Complete Genome Sequence of a Lineage IV Peste des Petits Ruminants Virus from Turkey, 2018

Hacıoğlu, Sabri; King, Simon; Çizmeci, Şirin; Yeşil, Öznur; Flannery, John; Baron, Michael D.; Batten, Carrie; Rajko-Nenow, Paulina

doi:10.1128/mra.01446-19

Cited by 5 publications

(3 citation statements)

References 7 publications

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“…The genome extremities are also amplified using rapid amplification of cDNA ends by polymerase chain reaction (RACE PCR) [74]. The amplified fragments are later confirmed by Sanger dideoxynucleotide cycle sequencing [69]. Similarly, a systematic drop out of problematic amplicons 18 and 76 was noticed during sequencing of SARS-CoV-2, which has led to the modification of the ARTIC nanopore sequencing protocol [75].…”

Section: Discussionmentioning

confidence: 99%

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses

Kinimi

Mahapatra

Kgotlele

et al. 2021

Animals

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Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic surveillance tools is critical where PPR is endemic. Genomic data can provide sufficient in-depth information to identify the pockets of endemicity responsible for PPRV persistence and viral evolution, and direct an appropriate vaccination response. Yet, access to the required sequencing technology is low in resource-limited settings and is compounded by the difficulty of transporting clinical samples from wildlife across international borders due to the Convention on International Trade in Endangered Species (CITES) of Wild Fauna and Flora, and Nagoya Protocol regulations. Oxford nanopore MinION sequencing technology has recently demonstrated an extraordinary performance in the sequencing of PPRV due to its rapidity, utility in endemic countries and comparatively low cost per sample when compared to other whole-genome (WGS) sequencing platforms. In the present study, Oxford nanopore MinION sequencing was utilised to generate complete genomes of PPRV isolates collected from infected goats in Ngorongoro and Momba districts in the northern and southern highlands of Tanzania during 2016 and 2018, respectively. The tiling multiplex polymerase chain reaction (PCR) was carried out with twenty-five pairs of long-read primers. The resulting PCR amplicons were used for nanopore library preparation and sequencing. The analysis of output data was complete genomes of PPRV, produced within four hours of sequencing (accession numbers: MW960272 and MZ322753). Phylogenetic analysis of the complete genomes revealed a high nucleotide identity, between 96.19 and 99.24% with lineage III PPRV currently circulating in East Africa, indicating a common origin. The Oxford nanopore MinION sequencer can be deployed to overcome diagnostic and surveillance challenges in the PPR Global Control and Eradication program. However, the coverage depth was uneven across the genome and amplicon dropout was observed mainly in the GC-rich region between the matrix (M) and fusion (F) genes of PPRV. Thus, larger field studies are needed to allow the collection of sufficient data to assess the robustness of nanopore sequencing technology.

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Section: Discussionmentioning

confidence: 99%

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses

Kinimi

Mahapatra

Kgotlele

et al. 2021

Animals

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“…Lineage IV seems the only lineage to be circulating in the whole region, as supported by molecular studies conducted in the Islamic Republic of Iran [ 38 , 39 ], Kazakhstan [ 40 ], Tajikistan [ 41 , 42 ], Georgia [ 43 ], Mongolia [ 10 , 44 ], Turkey [ 45 , 46 , 47 ] and China [ 48 , 49 , 50 , 51 , 52 ]. However, some PPRV strains from the region belong to distinct subclades of lineage IV, allowing the inference of separate patterns of local circulation and transboundary spread.…”

Section: Ppr Situation At Regional Levelmentioning

confidence: 92%

Peste des Petits Ruminants in Central and Eastern Asia/West Eurasia: Epidemiological Situation and Status of Control and Eradication Activities after the First Phase of the PPR Global Eradication Programme (2017–2021)

Legnardi

Raizman²,

Beltrán‐Alcrudo³

et al. 2022

Animals

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Peste des petits ruminants (PPR) is a highly contagious infectious disease of small ruminants caused by peste des petits ruminants virus (PPRV). PPR poses a significant threat to sheep and goat systems in over 65 endemic countries across Africa, the Middle East and Asia. It is also responsible for devastating outbreaks in susceptible wildlife, threatening biodiversity. For these reasons, PPR is the target of the Global Eradication Programme (PPR GEP), launched in 2016, which is aimed at eradicating the disease by 2030. The end of the first five-year phase of the PPR GEP (2017–2021) provides an ideal opportunity to assess the status of the stepwise control and eradication process. This review analyses 13 countries belonging to Eastern Europe, Transcaucasia, and Central and East Asia. Substantial heterogeneity is apparent in terms of PPR presence and control strategies implemented by different countries. Within this region, one country is officially recognised as PPR-free, seven countries have never reported PPR, and two have had no outbreaks in the last five years. Therefore, there is real potential for countries in this region to move forward in a coordinated manner to secure official PPR freedom status and thus reap the trade and socioeconomic benefits of PPR eradication.

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“…In 1987, PPR reached the northern part of India in Asia and spread to the Arabian Peninsula, the Middle East and other parts of India [ 6 ]. In 1999, initials PPR spread to Turkey in Europe [ 7 ]. So far, the PPR epidemic has spread to Europe, Asia and Africa, more than 70 countries have found PPR, among which Asia and Africa have the largest number of outbreaks, involving a wide range of regions [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Epidemiologic and import risk analysis of Peste des petits ruminants between 2010 and 2018 in India

et al. 2022

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Background Peste des petits ruminants (PPR) is a serious disease that affects goats, sheep and other small ruminants. As one of the earliest and most serious countries, PPR has seriously threatened India's animal husbandry economy. Results In this study, the spatiotemporal characteristics of the PPR in India outbreaks were analyzed. Between 2010 and 2018, the epidemic in India broke out all over the country in a cluster distribution. Epidemic clusters in northern and southern India are at higher risk, and the outbreak time of PPR has significant seasonality. The results of the analysis of the development and transmission of PPR under the natural infection conditions showed that the PPR outbreak in India reached a peak within 15 days. Finally, the quantitative risk analysis results based on scenario tree show showed that the average probability of infecting PPRV in live sheep exported from India was 1.45 × 10–4. Conclusions This study analyzed the prevalence of PPR in India. The analysis of transmission dynamics on the development of the epidemic provides a reference for the prevention and control of the epidemic. At the same time, it provides risk analysis and suggestions on trade measures for the trading countries of India.

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Complete Genome Sequence of a Lineage IV Peste des Petits Ruminants Virus from Turkey, 2018

Abstract: We report the whole-genome sequence of a peste des petits ruminants virus (PPRV) from a lamb exhibiting clinical signs in Turkey in September 2018. The genome of PPRV/Turkey/Central_Anatolia/2018 shows the highest nucleotide sequence identity (97.63%) to PPRV isolated in Turkey in 2000.

Cited by 5 publications

References 7 publications

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses

Peste des Petits Ruminants in Central and Eastern Asia/West Eurasia: Epidemiological Situation and Status of Control and Eradication Activities after the First Phase of the PPR Global Eradication Programme (2017–2021)

Epidemiologic and import risk analysis of Peste des petits ruminants between 2010 and 2018 in India

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