SARS-CoV-2 Infection in Beaver Farm, Mongolia, 2021.

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.

Phylogenetic analysis of Newcastle disease virus detected in Eritrea between 2017 and 2021.

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.

Evidence of coinfection of pigs with African swine fever virus and porcine circovirus 2.

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.

Coinfections of African swine fever virus, porcine circovirus 2 and 3, and porcine parvovirus 1 in swine in Nigeria.

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.

Three different genotypes of porcine circovirus 2 (PCV-2) identified in pigs and warthogs in Namibia.

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.

Co-circulation of genotypes XIV.2 and XVIII.2 of avian paramyxovirus-1 (Newcastle disease virus) in backyard poultry in Niger.

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.

Peste des petits ruminants in Africa: a review of currently available molecular epidemiological data, 2020.

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.

First molecular characterization of avian paramyxovirus-1 (Newcastle disease virus) in Botswana.

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).

Molecular characterization of rabies viruses from two western provinces of the Democratic Republic of the Congo (2008-2017).

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.

ICTV Virus Taxonomy Profile: Paramyxoviridae.

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.

Taxonomy of the order Mononegavirales: update 2019.

In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Mononegavirales: second update 2018.

In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Investigation of infectious laryngotracheitis outbreaks in Namibia in 2018.

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.

Seroprevalence of Rift Valley fever virus in cattle in the Democratic Republic of the Congo.

This study aimed at assessing the serological and virological status of Rift Valley fever virus (RVFV) in cattle from four climatically diverse zones of the Democratic Republic of the Congo (DRC). A total of 1675 sera samples collected between 2014 and 2015 from cattle without clinical manifestation of RVF infection were tested using competitive and capture enzyme ELISA to detect both IgG and IgM. RT-PCR was used for the detection of nucleic acid of RVFV. Out of the 1675 cattle sera tested, 203 were found to be IgG-positive, giving an overall true seroprevalence of 12.37% (95% CI 10.86-14.05). This seroprevalence varied between the four zones with a seroprevalence of 16.16% (95% CI 12.86-20.12), 14.70% (95% CI 11.72-18.29), 10.82% (95% CI 7.19-14.19), and 7.34% (95% CI 5.13-10.41) recorded in cattle sampled in the mountainous, humid savannah, dry savannah, and forest zones, respectively (p < 0.05, χ2 = 17.26). A higher true seroprevalence of 14.58% (95% CI 9.3-22.13) was found in animals aged 1 year compared to 10.43% (95% CI 8.12-13.30) and 13.16% (95% CI 11.19-15.42) in groups aged between 2-3 and > 3 years, respectively, although the difference was not statistically significant (p > 0.05, χ2 = 2.95). Similarly, no statistically significant difference (p > 0.05, χ2 = 0.04) was found between the sexes of the animals. Among the IgG-positive samples screened for anti-RVFV IgM, only 1.47% (3/203) was IgM-positive. One of the IgM-positive samples was positive by RT-PCR. These findings reveal country-wide distribution of RVF in the DRC for the first time.

Identification of Peste des Petits Ruminants Virus, Georgia, 2016.

A phylogenetic analysis of samples taken from reported outbreaks of peste des petits ruminants virus (PPRV) in Georgia revealed a closer relationship to viruses from northern and eastern Africa than to viruses from countries closer to Georgia. This finding has crucial implications for the control of PPRV in the region.

Pathotyping and genetic characterization of avian avulavirus-1 from domestic and wild waterfowl, geese and black swans in Pakistan, 2014 to 2017.

Twenty-nine avian avulavirus-1 viruses (AAvV-1s) from healthy domestic and wild ducks, geese and black swans collected in Pakistan between 2014-2017 have been pathotyped and genetically characterized. A phylogenetic analysis revealed that 21 of the isolates belonged to sub-genotype VIIi, whereas eight isolates were highly similar to vaccine-like viruses of genotype II. In addition to confirming the continued presence of sub-genotype VIIi AAvV-1s in Pakistan, this study identifies the probable spill-over of vaccine-like viruses from vaccinated poultry to wild and domestic waterfowl and, as such, has important implications for the control and management of Newcastle disease in Pakistan.

Molecular characterization of lumpy skin disease virus in Namibia, 2017.

Between January and July 2017, lumpy skin disease (LSD) outbreaks were reported in cattle in Namibia. DNA was extracted from skin biopsies taken from 32 cattle, and the RNA polymerase 30 kDa subunit (RPO30) gene of the LSD virus (LSDV) was successfully amplified by PCR. Phylogenetic analysis revealed that the newly sequenced LSDV isolates from Namibia were identical to LSDV isolates identified previously in Burkina Faso, Egypt, Greece, Niger, Serbia and South Africa. Given that only unvaccinated herds were affected by LSD, it is recommended that the current vaccination programmes in Namibia be re-evaluated to allow nationwide coverage.

Molecular characterization of avipoxviruses circulating in Mozambique, 2016-2018.

Samples from 45 chickens, two turkeys, one peacock and one quail with symptoms of fowlpox were collected in Mozambique between November 2016 and January 2018. Phylogenetic analysis revealed that the samples contained avipoxviruses belonging to both clade A1 and clade A2. In addition, all of the Clade A1 viruses were positive by PCR for the integration of reticuloendotheliosis virus, while the clade A2 avipoxvirus samples were negative. This study confirms the circulation of clade A1 avipoxviruses in Mozambique in addition to identifying clade A2 for the first time in the country.

Identification of Clade E Avipoxvirus, Mozambique, 2016.

Analysis of scab samples collected from poultry during outbreaks of fowlpox in Mozambique in 2016 revealed the presence of clade E avipoxviruses. Infected poultry were from flocks that had been vaccinated against fowlpox virus. These findings require urgent reevaluation of the vaccine formula and control strategies in this country.

First genetic characterization of newcastle disease viruses from Namibia: identification of a novel VIIk subgenotype.

The complete sequences of the fusion (F) protein genes of six Newcastle disease virus (NDV) isolates from backyard poultry in Namibia in 2016 have been determined. The F gene cleavage site motif for all of the isolates was 112RRQKRF117, indicating that the viruses are virulent. A phylogenetic analysis using the full F gene sequence revealed that the viruses belong to a novel subgenotype, VIIk. This is the first genetic characterization of NDV isolates from Namibia, and the findings have important implications for Newcastle disease management and control in the region.