William G. Dundon

First Complete Genome Sequence of a Lineage III Peste des Petits Ruminants Virus

ABSTRACT We report the first complete genome sequence of a lineage III peste des petits ruminants virus (KN5/2011) using RNA extracted from goat lung tissue collected in Kenya in 2011. The genome shows the highest nucleotide sequence identity with lineage II peste des petits ruminants viruses (PPRVs) (86.1 to 87.2%) and the lowest with lineage IV PPRVs (82.5 to 83.8%).

Complete Genome Sequence of a Lineage I Peste des Petits Ruminants Virus Isolated in 1969 in West Africa

ABSTRACT We report the complete genome sequence of a lineage I peste des petits ruminants virus (E32/1969) isolated in a Senegalese laboratory in 1969. This is the earliest peste des petits ruminants virus of any lineage sequenced to date and only the second lineage I virus available in public databases.

Detection and Genome Analysis of a Lineage III Peste Des Petits Ruminants Virus in Kenya in 2011

In May 2011 in Turkana County, north-western Kenya, tissue samples were collected from goats suspected of having died of peste des petits ruminant (PPR) disease, an acute viral disease of small ruminants. The samples were processed and tested by reverse transcriptase PCR for the presence of PPR viral RNA. The positive samples were sequenced and identified as belonging to peste des petits ruminants virus (PPRV) lineage III. Full-genome analysis of one of the positive samples revealed that the virus causing disease in Kenya in 2011 was 95.7% identical to the full genome of a virus isolated in Uganda in 2012 and that a segment of the viral fusion gene was 100% identical to that of a virus circulating in Tanzania in 2013. These data strongly indicate transboundary movement of lineage III viruses between Eastern Africa countries and have significant implications for surveillance and control of this important disease as it moves southwards in Africa.

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.

Phylogenetic analysis of Newcastle disease viruses isolated from commercial poultry in Mozambique (2011–2016)

The complete sequence of the fusion (F) protein gene from 11 Newcastle disease viruses (NDVs) isolated from commercial poultry in Mozambique between 2011 and 2016 has been generated. The F gene cleavage site motif for all 11 isolates was 112RRRKRF117 indicating that the viruses are virulent. A phylogenetic analysis using the full F gene sequence revealed that the viruses clustered within genotype VIIh and showed a higher similarity to NDVs from South Africa, China and Southeast Asia than to viruses previously described in Mozambique in 1994, 1995 and 2005. The identification of these new NDVs has important implications for Newcastle disease management and control in Mozambique.

First genetic characterization of peste des petits ruminants virus from Mongolia

Between August and September 2016 pathological samples were collected from sheep and goats following suspected peste des petits ruminants (PPR) outbreaks in western Mongolia. RT-PCR followed by sequencing and phylogenetic analysis of the samples confirmed the presence of a PPR virus belonging to lineage IV. A full genome analysis of the viral RNA from one of the samples revealed a high similarity (99.0-99.5%) with PPR viruses currently circulating in China (2013-2015) indicating a common origin. This is the first genetic characterization of PPR virus in Mongolia and the data generated will have important implications for control and management of the disease 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.

Enhanced immunosurveillance for animal morbilliviruses using vesicular stomatitis virus (VSV) pseudotypes

The measurement of virus-specific neutralising antibodies represents the “gold-standard” for diagnostic serology. For animal morbilliviruses, such as peste des petits ruminants (PPRV) or rinderpest virus (RPV), live virus-based neutralisation tests require high-level biocontainment to prevent the accidental escape of the infectious agents. In this study, we describe the adaptation of a replication-defective vesicular stomatitis virus (VSVΔG) based pseudotyping system for the measurement of neutralising antibodies against animal morbilliviruses. By expressing the haemagglutinin (H) and fusion (F) proteins of PPRV on VSVΔG pseudotypes bearing a luciferase marker gene, neutralising antibody titres could be measured rapidly and with high sensitivity. Serological responses against the four distinct lineages of PPRV could be measured simultaneously and cross-neutralising responses against other morbilliviruses compared. Using this approach, we observed that titres of neutralising antibodies induced by vaccination with live attenuated PPRV were lower than those induced by wild type virus infection and the level of cross-lineage neutralisation varied between vaccinates. By comparing neutralising responses from animals infected with either PPRV or RPV, we found that responses were highest against the homologous virus, indicating that retrospective analyses of serum samples could be used to confirm the nature of the original pathogen to which an animal had been exposed. Accordingly, when screening sera from domestic livestock and wild ruminants in Tanzania, we detected evidence of cross-species infection with PPRV, canine distemper virus (CDV) and a RPV-related bovine morbillivirus, suggesting that exposure to animal morbilliviruses may be more widespread than indicated previously using existing diagnostic techniques.

First report and characterization of peste des petits ruminants virus in Liberia, West Africa.

Peste des petits ruminants (PPR) is a contagious and often fatal disease affecting sheep and goats that is currently endemic in Africa, the Middle East, the Indian subcontinent and China. Understanding the molecular epidemiology and evolution of PPR virus (PPRV) can assist in the control of the transboundary spread of this economically important disease. Here we report the isolation of a PPRV from pathological and swab samples collected from goats in Liberia, West Africa in July 2015. The full genome of one of the isolates was sequenced and phylogenetic analysis showed that it clustered within viral lineage II. The full genome revealed a 99.2 % identity at the nucleotide level with the full genome of a PPRV isolated in neighbouring Côte d’Ivoire in 2009 indicating a common origin of the viruses. Peste des petits ruminants (PPR) is a highly contagious infectious viral disease of domestic and wild small ruminants. The control of PPR is considered an important element in the fight for global food security and poverty alleviation and it is for this reason that the disease has been chosen as the next animal disease for global eradication. In April 2015, in Abidjan, Côte d’Ivoire, the Food and Agricultural Organization of the United Nations (FAO) and the World Organization for Animal Health (OIE) met with high-level authorities from affected countries to agree on a global plan to eradicate PPR by 2030 (FAO 2015). The causative agent, the peste des petits ruminants virus (PPRV), is a member of the family Paramyxoviridae, genus Morbillivirus that includes rinderpest virus (RPV), measles virus (MV), canine distemper virus (CDV), phocine distemper virus (PDV), dolphin morbillivirus (DMV) and feline morbillivirus (Woo et al. 2012; Baron et al. 2016). The nonsegmented single-stranded, negative-sense RNA genome of PPRV is 15,948 nucleotides in size and encodes two nonstructural proteins C and V, and six structural proteins arranged in the order: nucleoprotein (N), phosphoprotein (P), matrix protein (M), fusion protein (F), hemagglutinin protein (H) and viral RNA-dependent polymerase (L) (Baron et al. 2016). Based on partial sequences of the N and F genes, PPRV strains have been classified into four genetically distinct lineages (I, II, III and IV) even though the virus is serologically monotypic (Libeau et al. 2014; Parida et al. 2015). PPRV strains that were first identified in Africa belong to lineages I, II and III while viruses belonging to lineage IV have been found in Asia including the Middle East (Libeau et al. 2014; Parida et al. 2015). Although, PPRV has been reported in several West African countries there has been no report of the virus in Liberia to * William G. Dundon w.dundon@iaea.org

WITHDRAWN: Identification of peste-des-petits ruminants virus (PPRV) lineage IV, the Asian lineage, in Nigeria and co-circulation with PPRV lineage II.

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