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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., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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.

Pig production is increasing annually in Africa as it is recognized as a significant source of income, livelihood and food security, particularly in rural communities. Understanding the circulating swine pathogens is crucial for the success of this emerging industry. Although there is extensive data available on the African swine fever virus due to its devastating impact on pig production, knowledge about the presence of other viral swine pathogens on the continent is still extremely limited. This review discusses what is currently known about six swine pathogens in Africa: classical swine fever virus, porcine reproductive and respiratory syndrome virus, porcine circovirus-2, porcine circovirus-3, porcine parvovirus-1, and pseudorabies virus. Gaps in our knowledge are identified and topics of future focus discussed., Competing Interests: Declaration of Competing Interest 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., (Copyright © 2024 Elsevier B.V. All rights reserved.)

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.

Introduction: The swine sector in Africa plays an important role in local economies, contributing to poverty alleviation and community subsistence. In addition, intensive farming is progressively becoming more important in the region. Therefore, any disease affecting swine populations can have detrimental effects on local communities. Porcine Reproductive and Respiratory Syndrome (PRRS) is among the most important infectious diseases affecting swine worldwide, but information on its epidemiology in Africa is extremely limited., Material and Methods: In the present study, 147 healthy butchered pigs, originating from 15 Namibian intensive and rural farms were tested by RT-PCR and the ORF7 genes of positive samples were sequenced for further genetic characterization and phylogenetic analysis. Additionally, 55 warthogs were also evaluated using the same approach., Results: Overall, 7 out of 147 pigs (4.76%) tested positive, all originating from 3 rural farms (with a within-herd detection frequency higher than 14%) characterized by strong epidemiological links. All industrial pig and warthog samples were negative. Sequence analysis revealed that all strains belonged to the Betaarterivirus suid1 species, previously known as PRRSV type I, and were likely imported from Europe at least 6 years ago, evolving independently thereafter. When and how the first introduction occurred could not be determined due to the absence of other African sequences for comparison., Discussion: The present work provides the first detection and characterization of PRRSV molecular epidemiology in Namibia. Based on the present findings, the presence of the PPRSV appears marginal and limited to backyard farms. While biosecurity measures applied in industrial farms appear to be effective in preventing viral introduction, PRRSV circulation in rural settings still represents a potential threat, and considering the socio-economical implication of livestock diseases decreasing animal performances in rural areas, active monitoring should be encouraged to promptly act against emerging menaces and guarantee the welfare of local pig populations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Molini, Coetzee, Hemberger, Chiwome, Khaiseb, Dundon and Franzo.)

Since its first identification in 2015, porcine circovirus 3 (PCV-3) has been reported worldwide with a high frequency and in the presence of several clinical conditions, although its impact on pig health and productivity is still debated. Data on the presence of PCV-3 in Africa are, however, limited. A previous study performed on commercial pigs in Namibia failed to identify the pathogen. In the present study, the viral circulation in backyard farms, characterised by lower biosecurity measures and frequent animal exchange between farms, was assessed. The susceptibility of warthogs to PCV-3 infection and their potential epidemiological role were also evaluated. Tonsils from 77 pigs from backyard piggeries and 55 warthogs were collected in different regions of Namibia and tested by PCR. Positive samples were sequenced and compared to PCV-3 strains circulating globally. Forty-two out of 77 pigs (54.54 %) and 12 out of 55 warthogs (21.82 %) tested positive, demonstrating the presence of PCV-3 in the country and suggesting that the high biosecurity measures implemented in the commercial farms that previously tested negative for PCV-3 probably prevented viral introduction. The partial ORF2 gene was successfully sequenced in samples from 27 pigs and 6 warthogs. Genetically, the identified strains were part of 3 distinct groups which included both backyard pigs and warthogs from different regions of Namibia. There is also evidence for the occurrence of multiple introduction events most likely from Asian countries, either directly into Namibia or through other African countries. Considering the strict Namibian regulations on live animal importation, understanding the source of viral introduction is challenging, although semen importation or the habit of feeding backyard pigs with human food waste might have played a role. Pig exchanges between farms for breeding purposes or wildlife movements could also have been involved in PCV-3 dispersal within Namibia. Despite the significant advances in the field, further studies should be undertaken to properly understand PCV-3 epidemiology in Namibia and its impact on pig productivity and wildlife health., Competing Interests: Declaration of Competing Interest 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., (Copyright © 2023. Published by Elsevier B.V.)

In February 2022, mortalities among great white pelicans (Pelecanus onocrotalus) were reported in the Parc National de Diawling, southwestern Mauritania. Samples were collected and processed, indicating the presence of high pathogenicity avian influenza subtype H5N1. A nearly complete genome was generated for one sample, revealing a high similarity [> 99.5% (H5) nucleotide sequence identity] with Clade 2.3.4.4b H5N1 identified in Europe in 2022., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Thirty-five samples collected from chickens in 13 commercial farms in Eritrea between 2017 and 2021 following reports of disease were screened for Newcastle disease virus. Seventeen samples (50%) were shown to be positive by RT-PCR. An initial analysis of partial fusion (F) gene sequences of 10 representative samples indicated that the viruses belonged to subgenotype VII.1.1. Subsequently, full F gene sequence analysis of four of these representative samples confirmed the genotype of the viruses but also revealed that they were not identical to each other suggesting different origins of the VII.1.1 subgenotype viruses circulating in Eritrea. These data have implications for the control of Newcastle disease within the poultry population in Eritrea.

Like in many other African countries, pig production is increasing in Tanzania. To support farmers and stakeholders, it is important to increase our understanding of porcine pathogens present in the country. Currently, little is known about the circulation of porcine circovirus-2 (PCV-2) and porcine circovirus-3 (PCV-3). For this reason, samples from 124 pigs collected throughout the country between 2018 to 2022 were screened by PCR for the presence of PCV-2 and PCV-3. Sequencing and phylogenetic analysis of positive amplicons identified two PCV-2 genotypes (a and d). Limited genetic heterogenicity was observed among the PCV-3. This study provides important data on pathogens present in pigs in Tanzania and should be of use veterinary authorities involved in porcine disease management.

Thirty swine samples collected from different regions of Namibia between 2019 and 2020 were screened for the presence of porcine parvovirus 1 (PPV1) by PCR. Eleven samples (37%) were positive. Phylogenetic analysis of a partial sequence of the structural protein gene (VP2) identified two distinct clusters, one which contained sequences that were highly similar to PPV1 previously identified in warthogs in Namibia. These results indicate possible PPV1 transmission between warthogs and domestic pigs and highlight the importance of wildlife as sources of pathogens., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

Monitoring the transboundary spread of peste des petits ruminants (PPR) virus is an essential part of the global efforts towards the eradication of PPR by 2030. There is growing evidence that Lineage IV is becoming the predominant viral lineage, replacing Lineage I and II in West Africa. As part of a regional investigation, samples collected in Burkina Faso, Côte d'Ivoire, Guinea and Ghana were screened for the presence of PPRV. A segment of the nucleoprotein gene from positive samples was sequenced, and phylogenetic analysis revealed the co-circulation of Lineage II and IV in Burkina Faso, Côte d'Ivoire and Guinea, and the identification of Lineage IV in Ghana. These data will be of importance to local and regional authorities involved in the management of PPRV spread.

The commercial farming and trading of parrots and ornamental birds as companion animals are important economic activities in many countries. Some of the bird species farmed/traded are captured from the wild or are closely related to wild birds and therefore represent a risk of pathogen exchange/introduction. Beak and feather disease virus (BFDV) and avian poliomavirus (APV) are among the viruses with the biggest impact on companion bird populations and have been detected in different hosts worldwide. Despite their relevance for both domesticated and wild birds, our knowledge of BFDV and APV epidemiology remains limited in several African countries. In the present study, 143 cloacal swabs were collected from companion birds in Windhoek, Namibia, and tested by polymerase chain reaction for BFDV and APV. Of the samples tested, 35/143 (24.48%) tested positive for BFDV; 11/143 (7.69%) were positive for APV; and 6/143 (4.2%) tested positive for both pathogens. Positive amplicons, consisting of segments of the ORF1 and VP1 genes, were sequenced and compared with sequences from viruses identified in other countries. Four Namibian-only clades of BFDV were identified, loosely related to foreign strains, which suggest the occurrence of multiple introduction events in the past, potentially from South Africa, followed by local, independent evolution. In contrast, the Namibian APV sequences were identical to each other and form a single clade. In both instances, no correlation was observed between the sampling host and the viral phylogeny, suggesting the absence of host-specific adaptation and a remarkable, unconstrained viral circulation within Namibian borders. Therefore, while regulations and control measures developed against foreign strain introduction have proven to be effective over time, the spread of BFDV and APV within Namibia's borders appears undeterred. Additional resources should be dedicated to limit strain circulation in commercial farming facilities, markets and small-scale traders., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011-2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence.

As pig production increases in Africa, it is essential to identify the pathogens that are circulating in the swine population to assess pig welfare and implement targeted control measures. For this reason, DNA samples collected from pigs in Nigeria in the context of African swine fever monitoring were further screened by PCR for porcine circovirus 2 (PCV-2), porcine circovirus 3 (PCV-3), and porcine parvovirus 1 (PPV1). Forty-seven (45%) pigs were positive for two or more pathogens. Sequence analysis identified PCV-2 genotypes a, b, and d, while limited genetic heterogenicity was observed among PCV-3 strains. All except one of the PPV1 sequences were genetically distinct from those previously identified in other countries., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Numerous outbreaks of high-pathogenicity avian influenza (HPAI) were reported during 2020-2021. In Africa, H5Nx has been detected in Benin, Burkina Faso, Nigeria, Senegal, Lesotho, Namibia and South Africa in both wild birds and poultry. Botswana reported its first outbreak of HPAI to the World Organisation for Animal Health (WOAH) in 2021. An H5N1 virus was detected in a fish eagle, doves, and chickens. Full genome sequence analysis revealed that the virus belonged to clade 2.3.4.4b and showed high identity within haemagglutinin (HA) and neuraminidase proteins (NA) for viruses identified across a geographically broad range of locations. The detection of H5N1 in Botswana has important implications for disease management, wild bird conservation, tourism, public health, economic empowerment of vulnerable communities and food security in the region.

Beak and feather disease virus (BFDV) infects domestic and wild psittacine species and is able to cause progressive beak, claw and feather malformation and necrosis. In addition to having an impact on the health and welfare of domesticated birds, BFDV represents a significant threat to wild endangered species. Understanding the epidemiology, dynamics, viral migration rate, interaction between wild and domestic animals and the effect of implemented control strategies is fundamental in controlling the spread of the disease. With this in mind, a phylodynamic and phylogeographic analysis has been performed on a database of more than 400 replication-associated protein (Rep) gene (ORF1) sequences downloaded from Genbank including some recently generated sequences from fifteen samples collected in Namibia. The results allowed us to reconstruct the variation of viral population size and demonstrated the effect of enforced international bans on these dynamics. A good correlation was found between viral migration rate and the intensity of animal trade between regions over time. A dominant flux of viral strains was observed from wild to domestic populations, highlighting the directionality of viral transmission and the risk associated with the capturing and trade of wild birds. Nevertheless, the flow of viruses from domestic to wild species was not negligible and should be considered as a threat to biodiversity. Therefore, considering the strong relationship demonstrated in this study between animal trade and BFDV viral fluxes more effort should be made to prevent contact opportunities between wild and domestic populations from different countries in order to control disease spread., (© 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Influenza D virus (IDV) was first isolated in 2011 in the USA and has since been shown to circulate in cattle, pigs, sheep, wild boar, and camels. In Africa, there is limited data on the epidemiology of IDV and, so, we investigated the presence of IDV among domestic ruminants and wild animals in Namibia by screening nasal swabs using an IDV-specific molecular assay. IDV RNA was detected in bovines (n=2), giraffes (n=2) and wildebeest (n=1). The hemagglutinin-esterase-fusion (HEF) gene from one of the bovine and the wildebeest samples was successfully sequenced as well as the full genome for the second bovine sample. Phylogenetic analysis of the HEF gene positioned the African virus variants within the D/OK lineage but with a long branch. The African variant had an amino acid diversity of 2.41% and most likely represents a distinct genotype within the lineage. Notably, the polymerase acidic protein gene (PA) was more closely related to a different lineage (D/660), indicative of potential reassortment. This is the first genetic characterization of IDV in Africa and it adds important data to our understanding of the global IDV distribution., (Copyright © 2022. Published by Elsevier B.V.)

Porcine circovirus-2 (PCV-2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV-2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV-2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV-2 were identified (i.e. PCV-2a, PCV-2b, PCV-2d and PCV-2 g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV-2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African-specific clusters and estimated the approximate time of introduction of PCV-2s into Africa from other continents. This is the first in-depth study of PCV-2 in Africa and it has important implications for pig production at both the small-holder and commercial farm level on the continent., (© 2021 Wiley-VCH GmbH.)

Understanding virus circulation in wild animals, particularly those that have contact with domestic animals, is crucial for disease management and control. In Africa, warthogs are known to be asymptomatic carriers of porcine pathogens; a recent study in Namibia has shown them to be positive for Porcine circovirus-2 (PCV-2). In this study, the same samples used for the PCV-2 investigation in Namibia were further screened for the presence of African swine fever virus (ASFV) and porcine parvovirus 1 (PPV1) by PCR. Of the 42 animals tested, 2 (4.8%) and 13 (31%) were positive for AFSV and PPV1, respectively. The two AFSV were also co-infected with PPV1. Combing the results of this study with the results of the previous PCV-2 investigation, four warthogs were shown to be co-infected with both PPV1 and PCV-2. Sequence and phylogenetic analysis revealed that the AFSV belonged to genotype (Ib) but were from different serogroups. Unexpectedly, the ASFVs from the warthogs were genetically distinct to those observed in an outbreak in the same region of Namibia that occurred less than fifteen months prior to the sampling of the warthogs. In fact, a stronger genetic relationship was observed between the warthog viruses and historical Namibian and South African ASFVs identified in 1980, 2004 and 2008. For the PPV1s, the closest relative to the Namibian PPV1 were viruses identified in wild boar in Romania in 2011. This study confirms that warthogs are carriers of porcine pathogens and the data should encourage further studies on larger populations of wild and domestic swine to more fully understand the epidemiology and transmission of viral pathogens from these species.

Porcine circovirus 3 (PCV-3) has been associated with an assortment of clinical conditions in pigs and has been reported in many countries worldwide. In Africa there is no data on the presence of PCV-3. In this study, DNA samples collected from 91 pigs between 2011 and 2019 in nine of the ten provinces of Mozambique in the context of African swine fever (ASF) monitoring were further screened for the presence of PCV-3. Of these samples, 7 (7.5%) animals were positive for PCV-3. Sequence and phylogenetic analysis of the capsid protein gene (ORF2) of the PCV-3s provided evidence of epidemiological links with PCV-3s identified in North and South America, Asia, and Europe. This is the first identification of PCV-3 in Mozambique (and Africa) and the first evidence of co-infection of PCV-3 and ASF virus. It should provide a starting point for further investigations into the presence and impact of PCV-3 in Africa., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Samples from eleven birds (chicken, dove and peacock) with symptoms of fowlpox, caused by the avipoxvirus (APV), were collected in seven different areas of the Windhoek district, Namibia between April and October 2021. A fragment of the 4b core protein and the DNA polymerase gene of APV were amplified by PCR from the DNA of the samples and sequenced. Phylogenetic analysis revealed that the viruses present in the chickens all belonged to clade A1 while the viruses in the doves and peacock were from subclade A3.1. This is the first report of subclade A3.1 avipoxvirus in peacock. In addition, all of the samples obtained from chickens were shown by PCR to be positive for the integration of reticuloendotheliosis virus while those from the doves and peacocks were negative. This study is the first characterization of avipoxvirus in Namibia and provides additional information on the presence of avipoxvirus in southern Africa.

Members of the genus Circovirus have been identified in several host species. While initially considered host-specific, there is growing evidence of their presence in unexpected hosts. Porcine circovirus 2 (PCV-2) is no exception, having been reported in animals belonging to different orders, including carnivores. Recently, PCV-2 was detected in domestic pigs, warthogs and antelopes in Namibia. Considering the potential contact between these populations and wild carnivores, the presence of PCV-2 was investigated in 32 black-backed jackals ( Lupulella mesomelas ) shot between February and July 2021 as part of predator control operations in Namibia. Two lung lymph nodes tested positive for PCV-2 by PCR, confirming the broader-than-expected PCV-2 host tropism and the susceptibility of canids. Sequence analysis demonstrated a close association between the PCV-2s identified in the jackals and PCV-2b strains collected from South African domestic pigs. Although several hypotheses regarding the source of the jackal's infection are proposed, further studies should be performed to properly assess how PCV-2 is acquired and maintained in the wild and its potential impact on wild and domestic species.

In April 2020, two Whooper Swans (Cygnus cygnus) and one Swan Goose (Anser cygnoides) were found dead at three different locations in western Mongolia. Virus isolation from organs taken from the carcasses and full genome sequencing revealed that all three birds were positive for highly pathogenic H5N6 avian influenza virus (HPAIV) belonging to subclade 2.3.4.4h. Confirming similar reports from central Mongolia and western China, these findings have important implications for the monitoring, control, and management of HPAIVs in wild bird and commercial poultry populations in Mongolia., (© Wildlife Disease Association 2022.)

Archival swine DNA samples from Indonesia and Mongolia, some of which were previously shown to be positive for African swine fever virus, were screened for the presence of porcine circovirus 2 (PCV-2) and porcine circovirus 3 (PCV-3) by PCR. Samples from both countries were positive for PCV-2 (three from Mongolia and two from Indonesia), while none were positive for PCV-3. The PCV-2 amplicons were sequenced, and phylogenetic analysis revealed that the PCV-2 strains belonged to four different genotypes: PCV-2a (Mongolia), PCV-2b (Mongolia and Indonesia), PCV-2d (Indonesia), and PCV-2g (Mongolia). This is the first report of ASFV/PCV-2 coinfection in pigs and the first report of the presence of PCV-2 in Mongolia., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

An in-depth knowledge of the molecular evolution of the peste des petits ruminants virus (PPRV) is critical for the success of the current global eradication program. For this reason, a molecular evolutionary analysis of PPRVs circulating in Bangladesh over a decade (2008-2020) was performed. The complete genome sequencing of three PPRV isolates from 2008 (BD2), 2015 (BD12) and 2017 (BD17) as well as full length nucleocapsid (N), matrix (M) and fusion (F) gene sequencing of seven more samples from 2015 to 2020 was performed. Phylogenetic analysis classified all ten PPRVs from Bangladesh as members of lineage IV and showed that they were closely related to PPRV strains detected in China and Tibet during 2007-2008, and India during 2014-2018. Time scale Bayesian Maximum Clade Credibility (MCC) phylogenetic analysis of the three complete genomes revealed a mean Time to Most Recent Common Ancestor (TMRCA) of 2000. Comparative deduced amino acid residue analysis at various functional motifs of PPRVs related to virus structure and function, virulence and host adaptation, receptor binding sites and polymerase activity revealed conserved residues among the PPRVs from Bangladesh. In total sixteen epitopes were predicted from four immunogenic proteins i.e. N, M, F and haemagglutinin (H). Interestingly, the predicted epitopes from the N and M proteins shared conserved epitopes with two vaccine strains currently being used, indicating that the strains from Bangladesh could be potentially used as alternative local vaccines., (Copyright © 2021. Published by Elsevier B.V.)

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

For several years after its discovery, Porcine circovirus 2 (PCV-2) represented a major threat to the swine industry through economic losses due to the associated clinical syndromes, decreased production performances in both symptomatic and asymptomatic animals and disease management costs. Widespread vaccination administration has largely reduced the impact of this infection and represents the most effective control measure. The efficacy of vaccination is threatened by the emergence of novel (or uncommon) PCV-2 genotypes. In addition to domestic pigs, PCV-2 has been detected in several other species, a fact which could have an impact on new variant emergence and maintenance. Considering this, the present study assessed the distribution of the minor PCV-2c genotype in non-Suidae ungulates in Namibia. Red hartebeests ( Alcelaphus buselaphus caama ) (n = 44), kudus ( Tragelaphus strepsiceros ) (n = 10) and oryxes ( Oryx gazella ) (n = 54), whose mediastinal lymph nodes were sampled after slaughtering during the period 2019-2021, were included in the study. Two oryxes (3.7%; 95% CI = 0.45-12.75%) were PCV-2-positive by PCR. Complete genome sequence was obtained for the two samples identifying them as PCV-2c genotype. The sequences were identical and shared a high percentage of identity (~99.9%) with those recently obtained from warthogs living in the same area. The present study confirms the presence of the PCV-2c genotype (previously considered extinct) in Namibian wild animal populations and demonstrates greater than expected PCV-2 host plasticity. Because of the role these niches can have in the maintenance and evolution of minor PCV-2 genotypes, more extensive and dedicated studies should be performed to prepare authorities to promptly react to potential emerging threats from these viruses.

African swine fever (ASF) is a severe haemorrhagic disease of domestic and wild pigs caused by the African swine fever virus (ASFV). In recent years, ASF has steadily spread towards new geographical areas, reaching Europe and Asia. On January 15th, 2019, Mongolia reported its first ASF outbreak to the World Organization for Animal Health (OIE), becoming, after China, the second country in the region affected by the disease. Following an event of unusual mortality in domestic pigs in Bulgan Province, a field team visited four farms and a meat market in the region to conduct an outbreak investigation and collect samples for laboratory analysis. Different organs were examined for ASF associated lesions, and total nucleic acid was extracted for real-time PCR, virus isolation and molecular characterization. The real-time PCR results confirmed ASFV DNA in 10 out of 10 samples and ASFV was isolated. Phylogenetic analysis established that ASFVs from Mongolia belong to genotype II and serogroup 8. The viruses were identical to each other, and to domestic pig isolates identified in China and Russia, based on the comparison of five genomic targets. Our results suggest a cross-border spread of ASFV, without indicating the source of infection., (© 2021 Wiley-VCH GmbH.)

African swine fever (ASF) is a highly lethal and contagious viral haemorrhagic disease of domestic and wild pigs, caused by the ASF virus (ASFV). After entering China in 2018, the disease has continued to spread through Asia. In September 2019, a team from the Indonesian Research Center for Veterinary Science, Bogor, investigated outbreaks in backyard pigs in the Dairi and Humbang Hasundutan districts of North Sumatra province. In January 2020, three pigs purchased from a pig seller in Bogor District, West Java province were also tested. Real-time PCR results confirmed ASFV DNA in sixteen out of twenty-nine samples, with nine positive samples from North Sumatra and seven from West Java. Four partial or full-length genes (i.e. p72, p54, pB602L and CD2v) and a 356-bp fragment between the I73R and I329L genes were sequenced from representative samples. Phylogenetic analysis established that the ASFV in the samples from both North Sumatra and West Java were identical, indicating a common source of infection, and that they belonged to the p72 genotype II and serogroup 8. The sequences from the Indonesian ASFVs were also identical to other genotype II ASFV from domestic pigs in Vietnam, China and Russia., (© 2021 Wiley-VCH GmbH.)

Transmission mitigation of SARS-CoV-2 requires the availability of accurate and sensitive detection methods. There are several commercial ad hoc molecular diagnostic kits currently on the market, many of which have been evaluated by different groups. However, in low resource settings the availability and cost of these commercial kits can be a limiting factor for many diagnostic laboratories. In such cases alternatives need to be identified. With this in mind, eight commercial reverse transcription quantitative real-time PCR (RT-qPCR) master mixes from Applied Biosystems (Thermo Fisher Scientific), Bio-Rad, Biotech Rabbit, Promega, Qiagen, QuantaBio, Invitrogen (Thermo Fisher Scientific) and Takara using the same commercial primer and probe mix [LightMix® Modular SARS and Wuhan CoV E-gene mix (TIB MolBiol, Germany)] were evaluated. Three ad hoc molecular diagnostic kits [GeneFinder™ COVID-19 Plus RealAmp kit (Osang Healthcare); genesig® Real-Time PCR Coronavirus COVID-19 (Primerdesign); and ViroReal® Kit SARS-CoV-2 & SARS-CoV (Ingenetix)] were also included in the study. The limit of detection was calculated for each assay using serial dilutions of a defined clinical sample. The performances of the assays were compared using a panel of 178 clinical samples and their analytical specificity assessed against a panel of human betacoronaviruses. Inter assay agreement was assessed using statistical tests (Bland-Altman, Fleiss-Kappa and Cohen's Kappa) and was shown to be excellent to good in all cases. We conclude that all of the assays evaluated in this study can be used for the routine detection of SARS-CoV-2 and that the RT-qPCR master mixes are a valid alternative to ad hoc molecular diagnostic kits., (Copyright © 2021 The Author(s). Published by Elsevier B.V. All rights reserved.)

The recent emergence of SARS-CoV-2 in humans from a yet unidentified animal reservoir and the capacity of the virus to naturally infect pets, farmed animals and potentially wild animals has highlighted the need for serological surveillance tools. In this study, the luciferase immunoprecipitation systems (LIPS), employing the spike (S) and nucleocapsid proteins (N) of SARS-CoV-2, was used to examine the suitability of the assay for antibody detection in different animal species. Sera from SARS-CoV-2 naturally-infected mink ( n = 77), SARS-CoV-2 experimentally-infected ferrets, fruit bats and hamsters and a rabbit vaccinated with a purified spike protein were examined for antibodies using the SARS-CoV-2 N and/or S proteins. From comparison with the known neutralization status of the serum samples, statistical analyses including calculation of the Spearman rank-order-correlation coefficient and Cohen's kappa agreement were used to interpret the antibody results and diagnostic performance. The LIPS immunoassay robustly detected the presence of viral antibodies in naturally infected SARS-CoV-2 mink, experimentally infected ferrets, fruit bats and hamsters as well as in an immunized rabbit. For the SARS-CoV-2-LIPS-S assay, there was a good level of discrimination between the positive and negative samples for each of the five species tested with 100% agreement with the virus neutralization results. In contrast, the SARS-CoV-2-LIPS-N assay did not consistently differentiate between SARS-CoV-2 positive and negative sera. This study demonstrates the suitability of the SARS-CoV-2-LIPS-S assay for the sero-surveillance of SARS-CoV-2 infection in a range of animal species.

Nasal swabs collected from 40 wild ruminants in Namibia were analyzed by PCR for the presence of lumpy skin disease virus (LSDV) DNA. One sample from an asymptomatic eland (Taurotragus oryx) tested positive, providing the first evidence of the presence of LSDV DNA in an eland., (© Wildlife Disease Association 2021.)

Porcine circovirus 2 (PCV-2) is the causative agent of porcine circovirus diseases (PCVD). A study was undertaken to determine whether PCV-2 was present in samples collected from commercial pigs (n = 46) and warthogs (n = 42) in Namibia between 2019 and 2020. Twenty-three of the collected samples were positive by PCR (13 from pigs and 10 from warthogs), and a phylogenetic analysis of ORF2 identified three genotypes (PCV-2b and PCV-2d in pigs and PCV-2c in warthogs). This is the first time that PCV-2 has been identified in warthogs and in Namibia. It is also the first report of PCV-2c in Africa.

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.)

The causative agent of Newcastle disease (ND) of poultry is the avian paramyxovirus-1, also commonly known as ND virus (NDV). Like in many developing countries, ND is endemic in Niger and has significant economic impact on commercial and backyard poultry production. NDVs were characterized in Niger between 2006 and 2008 and shown to belong to genotypes XIV.1 and XVII. In order to determine the current situation regarding the virus in Niger, tracheas (n = 384) were collected for the detection of NDV from both healthy (n = 335) and sick (n = 49) backyard poultry in 2019. Of these samples, 24 from sick chickens were positive for NDV by conventional RT-PCR. Sequencing of the fusion protein gene and phylogenetic analysis revealed that the viruses belonged to either genotype XIV.2 or XVIII.2. No NDVs of genotype XIV.1 or XVII were identified in the current study highlighting the dynamic nature of NDV circulation in Niger and the region.

Avian paramyxovirus-1 (APMV-1), the causative agent of Newcastle disease (ND) in domestic and wild avian species, has recently been reported and characterized in five southern African countries (i.e. Mozambique, Namibia, South Africa, Zambia and Zimbabwe). Since APMV-1s have never been characterized in Botswana, this study was undertaken to determine the genotype circulating in the country. Fourteen samples were collected from ND outbreaks in poultry in 2014, 2018 and 2019 and the complete fusion protein gene was sequenced. Phylogenetic analysis revealed that all of the viruses from Botswana clustered in genotype VII.2 (previously subgenotype VIIh) and that they were more related to viruses from South Africa and Mozambique than the other southern African countries (i.e. Namibia, Zambia and Zimbabwe).

Small ruminants (e.g., sheep and goats) contribute considerably to the cash income and nutrition of small farmers in most countries in Africa and Asia. Their husbandry is threatened by the highly infectious transboundary viral disease peste des petits ruminants (PPR) caused by peste-des-petits-ruminants virus (PPRV). Given its social and economic impact, PPR is presently being targeted by international organizations for global eradication by 2030. Since its first description in Côte d'Ivoire in 1942, and particularly over the last 10 years, a large amount of molecular epidemiological data on the virus have been generated in Africa. This review aims to consolidate these data in order to have a clearer picture of the current PPR situation in Africa, which will, in turn, assist authorities in global eradication attempts.

Although rabies is enzootic in the Democratic Republic of the Congo, there is very little molecular epidemiological information about the viruses circulating in animals. In this study, a fragment of the rabies virus (RABV) nucleoprotein gene was amplified and sequenced from 21 animal brain samples collected in two western provinces of the country between 2008 and 2017. The samples tested were from cat (n = 1), dog (n = 17), goat (n = 2), and sheep (n = 1). Phylogenetic analysis revealed that the sequences generated were highly similar to each other and belonged to lineage Africa 1b clustering with a single sample identified in a canine in the Republic of Congo in 2014. This is the first molecular epidemiological study of RABV in the DRC and the data generated will assist authorities in the development of effective control strategies for rabies in the country.

Like many West African countries, outbreaks of peste des petits ruminants (PPR), an economically important disease of goats and sheep, are regularly reported in Niger. The causative virus, peste des petits ruminants virus (PPRV), can be differentiated into four genetically distinct lineages. A publication in 2018 identified three PPRV lineages circulating in the country in 2001 (lineages I and II) and 2013 (lineage IV), respectively. In this present study, more recent samples were collected from goats and sheep in locations throughout Niger between 2011 and 2017. Twelve PPRV-positive samples were characterized by sequencing of a segment of the nucleocapsid protein (N) gene. Phylogenetic analysis of the sequences identified viruses from lineages II and IV only. The analysis also indicated a shared origin of the viruses from Niger with PPRVs from neighbouring countries suggesting transboundary movement., (© 2019 Blackwell Verlag GmbH.)

Five samples were collected from four suspected outbreaks of African swine fever in Namibia in 2018. Sequencing of the C-terminus of the B646L gene (p72 protein), the central hypervariable region (CVR) of the B602L gene, the E183L gene (p54 protein) and the CD2v (used to determine the serogroup) was performed on DNA isolated from the samples. Phylogenetic analyses of the B646L (p72) revealed that one of the samples belonged to genotype I while the remaining samples could not be assigned to any currently known genotype. In contrast, by using the E183L gene three of the samples were shown to belong to genotype Id and only two were of unknown genotype. Based on the analysis of the partial CD2v amino acid sequences of four of the samples, one of the viruses clustered with serogroup 2 while the other three did not cluster within any of the eight known serogroups. Examination of the CVR identified three variants with 8, 18 and 24 tetrameric tandem repeat sequences. This study indicates that at least three different genetically distinct ASFV are currently present in Namibia., (© 2019 Blackwell Verlag GmbH.)

In January 2019, high mortalities were reported among African Penguins ( Spheniscus demersus ) in a breeding colony on Halifax Island, Namibia, Africa. Analysis of samples by reverse transcription quantitative PCR indicated the presence of highly pathogenic avian influenza (HPAI) subtype H5N8. Sequence analysis of the hemagglutinin and neuraminidase genes confirmed the presence of the virus in the birds and its high similarity to HPAI subtype H5N8 identified in South Africa in 2017. There have been no previous reports of HPAI H5N8 in Namibia.

Understanding the molecular epidemiology and evolution of peste des petits ruminants virus (PPRV), the causative agent of Peste des petits ruminants, can assist in the control of the transboundary spread of this economically important disease. To date, despite having been reported in the majority of northern and central African countries, no molecular epidemiological data on PPRVs are available for the Democratic Republic of the Congo (DRC). This study reports the collection and analysis of 11 samples collected from three provinces of the DRC in 2016 and 2018. Sequence analysis identified two (i.e. II and III) of the four known lineages of PPRV in the country providing important information that will assist in the global eradication of PPR., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Avian influenza (AI) virus (AIV) subtype H9N2 continues to cause significant outbreaks among commercial and backyard poultry in Pakistan. Despite this, the characterization of H9N2 viruses in avian hosts other than chickens in Pakistan has not been thoroughly investigated. In this study, 12 low pathogenicity avian influenza viruses subtype H9N2 were isolated from peacocks ( n = 4), ducks ( n = 4), pheasants ( n = 2), geese ( n = 1), and black swans ( n = 1) in Pakistan during 2016 and were characterized on the basis of the hemagglutinin (HA) and neuraminidase genes. All of the viruses possessed an amino acid substitution Q226L in the receptor-binding site of the HA protein, which is known to contribute to increased viral replication and virulence in mammals. In addition, phylogenetic studies showed that these H9N2 AIVs belonged to the Middle East B genetic group of sublineage G1 and were very similar to viruses isolated from an outbreak in chickens in Pakistan in 2017. This demonstrates an epidemiologic link between poultry and other avian species, which is a fact to consider in future H9N2 disease management programs.

The family Paramyxoviridae consists of large enveloped RNA viruses infecting mammals, birds, reptiles and fish. Many paramyxoviruses are host-specific and several, such as measles virus, mumps virus, Nipah virus, Hendra virus and several parainfluenza viruses, are pathogenic for humans. The transmission of paramyxoviruses is horizontal, mainly through airborne routes; no vectors are known. This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) Report on the family Paramyxoviridae . which is available at ictv.global/report/paramyxoviridae.

Rift Valley fever (RVF) is a zoonotic viral disease caused by the RVF phlebovirus (RVFV) that infects a variety of animal species including sheep and goats. Sera (n = 893) collected between 2013 and 2015 from randomly selected indigenous sheep and goats in seven provinces of the Democratic Republic of the Congo (DRC) were tested for the presence of specific immunoglobulin G (IgG) and M (IgM) against RVFV, using two commercially available enzyme-linked immunosorbent assays. The reverse transcription polymerase chain reaction (RT-PCR) was also used to detect RVFV nucleic acid. There was significant variation in true seroprevalence of RVFV for both sheep and goats between the seven provinces investigated. Values ranged from 0.0 (95% confidence interval [CI] 0.0-6.55) to 23.81 (95% CI 12.03-41.76) for goat and 0.0 (95% CI 0.0-7.56) to 37.11 (95% CI 15.48-65.94) for sheep, respectively. One serum (1.85%) out of 54 that tested positive for IgG was found to be IgM-positive. This same sample was also positive by RT-PCR indicating an active or recent infection. These findings report the presence of RVFV in small ruminants in the DRC for the first time and indicate variations in exposure to the virus in different parts of the country.

In December 2017, Peste des Petits Ruminants (PPR) emerged in Burundi (East Africa) and rapidly spread to five provinces (Gitega, Kirundo, Mwaro, Muramvya and Karuzi) in the country, causing severe disease and killing more than 4,000 goats in the province of Gitega alone. An initial outbreak investigation was conducted in December 2017 by the Burundi Government Veterinary Services and samples were collected for laboratory confirmation. A competitive Enzyme Linked Immuno-Sorbent Assay (cELISA: Chinese Patent No. ZL201210278970.9) supplied by the Lanzhou Veterinary Research Institute was used to test 112 sera and results showed around 37.5% positive samples. This high level of PPR positive sera in an animal population where PPR infection and vaccination had not been previously reported indicated the exposure of the animals to PPRV. Subsequently in January 2018, the laboratory tests conducted at the African Union-Pan African Veterinary Vaccine Centre (AU-PANVAC) laboratories following a joint investigative mission by the African Union-Interafrican Bureau for Animal Resources (AU-IBAR), AU-PANVAC and the East African Community (EAC) confirmed the presence of PPR in Burundi. Samples tested by conventional RT-PCR indicated the presence of the PPR virus (PPRV). Confirmatory isolation of the virus was also performed. Phylogenetic analysis revealed that the virus belongs to lineage III and shows a close relationship with PPRV isolates from Kenya in 2011 and Uganda in 2012. A possible explanation for the outbreaks of PPR in Burundi between December 2017 and February 2018 is presented., (© 2019 Blackwell Verlag GmbH.)

Between July and August 2018, two outbreaks of infectious laryngotracheitis caused the death of over 116,000 commercial poultry (layers and broilers) near the city of Windhoek, Namibia. A third outbreak occurred in September 2018 in the north of the country approximately 800 km from the original outbreaks. Sample collection and molecular epidemiological analyses revealed that the outbreaks were most likely caused by poor vaccination practices leading to the reversion to virulence of an ILT vaccine strain. The analyses also indicate that inaccurate declarations were made by one of the farms involved and that illegal movement of animals most likely occurred.