense against S. suis. In addition, ATOMSSUISpenta conferred significant protection in a S. suis serotype 2 infection and induced opsonic antibodies against serotypes 4 and 9. CONCLUSIONS:These findings highlight ATOMSSUISpenta as a subunit vaccine strategy with potential for broader protection and demonstrate the effectiveness of epitope-based multimeric design against antigenically diverse Gram-positive pathogens.

Introduction:Lumpy skin disease (LSD) threatens cattle health and productivity in Ivory Coast, where limited resources for livestock management hinder disease control. Moreover, the lack of studies on its prevalence and genetic profile leaves critical gaps in understanding its epidemiology and local risk factors. This study addresses these gaps by investigating LSD viruses' prevalence, its molecular characteristic and the associated risk factors among cattle in the Poro Region of northern Ivory Coast. Methods:Using a cross-sectional design, nodule and nasal swab samples were collected from 405 cattle across 36 villages between September 2023 and December 2024 based on syndromic surveillance. The samples were analyzed PCR to confirm LSD virus presence, followed by sequencing of four viral genes: RPO30, GPCR, EEV glycoprotein, and B22R. Results:Overall, LSD prevalence among cattle showing pox-like lesions and clinical symptoms was found to be 51.85% and varied significantly across localities, reaching 66.67% in M'bengué and 70.87% in Dikodougou. Larger herds (over 50 cattle) had a higher prevalence (76.51%) compared to smaller herds (34.72%), and transhumant herds showed increased prevalence (p < 0.001). No significant associations were identified between sex, age, or breed. Phylogenetic analysis indicated that the Ivory Coast LSDV strains clusters with other African field strains, distinct from South-East Asian and Russian recombinants. Discussion:The present study shows a notable regional difference in the prevalence of LSD in cattle in Ivory Coast, with big and transhumant herds having a higher prevalence rate making the herd size and movement a major risk factor. Molecular analysis demonstrated that Ivory Coast LSD strains are in the same group with other strains found in the African field, indicating that it is necessary to take control measures within the region and provide further surveillance.

Lumpy Skin Disease (LSD) is an economically significant viral disease of cattle, widely prevalent across Africa, particularly in sub-Saharan regions. In 2024, Tunisia reported its first outbreak. Understanding the genetic characteristics of lumpy skin disease virus (LSDV) and related poxviruses is critical for surveillance and control. Twenty-nine samples from 26 suspected cases were screened for LSDV using qPCR, followed by a High-Resolution Multiplex Melting (HRM) assay. Three representative samples, two LSDV-positive and one bovine papular stomatitis virus (BPSV)-positive, were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) HiFi long-read technology. Phylogenetic analyses of the LSDV-marker gene RPO30 and complete genomes were performed alongside SNP and InDel profiling. The Tunisian LSDV isolates clustered with Clade 1.2.2 field strains and were 100% identical to each other and to the Italian isolate LSDV_Italy_Sardinia_2025, sharing 99.99% nucleotide identity with LSDV_V281_Nigeria. Although only two LSDV isolates were sequenced which showed no genetic differences, these findings suggest genomic stability within Clade 1.2.2. The Tunisian BPSV isolate showed high similarity (98.15-98.59%) to strains reported in Germany and Switzerland. This study presents the first genetic characterization of LSDV and BPSV in Tunisia, highlighting the importance of accurate differential diagnosis among poxviruses and continuous genomic surveillance to inform control strategies.

Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for initial virus identification. This study introduces a multiplex family-wide PCR coupled with Nanopore sequencing of amplicons (FP-NSA) for surveillance of novel and known zoonotic respiratory viruses, including influenza A and D viruses (IAV and IDV), alpha (α-), beta (β-), and gamma (γ-) coronaviruses (CoVs). This assay utilized primers in conserved regions of each virus group for multiplex reverse transcription (RT)-PCR coupled with the portable MinION device for rapid Nanopore sequencing. The FP-NSA was optimized using seven IAV subtypes, IDVs, and α- and β-CoVs. The analytical sensitivity of the FP-NSA was assessed using positive controls of known concentrations from each targeted viral family and validated using clinical samples and cell culture isolates from various host species and geographical origins. Potential novel viruses detected in the clinical samples, based on the FP-NSA, were further analyzed using metagenomics sequencing with the Sequence-Independent Single Primer Amplification (SISPA) approach. The optimized FP-NSA assay efficiently detected all the targeted viruses singly as well as in co-infection scenarios of multiple respiratory viruses. Evaluation of the assay on 78 selected clinical and cell culture samples (from 184 initially screened) successfully detected IAVs; α-CoVs: porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) NL63, and HCoV-229E; β-CoVs: HCoV-OC43, severe acute respiratory syndrome (SARS)-CoV-(1), SARS-CoV-2, and MERS-CoV; and γ-CoV infectious bronchitis virus (γ-CoV_IBV) infections. Additionally, the FP-NSA assay discovered a novel γ-CoV_IBV from Guinea that is phylogenetically distant from known genotypes using a SISPA metagenomics approach. The assay’s short PCR amplicons enable screening of samples within 4 h, from PCR to sequencing and bioinformatics analysis, providing an adequate number of pathogens’ reads. The portable MinION device makes the assay suitable for pathogen surveillance in disease hotspots and resource-limited regions such as low- and middle-income countries. Thus, the FP-NSA assay is a valuable tool for detecting potential novel and known zoonotic respiratory viruses in the targeted families across various host species.

Lumpy Skin Disease (LSD) is an emerging bovine vector-borne disease of important economic impact on the cattle industry. Since its first identification in 1929, the disease was restricted for decades, to Sub-Saharan regions before its spread into new areas. In 2023 and 2024, LSD cases were identified for the first time in north African countries, Libya and Algeria, respectively. From June 2024, many LSD suspected cases were investigated in Tunisia. From June to October 2024, one hundred and twenty-one samples were investigated. Most of samples consist of blood samples, nasal and oral swabs from 49 suspected cattle from different parts of Tunisia. All samples were tested using Real-Time PCR and High Resolution Melting assay (HRM). On August 7, 2024, we reported the first LSD case in Tunisia. Two months later, other positive cases were confirmed by the two molecular techniques. The HRM technique allow the identification of a positive Bovine Papular Stomatitis animal presenting LSD clinical signs. Among the 49 tested cattle, eighteen were confirmed LSD positive. Most of LSD cases were from north western regions, close to Algerian border. The number of positive cases highly increased from October, period corresponding to increased LSD vectors’ activity. This is the first report on the identification of LSD in Tunisian cattle. Our findings confirm the progressive spread of LSD into new areas, and highlight the need of the implementation of control and surveillance measures to face such diseases.

In February 2024, an outbreak of African Swine Fever (ASF) was reported in a commercial pig farm in southwestern Angola. Five clinical samples were collected and sent to the Central Veterinary Laboratory in Windhoek, Namibia and the presence of ASF virus (ASFV) was confirmed. Sequencing of the C-terminus of the B646L gene (p72 protein), the complete E183L gene (p54 protein), the central hypervariable region (CVR) of the B602L gene, and the partial CD2v gene (used for serotyping) was performed on DNA isolated from the samples. Phylogenetic analyses of the B646L (p72) and the E183L gene (p54) revealed that the samples were identical to each other and belonged to genotype I. The viruses belonged to serotype 2 and had CVR profiles similar to those commonly found in ASFVs of genotype I. This is the first detailed report of ASFV in Angola and will be of interest to regional veterinary authorities.

Background Lumpy Skin Disease (LSD) is endemic in sub-Saharan countries and is currently a global threat to the cattle industry. Information on the circulating Capripoxvirus lumpyskinpox, formerly known as Lumpy Skin Disease Virus (LSDV), and other poxviruses infecting cattle is very scant in Tanzania. The current study aimed to confirm and characterize LSDV and other poxviruses infecting cattle, from LSD suspected outbreaks in Tanzania. Methods A total of 24 samples were collected from four LSD suspected outbreaks reported in Tanzania between February and May 2023. Samples were screened for LSDV genome by real-time PCR and then subjected to a high-resolution multiplex melting (HRM) assay where 10 samples were positive for Capripoxvirus (CaPV) and one sample was Parapoxvirus (PPV) positive. Four LSDV genes; RPO30, GPCR, EEV glycoprotein and B22R and the partial B2L gene of PPVs were analyzed. Results All targeted LSDV genes from the Tanzanian isolates showed 100% similarity and isolates clustered with commonly circulating LSDV field isolates. Furthermore, the single nucleotide polymorphism (SNP) at position 240 (A-> G) of the EEV gene differentiates the Tanzanian LSDVs from the group of ancient Kenyan LSDV isolates while the B22R sequences of the Tanzanian LSDV isolates differed from the LSDV Neethling and LSDV KSGP-0240 derived vaccines. Sequence analysis of the partial B2L gene of the Tanzanian parapoxvirus bovinestomatitis, formerly known as Bovine papular stomatitis virus (BPSV) showed a different BPSV strain circulating compared to publicly available sequences. Conclusion These findings confirm the presence of LSDV in Tanzania, which suggesting the need for establishing an effective control program and continuous monitoring. The presence of a typical profile for Tanzania BPSV is an indication that, although never reported before, BPSV is established in the country therefore this virus should be included in the differential diagnosis of LSDV.

Global eradication of peste des petits ruminants (PPR) is planned for 2030 by international animal health organizations in collaboration with national partners. As the deadline approaches, it is fundamental that the PPR status in each country is determined. In addition, the identification of other pathogens of small ruminants that share common geographical locations and can produce similar clinical signs is also important for differential diagnosis. With this in mind, 37 samples collected from goats and sheep presenting respiratory symptoms in Mauritania in 2023 were screened for the presence of PPR virus, Capripoxvirus, Pasteurella multocida and Mycoplasma capricolum subspecies capripneumoniae (Mccp) using a one-step multiplex RT-qPCR assay. None of the samples were positive for Capripoxvirus or P. multocida. Nine of them were positive for PPRV and sequence analysis of a segment of the PPRV nucleoprotein revealed that they belonged to lineage IV and were similar to viruses recently identified in Côte D’Ivoire, Guinea, and Niger indicating transboundary movement. The full genome of one representative virus was also generated. Mccp was identified in eight samples and multi-locus sequence analysis (MLSA) identified them as belonging to MLSA Group 3 together with Mccps identified in China, Tajikistan, Turkey and the United Arab Emirates. This is the first time that such a study has been undertaken in Mauritania and the data generated should be of interest to those involved in the management of goat diseases in Mauritania and neighbouring countries.

Abortion is one of the major causes of economic losses in livestock production worldwide. Because several factors can lead to abortion in cattle, sheep and goats, laboratory diagnosis, including the molecular detection of pathogens causing abortion, is often necessary. Bacterial zoonotic diseases such as brucellosis, coxiellosis, leptospirosis, and listeriosis have been implicated in livestock abortion, but they are under diagnosed and under-reported in most developing countries, including Botswana. This study applied a recently developed multiplex high-resolution melting analysis technique, coupled with singleplex qPCR assays, to investigate abortions in livestock in Botswana, using 152 samples from cattle, sheep, and goat abortion cases. Brucella spp. were the most frequent pathogen detected, with an overall frequency of 21.1%, followed by Coxiella burnetii with 19.1%. Listeria monocytogenes and Leptospira spp. were not detected in any of specimens samples investigated. Mixed infections with Brucella spp. and C. burnetii were observed in 35% specimes examined. There was a good agreement between the multiplex qPCR-HRM and singleplex qPCR for detecting Brucella spp. and C. burnetii. This study is the first report on the syndromic testing of abortion-causing pathogens in Botswana. It shows the importance of molecular methods in the differential diagnosis of abortion-causing diseases in domestic ruminants.

We report an outbreak of COVID-19 in a beaver farm in Mongolia in 2021. Genomic characterization revealed a unique combination of mutations in the SARS-CoV-2 of the infected beavers. Based on these findings, increased surveillance of farmed beavers should be encouraged.

Lumpy skin disease (LSD) is a transboundary viral disease of cattle and water buffaloes caused by the LSD virus, leading to high morbidity, low mortality, and a significant economic impact. Initially endemic to Africa only, LSD has spread to the Middle East, Europe, and Asia in the past decade. The most effective control strategy for LSD is the vaccination of cattle with live-attenuated LSDV vaccines. Consequently, the emergence of two groups of LSDV strains in Asian countries, one closely related to the ancient Kenyan LSDV isolates and the second made of recombinant viruses with a backbone of Neethling-vaccine and field isolates, emphasized the need for constant molecular surveillance. This current study investigated the first outbreak of LSD in Indonesia in 2022. Molecular characterization of the isolate circulating in the country based on selected LSDV-marker genes: RPO30, GPCR, EEV glycoprotein gene, and B22R, as well as whole genome analysis using several analytical tools, indicated the Indonesia LSDV isolate as a recombinant of LSDV_Neethling_vaccine_LW_1959 and LSDV_NI-2490. The analysis clustered the Indonesia_LSDV with the previously reported LSDV recombinants circulating in East and Southeast Asia, but different from the recombinant viruses in Russia and the field isolates in South-Asian countries. Additionally, this study has demonstrated alternative accurate ways of LSDV whole genome analysis and clustering of isolates, including the recombinants, instead of whole-genome phylogenetic tree analysis. These data will strengthen our understanding of the pathogens’ origin, the extent of their spread, and determination of suitable control measures required.

Sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV) are the three members of the genus Capripoxvirus within the Poxviridae family and are the etiologic agents of sheeppox (SPP), goatpox (GTP), and lumpy skin disease (LSD), respectively. LSD, GTP, and SPP are endemic in Africa and Asia, causing severe disease outbreaks with significant economic losses in livestock. Incursions of SPP and LSD have occurred in Europe. Vaccination with live attenuated homologous and heterologous viruses are routinely implemented to control these diseases. Using the gold standard virus neutralization test, we studied the ability of homologous and heterologous sera to neutralize the SPPV and LSDV. We found that LSD and SPP sera effectively neutralize their homologous viruses, and GTP sera can neutralize SPPV. However, while LSD sera effectively neutralizes SPPV, SPP and GTP sera cannot neutralize the LSDV to the same extent. We discuss the implications of these observations in disease assay methodology and heterologous vaccine efficacy.

On 13 October 2023, the National Directorate for Livestock Development in Mozambique was notified of a suspected outbreak of avian influenza in commercial layers. Samples were screened by real-time and conventional RT-PCR and were positive for both H7 and N6. Full genome sequences were obtained for three representative samples. Sequence analysis of the H7 cleavage site confirmed that the viruses were highly pathogenic (i.e. 333- PEPPKGPRFRR/GLF-346). In addition, the H7 and N6 sequences were highly similar (from 99.4-99.5% and 99.6-99.7% for the HA gene and the NA gene, respectively) to the sequences of a H7N6 virus identified in the Republic of South Africa in May 2023 indicating a similar origin of the viruses. The identification of H7N6 HPAIV in Mozambique has important implications for disease management and food security in the region.

The three members of the genus capripoxvirus (CaPV), lumpy skin disease virus (LSDV), sheeppox virus (SPPV), and goatpox virus (GTPV) have common hosts and areas of overlapping geographical distribution with Rift Valley fever virus (RVFV). Hence, to ensure more cost-effective disease surveillance we developed and evaluated a Luminex assay for the simultaneous detection of antibodies against CaPV and RVFV in domestic ruminants. In cattle, the assay had a sensitivity (Se) of 98.7% and a specificity (Sp) of 98.3% in detecting anti-LSDV antibodies; both diagnostic parameters were 100% for the detection of anti-RVFV antibodies in this species. In sheep and goats, Se and Sp were 100% for the detection of anti-SPPV and anti-GTPV antibodies while they were 100% and 98.9%, respectively for the detection of anti-RVFV antibody. The assay did not cross react with anti-parapoxvirus antibodies of cattle, sheep, and goats. This multiplex serological assay offers a practical tool for accurate detection and monitoring of the immunological status of domestic ruminant populations against veterinary and socio-economically important capripox- and phleboviral infections, thus has the potential to aid in the strategic application of vaccination programmes.

This paper explores the significance of quality vaccines in managing ASF in Asia, where it poses a substantial threat to the pork industry. It emphasizes the risks associated with substandard vaccines, including the emergence of new virus strains that complicate disease control. Highlighting recent advancements in vaccine deployment in Vietnam, the paper calls for rigorous testing and regulations to guarantee vaccine effectiveness and safety. The authors advocate for the implementation of vaccines with the inclusion of differentiating infected from vaccinated animals (DIVA), which enhances disease management strategies in both endemic and non-endemic regions. The conclusion underscores the necessity of stringent standards in vaccine development and strict adherence to regulatory guidelines to ensure successful ASF management and maintain public trust in the vaccines.

Lumpy skin disease is one of the fast-spreading viral diseases of cattle and buffalo that can potentially cause severe economic impact. Lesotho experienced LSD for the first time in 1947 and episodes of outbreaks occurred throughout the decades. In this study, eighteen specimens were collected from LSD-clinically diseased cattle between 2020 and 2022 from Mafeteng, Leribe, Maseru, Berea, and Mohales’ Hoek districts of Lesotho. A total of 11 DNA samples were analyzed by PCR and sequencing of the extracellular enveloped virus (EEV) glycoprotein, G-protein-coupled chemokine receptor (GPCR), 30 kDa RNA polymerase subunit (RPO30), and B22R genes. All nucleotide sequences of the above-mentioned genes confirmed that the PCR amplicons of clinical samples are truly LSDV, as they were identical to respective LSDV isolates on the NCBI GenBank. Two of the elevem samples were further characterized by whole-genome sequencing. The analysis, based on both CaPV marker genes and complete genome sequences, revealed that the LSDV isolates from Lesotho cluster with the NW-like LSDVs, which includes the commonly circulating LSDV field isolates from Africa, the Middle East, the Balkans, Turkey, and Eastern Europe.

In January 2022, significant mortality was observed among Cape cormorants (Phalacrocorax capensis) on the west coast of Namibia. Samples collected were shown to be positive for H5N1 avian influenza by multiplex RT-qPCR. Full genome analysis and phylogenetic analysis identified the viruses as belonging to clade 2.3.4.4b and that it clustered with similar viruses identified in Lesotho and Botswana in 2021. This is the first genomic characterization of H5N1 viruses in Namibia and has important implications for poultry disease management and wildlife conservation in the region.

Abortifacient pathogens induce substantial economic losses in the livestock industry worldwide, and many of these pathogens are zoonotic, impacting human health. As Brucella spp., Coxiella burnetii , Leptospira spp., and Listeria monocytogenes cause abortion, rapid differential molecular diagnostic tests are needed to facilitate early and accurate detection of abortion to establish effective control measures. However, the available molecular methods are laborious, time-consuming, or costly. Therefore, we developed and validated a novel multiplex real-time polymerase chain reaction (qPCR) method based on high-resolution melting (HRM) curve analysis to simultaneously detect and differentiate four zoonotic abortifacient agents in cattle, goats, and sheep. Our HRM assay generated four well-separated melting peaks allowing the differentiation between the four zoonotic abortifacients. Out of 216 DNA samples tested, Brucella spp. was detected in 45 samples, Coxiella burnetii in 57 samples, Leptospira spp. in 12 samples, and Listeria monocytogene s in 19 samples, co-infection with Brucella spp . and Coxiella burnetii in 41 samples, and 42 samples were negative. This assay demonstrated good analytical sensitivity, specificity, and reproducibility. This is a valuable rapid, cost-saving, and reliable diagnostic tool for detecting individual and co-infections for zoonotic abortifacient agents in ruminants.

Since anthropo-zoonotic outbreaks of SARS-CoV-2 have been reported in mink farms, it is important to monitor the seroprevalence within this population. To investigate the accuracy of nucleo (N) or spike (S) protein-based assays to detect anti-SARS-CoV-2 antibodies in animal serum, we compared four assays, two commercial N-based enzyme-linked immunosorbent assays (ELISA) validated for animal sera and two luciferase immunoprecipitation systems (LIPS-N and LIPS-S), to the reference standard plaque reduction neutralisation test (PRNT). Samples included in this study were derived from a naturally infected mink population. For the first time in this study, serum samples of mink were collected over a 307-day period, at different time points, thus providing an overview of performances of four different rapid serological tests over time. The assays were compared by performing a correlation analysis using R2, Spearman’s rank-order correlation coefficient, and Fleiss’ and Cohen’s kappa for analysis of agreement to PRNT, and an UpSet chart was created to visualize the number of shared positive samples between assays. Cohen’s kappa test on categorical data showed an excellent agreement between PRNT and LIPS-S, while agreements between PRNT and N-based methods decreased from fair for LIPS-N to poor agreements for the ELISA kits. In addition, LIPS-S revealed the highest number of true-positive SARS-CoV-2 samples compared to N-based methods. Despite an excellent agreement between LIPS-S and PRNT, a weak correlation was detectable between PRNT titres and relative light units. This study shows that the LIPS-S assay can be used for serological surveillance within a naturally exposed mink population, while N-based serological assays are less accurate providing a higher number of false-negative results, especially at a later stage of infection, thus indicating that N antibodies are less persistent in naturally exposed mink. Our findings provide crucial information for veterinarians and competent authorities involved in surveillance and outbreak investigation in wild and farmed minks.