# Genomic analysis of peste des petits ruminants virus in Europe: Common origin for emergence in Greece, Romania, and Bulgaria

Samia Guendouz, Olivier Kwiatek, Aikaterini Kirtzalidou, Angeliki Katsifa, Maria Gianniou, Corina Ancuceanu, Mona Ghiță, Cristian Laurențiu Mortasivu, Anna Zdravkova, Iliyan Kostov, et al.

► To cite this version:

Samia Guendouz, Olivier Kwiatek, Aikaterini Kirtzalidou, Angeliki Katsifa, Maria Gianniou, et al. Genomic analysis of peste des petits ruminants virus in Europe: Common origin for emergence in Greece, Romania, and Bulgaria. Infection, Genetics and Evolution, 2025, 132, pp.105774. 10.1016/j.meegid.2025.105774. hal-05346892

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# Genomic analysis of peste des petits ruminants virus in Europe: Common origin for emergence in Greece, Romania, and Bulgaria

Samia Guendouz<sup>a,b,1</sup>, Olivier Kwiatek<sup>a,b,1</sup>, Aikaterini Kirtzalidou<sup>c</sup>, Angeliki Katsifa<sup>c</sup>, Maria Gianniou<sup>d</sup>, Corina Ancuceanu<sup>e</sup>, Mona Ghiță<sup>e</sup>, Cristian Laurențiu Mortasivu<sup>f</sup>, Anna Zdravkova<sup>g</sup>, Iliyan Kostov<sup>h</sup>, Emilia Ivanova<sup>i</sup>, Florica Bărbuceanu<sup>e,j</sup>, Konstantia E. Tasioudi<sup>c</sup>, Arnaud Bataille<sup>a,b,*</sup>

## ARTICLE INFO

### Keywords:

- Morbillivirus

- Small ruminant

- Transboundary disease

- Phylogenomics

## ABSTRACT

Outbreaks of the highly pathogenic small ruminant disease peste des petits ruminants (PPR) were reported in Greece and Romania in July 2024, and central Bulgaria in November 2024. The origin and the link between these outbreaks are not clear. In this study, genome sequences of PPR virus were obtained from samples collected by veterinary authorities in the first farms notified as infected in the three European countries. Genomic analyses confirmed that the emergence of PPR across Europe has a common origin, pointing towards an introduction from Northern Africa, although additional sequencing from the virus currently circulating globally is needed to confirm this hypothesis. More sequencing from the different outbreaks in Europe could also help to resolve the pathway of PPR transmission between and within European countries. Multiple nucleotide and amino acid differences separate the genomes from Europe from other sequences, with potential impact on the functionality of viral proteins to be investigated.

## 1. Introduction

Peste des petits ruminants (PPR) is a highly infectious viral disease affecting mainly sheep and goats in large parts of Africa, the Middle East, and Asia (Baron et al., 2016). PPR has a large impact on the global economy and represents a threat to food security, as it affects mainly low-income livestock owners (Jones et al., 2016). Despite ongoing eradication efforts, risks of emergence of this transboundary disease in new areas remain high, mostly through livestock movements (Bataille and Baron, 2024). The risk of PPR emergence in Europe has been

considered important for at least a decade, notably with the presence of the disease in North Africa and Turkey (Parida et al., 2016). PPR first emerged in Europe in 2018, with outbreaks in Bulgaria, close to the border with Turkey, although the outbreak was rapidly controlled (WOAH, 2018). No more outbreaks were reported in Europe until July 2024, when PPR infections were reported in Greece, then in Romania (WOAH, 2024a, 2024c). Other outbreaks have recently been reported in Bulgaria and Hungary, in November 2024 and January 2025, respectively (WOAH, 2024b, 2025). This is the first major emergence in the European Union and the multiplication of notifications is worrying. No

<footnote><sup>a</sup> ASTRE, University of Montpellier, CIRAD, INRAE, F-34398 Montpellier, France</footnote>

<footnote><sup>b</sup> CIRAD, UMR ASTRE, F-34398 Montpellier, France</footnote>

<footnote><sup>c</sup> National Reference Laboratory for Peste des Petits Ruminants, Department of Molecular Diagnostics, FMD, Virological, Rickettsial & Exotic diseases, Directorate of Veterinary Center of Athens, Ministry of Rural Development and Food, 25, Neapoleos str, 15341, Agia Paraskevi, Athens, Greece</footnote>

<footnote><sup>d</sup> Animal Health Directorate, Directorate General of Veterinary Services, Ministry of Rural Development and Food, 47 Veranzerou street, 10438 Athens, Greece.</footnote>

<footnote><sup>e</sup> Institute for Diagnosis and Animal Health, Bucharest, Romania</footnote>

<footnote><sup>f</sup> National Sanitary Veterinary and Food Safety Authority, Romania</footnote>

<footnote><sup>g</sup> Animal Health Department, Bulgarian Food Safety Agency, Sofia, Bulgaria</footnote>

<footnote><sup>h</sup> Ministry of Agriculture and Food, Sofia, Bulgaria</footnote>

<footnote><sup>i</sup> National Diagnostic and Research Veterinary Medical Institute, Sofia, Bulgaria</footnote>

<footnote><sup>j</sup> Faculty of Veterinary Medicine, Bucharest, Romania</footnote>

<footnote>* Corresponding author at: ASTRE, University of Montpellier, CIRAD, INRAE, F-34398 Montpellier, France.
E-mail address: arnaud.bataille@cirad.fr (A. Bataille).</footnote>

<footnote n="1">¹ Have contributed equally.</footnote>
vaccination against PPR have been implemented in the European Union, with efficient control of the emergence based on stamping out and movement control. A major question concerns the origin of these outbreaks and whether emergences in the four European countries are related. It is important to determine if the emergences correspond to separate events or represent the spread of a virus from a common origin.

Viral genome sequencing represents a powerful tool to resolve these questions, notably with RNA viruses like PPRV and other morbilliviruses, as mutations are quickly generated during viral replication. Based on genomic differences, phylogenetic analyses can provide information on the relationship between virus strains circulating in different parts of the world and mutations of potential importance for virus spread and virulence can be identified (Courcelle et al., 2024; Pybus and Rambaut, 2009). In the case of PPR virus, four different genetic lineages have been identified, with lineages I (LI), II (LII), and III (LIII) having limited distribution within Africa, while lineage LIV is widespread across Africa, the Middle East, and Asia (Bataille and Baron, 2024). The lineage IV shows high genetic diversity and can be separated into well-defined groups corresponding in most part to geographical regions (Courcelle et al., 2024). Despite this genetic diversity, there is only one serotype for PPRV, allowing for the use of efficient vaccines in current efforts to eradicate the disease (Bataille and Baron, 2024).

This study describes the sequencing of the full genome of PPR virus obtained from animals infected in the first outbreaks reported in Greece, Romania, and Bulgaria. We use phylogenomic analyses and comparative genomic analyses to investigate whether these outbreaks have a common origin, what this origin might be, and if the virus strains circulating in Europe present genomic characteristics that may influence their virulence and capacity for transmission.

## 2. Material and methods

CIRAD (Montpellier, France), within the frame of its role as Reference Laboratory of the European Union for PPR (EURL-PPR, https://eurl-ppr.cirad.fr/), received samples from infected farms collected by

Veterinary Services in Greece, Romania, and Bulgaria and tested positive for presence of genomic material of PPR virus by the National Reference Laboratories using real-time RT-PCR (WOAH, 2024a, 2024b, 2024c) (Fig. 1). Samples received included blood, organs, ocular, nasal, and rectal swabs. Full genome sequencing was performed on a selection of 10 samples presenting the lowest Ct value in the real-time PCR assay (range: 11.7–26.3; Table 1), including 3 samples from Greece, 3 from Romania, and 4 from Bulgaria (Table 1).

Samples were first treated with a cocktail of nucleases to digest unwanted nucleic acids except viral RNA as described in a publication by Gil et al. (Gil et al., 2021). RNA was then extracted using a magnetic bead-based extraction kit (IndiMag Pathogen INDICAL BIOSCIENCE) on an IDEAL32 platform (IDEAL32, Innovative Diagnostics) according to the manufacturer's instructions, except for the replacement of the carrier by 1 µl of linear acrylamide (5 mg/ml, Invitrogen). Library preparation for high-throughput sequencing was carried out using a protocol based on random amplification developed to sequence rinderpest virus genomes (King et al., 2020) with some modifications. First strand cDNA was generated from PPR RT-qPCR positive RNA using random hexamer primers with RevertAid first strand cDNA synthesis kit (Thermo Scientific) according to the manufacturer's protocol except for the addition of 1 µl of 100 % DMSO at the denaturation step. RNA was then digested at 37 °C for 20 min with 2 U RNase H and double-stranded cDNA synthesised using DNA Polymerase I, Large (Klenow) Fragment kit (New England Biolabs) in a final volume of 30 µl incubated at 25 °C for 15 min followed by 75 °C for 20 min. Double stranded cDNA was purified using the Nucleospin PCR clean up and gel extraction kit (Macherey-Nagel) according to the manufacturer's instructions in a final volume of 30 µl. The purified double-strand cDNA concentration was assessed using the Qubit dsDNA HS (Invitrogen) assay kit and adjusted to a final concentration of 0.2 ng/µl. Libraries were generated from 1 ng double-stranded cDNA using the Nextera XT DNA Library Prep kit according to the manufacturer's instructions in "dual index" by using two indexes for each sample. The quantitative PCR (Q-PCR) "Library quantification kit" (Takara Clonetech) was performed on a LightCycler instrument (Roche)

<figure><img src="image_3.png" /><figcaption>**Fig. 1.** Map showing in dark grey the regions in Africa and Asia neighboring Europe, reporting PPR circulation within the last 10 years. Black areas represent the first notified outbreaks in Greece, Romania, and Bulgaria (2024), from which samples were collected for this study.</figcaption></figure>
<table><caption>**Table 1**

List of PPR virus samples with summary of the results of the genomic sequencing effort.</caption><thead><tr><th>Country</th><th>Region/village</th><th>Outbreak number</th><th>Sample ID</th><th>Sample type</th><th>Ct value</th><th>Coverage (%)</th><th>Mean depth</th><th>Accession number</th></tr></thead><tbody><tr><td rowspan="3">Greece</td><td rowspan="3">Thessalia/Kalampaka</td><td>ADIS-1</td><td>3</td><td>ocular swab</td><td>23.1</td><td>21</td><td>0.39</td><td>-</td></tr><tr><td>ADIS-5</td><td>6</td><td>lung</td><td>22.0</td><td>72.9</td><td>3</td><td>-</td></tr><tr><td>ADIS-5</td><td>7</td><td>lung</td><td>14.9</td><td>99.5</td><td>834</td><td>PV385049</td></tr><tr><td rowspan="3">Romania</td><td rowspan="3">Tulcea/Baia</td><td>ADIS-1</td><td>7*</td><td>lung</td><td>12.0</td><td>99.5</td><td>659</td><td>PV385050</td></tr><tr><td>ADIS-1</td><td>8*</td><td>Lymph node</td><td>11.7</td><td>99.7</td><td>750</td><td>PV385051</td></tr><tr><td>ADIS-1</td><td>13</td><td>lung</td><td>11.7</td><td>99.5</td><td>21,000</td><td>-</td></tr><tr><td rowspan="5">Bulgaria</td><td rowspan="5">Pazardzhik/Velingrad</td><td>ADIS-1</td><td>1</td><td>blood</td><td>26.3</td><td>2.6</td><td>0.04</td><td>-</td></tr><tr><td></td><td>12*</td><td>blood</td><td>24.7</td><td>12.9</td><td>0.2</td><td>-</td></tr><tr><td></td><td>42*</td><td>ocular swab</td><td>17.8</td><td>83.4</td><td>5</td><td>-</td></tr><tr><td></td><td>53</td><td>ocular swab</td><td>20.3</td><td>56.1</td><td>1.5</td><td>-</td></tr><tr><td></td><td>42 + 53</td><td>ocular swab</td><td>-</td><td>93.7</td><td>10</td><td>PV385052</td></tr></tbody></table>

to assess the exact quantity of ligated DNA molecules for each library. The distribution of fragment sizes within each library was analyzed on an Agilent 2100 Bioanalyzer with the Agilent high sensitivity DNA kit (Agilent Technologies). The quantity and average size of each library were used to pool the libraries in an equimolar manner. Sequencing was performed on a Miniseq Illumina machine at MGX sequencing platform (MGX-CNRS, Montpellier, France).

Raw sequencing reads were cleaned and aligned to a reference PPRV genome (Georgia/Tbilisi/2016; GenBank: MF737202) to produce a consensus genome following a bioinformatic pipeline described earlier (Courcelle et al., 2024). If the percentage of genome coverage was low (<90 %), raw sequencing reads from multiple samples collected from the same farm were combined and this combined data was run through

the pipeline in an attempt to obtain a complete or almost complete genome sequence from each infected establishment. The consensus genomes obtained were checked to ensure absence of contamination using recombination analyses (Baron and Bataille, 2022), then aligned with a curated dataset of full PPRV genome sequences (available at https://eurl-ppr.cirad.fr/). A phylogenetic analysis was carried out on the aligned dataset using Maximum Likelihood inference as implemented in W-IQ-TREE (Trifinopoulos et al., 2016), with branch support analysis performed with 5000 bootstrap iterations. Genetic and amino acid differences between the consensus genomes obtained from PPRV outbreaks in Europe and the most closely related genome virus in the dataset were identified using Geneious 10.2.6 (https://www.geneious.com).

<figure><img src="image_4.png" /><figcaption>**Fig. 2.** Phylogenetic tree obtained by Maximum Likelihood method using PPRV full genome sequences. Sequences from major genetic lineages and sub-lineages with no direct relevance for this analysis have been collapsed. Confidence support for tree nodes was of 100 % for all nodes presented in this tree based on bootstrap analysis (5000 replications). Sequence from Greece, Bulgaria and Romania are shaded in grey. The full tree showing all branches is available in supplementary material Fig. S1.</figcaption></figure>

<footnote>(*) Sample coming from the same animal; Ct value: Ct value obtained for each sample using the quantitative Real-time PCR method validated by the EURL-PPR (https://eurl-ppr.cirad.fr/); Mean Depth, mean number of sequencing read per genome position in the reference PPRV genome used for the alignment.</footnote>
## 3. Results

An almost complete genome sequence (99.5–99.7 % coverage from total size of 15,948 bp) was obtained for one organ sample from the PPR outbreak in Greece and all samples tested from Romania, with a good mean depth per site (Table 1). Two sequences, obtained from samples taken from the same animal (samples 7 and 8), were identical, as expected. Sequencing attempts on samples received from the outbreak in Bulgaria gave poor genome coverage, especially with blood samples (2.6–12.9 %; Table 1). Sequencing from ocular swabs gave better results, and, after combining raw reads from two ocular swab samples, an almost complete consensus genome could be generated (93.7 % coverage), although with mean depth limited to 10 reads per site (Table 1). For all consensus genome sequences, the same regions were missing, i.e., a portion of the non-coding region separating the regions coding for the M and F proteins, well known to be difficult to sequence due to high GC content but which has limited impact on phylogenetic analyses (Baron and Bataille, 2022). All raw sequencing reads and genome sequences were deposited into the Sequencing Read Archive (PRJNA717034) and GenBank, respectively (PV385049-PV385052; Table 1).

All genomes obtained from the emergences in Europe had a high percentage of similarity (99.7–100 %). Results of the phylogenetic analyses showed that all viral genome sequences from the emergence in Greece, Romania, and Bulgaria belonged to PPRV genetic lineage IV, and grouped with sequences from the North and East Africa sub-lineage (Fig. 2). The most closely related sequence was from the PPR virus isolated during the outbreak in Georgia in 2016 (Georgia/Tbilisi/2016) whose origin has never been fully elucidated (Donduashvili et al., 2018). The number of nucleotide differences separating the Georgia/Tbilisi/ 2016 strain from European strains ranged between 173 and 178, with 30–35 differences leading to a change in amino acids in multiple proteins of the virus (Table 2). Some of these amino acid changes appear unique to the European strains, as they are not found in other PPRV genomes publicly available (Table 2). Genomes of PPR virus isolated in the three European countries differ by 8 to 32 nucleotide substitutions leading to 1 to 7 amino acid changes, with higher similarity between genomes isolated from the same farm in Romania and more differences between genomes from Bulgaria and Romania (Table 2). Some amino acid differences lead to a change in the property of the amino acid (e.g., charge or structure) and could impact the function of the proteins (Table S1 in supplementary materials). The majority of these changes are situated in the P protein, involved in viral replication and in the hemagglutinin protein (H), responsible for the attachment to the host cells (Table S1 in supplementary materials).

<caption>**Table 2**</caption>

Number of nucleotide and amino acid differences separating PPR virus from outbreaks in Europe in 2024 and Georgia in 2016.

<table><thead><tr><th></th><th>Nuc diff</th><th>AA diff</th><th>Unique AA diff</th></tr></thead><tbody><tr><td>Georgia/2016 vs Greece/2024</td><td>176</td><td>30</td><td>12</td></tr><tr><td>Georgia/2016 vs Romania/7/2024</td><td>177</td><td>35</td><td>14</td></tr><tr><td>Georgia/2016 vs Romania/13/2024</td><td>173</td><td>34</td><td>14</td></tr><tr><td>Georgia/2016 vs Bulgaria/2024*</td><td>178</td><td>32</td><td>13</td></tr><tr><td>Greece/2024 vs Romania/7/2024</td><td>22</td><td>4</td><td>2</td></tr><tr><td>Greece/2024 vs Romania/13/2024</td><td>20</td><td>5</td><td>2</td></tr><tr><td>Greece/2024 vs Bulgaria/2024*</td><td>19</td><td>3</td><td>2</td></tr><tr><td>Romania/7/2024 vs Romania/13/2024</td><td>8</td><td>1</td><td>0</td></tr><tr><td>Romania/7/2024 vs Bulgaria/2024*</td><td>32</td><td>7</td><td>4</td></tr></tbody></table>

Nuc diff, number of Nucelotide differences; AA diff, number of amino acid differences; unique AA diff, number of amino acid differences in genome positions were no polymorphism has been observed in publicly available PPRV genomes; (*) The genome of Bulgaria/2024 is less covered (93.7 %) than genomes from other European countries (99.5 %), so some nucelotide and amino acid differences may be missing.

## 4. Discussion

An almost complete genome of PPR virus at the origin of the outbreaks in Romania, Greece, and Bulgaria could be obtained. Analyses performed in this study confirm that the emergence of PPR in the three countries has a common origin. Phylogenetic analyses point towards an origin in Northern Africa, instead of Turkey, as earlier risk assessments had expected (Parida et al., 2016). Phylogenetic analyses on the partial N gene for the PPR outbreak in Georgia in 2016 also pointed to an introduction from the same region, suggesting that there is a recurrent link between the two regions representing a risk of PPR spread into new areas. It can be noted that Georgia and Romania are the 13rd and 4th largest exporters of live small ruminants, respectively, according to the Observatory of Economic Complexity (www oe world), reaching multiple countries, including in North Africa and Middle East, although it remains to be explored if such export activities can really represent a risk of PPR transmission into the country organizing the exports. Sequencing of samples from the recent PPR outbreak in Hungary (WOAH, 2025) is needed to assess whether it has the same origin or represents a separate incursion of PPR into Europe.

It is important to acknowledge the lack of recent PPRV genomic data in many countries where PPR is currently circulating, including Turkey, the Middle East, Central Asia, and Northern Africa (Bataille and Baron, 2024). Additional sequencing from recent outbreaks in Turkey and Northern Africa is especially needed to further investigate the question of the exact origin of this emergence in Europe. In addition, one or two sequences from the three European countries are not enough data to investigate the pathway of transmission between the countries. The samples collected come from the first establishments officially notified as infected by PPR, but due to delays in identifying the diseases, it is apparent that these farms may not be the first ones to have been infected, and links between different infected farms are difficult to identify.

Systematic sequencing of a representative sample from affected farms from various regions infected in Greece, Romania, and Bulgaria could help determine the dynamic of PPR spread within and between the three countries. Indeed, our results show that nucleotide mutations have quickly accumulated in the virus circulating in Europe. Even within one infected farm in Romania, two genomes with 8 nucleotide differences could be obtained from two different animals. It suggests that genetic diversity is large enough to use genomic analyses to investigate pathways of transmission between establishments in Europe, providing valuable information to improve control measures in case of new outbreaks. However, our sequencing method appears to be more efficient in obtaining the full genome from organ samples with high viral load (Ct < 20), but does not perform well for samples with lower viral load, especially for blood samples already shown not to be recommended for PPR virus detection (Halecker et al., 2020). Modification of the method, notably with the addition of steps to deplete host genetic material, may help improve our yield. Such work is important if we want to support epidemiological investigation with genomic analyses, as good quality organ samples are not always collected or properly stored in the field during investigation.

Many nucleotide and amino acid differences separate the genomes obtained from outbreaks in Europe from the most closely related genome available in the public database, Georgia/Tbilisi/2016. Also, more mutations leading to amino acid changes have been accumulating during the past few months of PPR circulation in Europe. It is possible that some of the amino acid changes observed have impacted the function of viral proteins, and therefore the capacity of this PPRV strain to replicate and circulate in European small ruminant breeds. This hypothesis should be further investigated with experimental studies. Our findings indicate that uncontrolled PPRV replication in infected farms prior to detection and control may lead to increased accumulation of virus mutations. This elevated mutation rate could potentially facilitate the emergence of more virulent and transmissible strains, posing a significant risk for the spread of PPR across Europe. Therefore, enhancing
rapid detection capabilities in the field is crucial. This necessitates widespread communication and training for both private and public veterinarians across Europe, focusing on the specific clinical manifestations of PPR observed during recent outbreaks.

The unexpected emergence of PPR in Europe has presented a significant challenge, despite the rapid and effective responses from veterinary services and laboratories. The origins and transmission pathways of this incursion across EU member states remain under active investigation. This study demonstrates the crucial role of viral genomic analyses in elucidating these epidemiological mysteries, thereby enhancing our capacity to effectively control the current outbreak and ultimately eliminate PPR from Europe.

Supplementary data to this article can be found online at https://doi.org/10.1016/j.meegid.2025.105774.

### CRediT authorship contribution statement

**Samia Guendouz:** Writing – review & editing, Methodology, Investigation, Formal analysis. **Olivier Kwiatek:** Writing – review & editing, Methodology, Investigation, Formal analysis, Data curation. **Aikaterini Kirtzalidou:** Writing – review & editing, Investigation. **Angeliki Katsifa:** Formal analysis, Investigation, Writing – review & editing. **Maria Gianniou:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Corina Ancucean:** Writing – review & editing, Investigation. **Mona Ghiţă:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Cristian Laurenţiu Mortasivu:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Anna Zdravkova:** Writing – review & editing, Investigation. **Iliyan Kostov:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Emilia Ivanova:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Florica Bărbucean:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition. **Konstantia E. Tasioudi:** Writing – review & editing, Supervision, Resources, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization.

### Funding statement

AB, OK and SG are supported by a grant (SI2.756606) from the European Commission Directorate General for Health and Food Safety awarded to the European Union Reference Laboratory for peste des petits ruminants (EURL-PPR, https://eurl-ppr.cirad.fr/).

### Declaration of competing interest

The authors declare no conflict of interest.

### Acknowledgments

The authors would like to thank the dedicated staff of the NRLs from Greece, Romania and Bulgaria for their diagnostic contributions as well

as the respective Veterinary Services for providing the samples.

### Data availability

All raw sequencing reads and genome sequences were deposited into the Sequencing Read Archive (PRJNA717034) and GenBank, respectively (PV385049-PV385052).

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