Phylodynamic analysis of foot-and-mouth disease virus evolution in Mar Chiquita, Argentina.

Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10- 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread.

Identification and molecular characterization of Orfvirus infection in occupationally exposed women inSouth America

Abstract Contagious Ecthyma (CE) is a severe exanthematous dermatitis caused by the Orf virus (ORFV) that mainly affects domestic small ruminants such as sheep and goats. It is a worldwide-distributed occupational zoonosis, particularly infecting those in close contact with animals or animal products such as shepherds, farmers and veterinarians, among others. In the present work, we report the first human CE case confirmed in Argentina. A phylogenetic analysis based on four gene sequences of the isolated strain responsible for the disease showed that this isolate grouped with other ORFV sequences that caused reported CE cases in sheep from the same Argentine province. We also sequenced a sample from a Chilean human case reported in 2017, whose phylogenetic analysis showed that it groups together with other Argentine isolates from locations close to the border with Chile. Keywords: Contagious Ecthyma; Dermatitis; Human Orf; Zoonosis; Molecular characterization.

Resumen El ectima contagioso (EC) es una dermatitis exantemática grave causada por el virus Orf (ORFV), que afecta mayormente a pequeños rumiantes domésticos, como ovinos y caprinos. Es una zoonosis ocupacional con distribución mundial, infecta a humanos en estrecho contacto con animales o sus productos, como granjeros, esquiladores y veterinarios, entre otros. En este trabajo se informa el primer caso humano de EC confirmado en Argentina. Un análisis filogenético basado en cuatro genes de la cepa responsable de este caso mostró que el aislamiento agrupa con otras secuencias de ORFV que causaron casos en ovinos en la misma provincia argentina. También se secuenció una muestra del caso de ectima humano reportado en Chile en 2017 y el análisis filogenético mostró que dicho aislamiento forma un grupo con otros aislamientos argentinos de localidades cercanas a la frontera con Chile. Palabras clave: Ectima contagioso; Dermatitis; Orf en humanos; Zoonosis; Caracterización molecular.

Identification and molecular characterization of Orf virus infection in occupationally exposed women in South America.

Contagious Ecthyma (CE) is a severe exanthematous dermatitis caused by the Orf virus (ORFV) that mainly affects domestic small ruminants such as sheep and goats. It is a worldwide-distributed occupational zoonosis, particularly infecting those in close contact with animals or animal products such as shepherds, farmers and veterinarians, among others. In the present work, we report the first human CE case confirmed in Argentina. A phylogenetic analysis based on four gene sequences of the isolated strain responsible for the disease showed that this isolate grouped with other ORFV sequences that caused reported CE cases in sheep from the same Argentine province. We also sequenced a sample from a Chilean human case reported in 2017, whose phylogenetic analysis showed that it groups together with other Argentine isolates from locations close to the border with Chile.

Optimization and application of a high-resolution melting protocol in the characterization of avian infectious laryngotracheitis virus

Resumen En un estudio epidemiológico realizado previamente en Argentina, se analizó la secuencia de un fragmento del gen US5 del virus de la laringotraqueítis infecciosa (ILTV), lo que permitió diferenciar las cepas de campo de las vacunales. También esto permitió definir cinco haplotipos del ILTV, con variaciones específicas en las posiciones 461, 484, 832, 878 y 894 del gen US5. La caracterización de las cepas virales también puede lograrse mediante el análisis de la disociación de alta resolución o high-resolution melting analysis (HRMA), descripto como un método efectivo, rápido y sensible para detectar mutaciones en productos de PCR. En el presente estudio se desarrolló un protocolo de disociación de alta resolución con el objetivo de caracterizar cepas del ILTV circulantes en Argentina. Para ello,se confirmó la especificidad de esta herramienta en diferentes diluyentes del ADN de las muestras, sin observarse interferencias en presencia de ADN heterólogo u otros metabolitos celulares. Asimismo, la concentración de sales en el buffer de elución utilizado durante la extracción de ADN no alteró los perfiles de las curvas. Se obtuvieron perfiles bien definidos con concentraciones de ADN más elevadas (Ct = 26.0), mientras que concentraciones más bajas presentaron curvas heterogéneas (Ct = 32.5). El HRMA mostró una concordancia del 97.49% con la técnica de referencia, la secuenciación. El protocolo de disociación de alta resolución amplifica el ADN antes de su caracterización, por lo que esta técnica podría ser eventualmente utilizada para confirmar la presencia del ILTV y, al mismo tiempo, distinguir haplotipos, optimizando su valor como herramienta de diagnóstico. Esta característica implica una reducción significativa en el tiempo dedicado al procesamiento de muestras.

Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site.

Molecular knowledge of virus-antibody interactions is essential for the development of better vaccines and for a timely assessment of the spread and severity of epidemics. For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigen-antibody (Ag-Ab) interaction, and cross-antigenicity characterization and prediction are critical to design engineered vaccines with robust, long-lasting, and wider response against different strains. We integrated existing structural modeling and prediction algorithms to study the surface properties of FMDV Ags and Abs and their interaction. First, we explored four modeling and two Ag-Ab docking methods and implemented a computational pipeline based on a reference Ag-Ab structure for FMDV of serotype C, to be used as a source protocol for the study of unknown interaction pairs of Ag-Ab. Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two peptide ELISAs for their fine epitope mapping. Then, we applied the previous Ag-Ab molecular structure modeling and docking protocol further scored by functional peptide ELISA data. This work highlights a possible different behavior in the immune response of IgG and IgM Ab isotypes. The present method yielded reliable Ab models with differential paratopes and Ag interaction topologies in concordance with their isotype classes. Moreover, it demonstrates the applicability of computational prediction techniques to the interaction phenomena between the FMDV immunodominant AgSA and Abs, and points out their potential utility as a metric for virus-related, massive Ab repertoire analysis or as a starting point for recombinant vaccine design.

Optimization and application of a high-resolution melting protocol in the characterization of avian infectious laryngotracheitis virus.

A previous sequence analysis of a US5 gene fragment of infectious laryngotracheitis virus (ILTV) performed in an Argentinian epidemiological study allowed to differentiate between wild and vaccine strains. This analysis also defined five ILTV haplotypes with specific variations at positions 461, 484, 832, 878 and 894 of the US5 gene. This characterization of viral strains may also be accomplished using the High-Resolution Melting Analysis (HRMA), which has been described as an effective, fast and sensitive method to detect mutations in PCR products. In the present study, an HRM protocol was developed with the aim of characterizing the circulating ILTV strains in Argentina. The specificity of this tool was confirmed in different DNA diluents, without interference from heterologous DNA or other cellular metabolites. Additionally, the salt concentration in the elution buffer used for DNA extraction did not alter the curve profiles. Higher concentrations of DNA (Ct≅26.0) displayed well-defined curve profiles, whereas lower concentrations (Ct≅32.5) exhibited more heterogeneous curves. The HRMA showed 97.49% concordance with the reference technique, i.e., sequencing. The HRM protocol has the capability to perform DNA amplification prior to its characterization. Thus, eventually this technique may be used simultaneously as a diagnostic tool. This advantage implies a significant reduction in the time and effort involved in sample processing.

Phylogenetic Analysis of ORF Viruses From Five Contagious Ecthyma Outbreaks in Argentinian Goats.

Orf virus (ORFV) is the etiological agent of Contagious Ecthyma (CE) disease that mainly affects sheep, goats, wild ruminants, and humans with a worldwide distribution. To date, only two strains from Argentinian sheep have been characterized at the molecular level and there is little information on ORFV strains circulating in Argentina. Here we describe and analyze five outbreaks of CE in goats in three geographic regions of the country: Northwest, Center, and Southwest. The phylogenetic analysis based on four molecular markers of ORFV (orf011 partial sequence and orf020, orf109, and orf127 complete sequence genes) revealed that there are different strains circulating in Argentina and pointed out the importance of knowing the health status of animals traded between farms.

Molecular Characterization and Cluster Analysis of Field Isolates of Avian Infectious Laryngotracheitis Virus from Argentina.

Avian infectious laryngotracheitis (ILT) is a worldwide infectious disease that causes important economic losses in the poultry industry. Although it is known that ILT virus (ILTV) is present in Argentina, there is no information about the circulating strains. With the aim to characterize them, seven different genomic regions (thymidine kinase, glycoproteins D, G, B, C, and J, and infected cell polypeptide 4) were partially sequenced and compared between field samples. The gJ sequence resulted to be the most informative segment, it allowed the differentiation among field sample strains, and also, between wild and vaccine viruses. Specific changes in selected nucleotidic positions led to the definition of five distinct haplotypes. Tests for detection of clustering were run to test the null hypothesis that ILTV haplotypes were randomly distributed in time in Argentina and in space in the most densely populated poultry region of this country, Entre Rios. From this study, it was possible to identify a 46 km radius cluster in which higher proportions of haplotypes 4 and 5 were observed, next to a provincial route in Entre Rios and a significant decline of haplotype 5 between 2009 and 2011. Results here provide an update on the molecular epidemiology of ILT in Argentina, including data on specific genome segments that may be used for rapid characterization of the virus in the field. Ultimately, results will contribute to the surveillance of ILT in the country.

A computational study of the interaction of the foot and mouth disease virus VP1 with monoclonal antibodies.

Foot and mouth disease is caused by a non-enveloped virus (FMDV), which disposes several antigenic sites at the surface of their capsid proteins. The most relevant and immunodominant antigenic site of FMDV (site A or AnSA) includes a key virus-cell interaction element (RGD motif) located in the Viral Protein 1 (VP1), more precisely at the GH loop. AnSA includes a set of overlapped and mainly linear epitopes, which are the main targets of the humoral immune response. Taking advantage over specific structural features of the GH loop, we have evaluated the influence of every amino acid residue at AnSA in the interaction with 2 neutralizing antibodies by molecular modeling techniques. Additionally, we constructed diverse interaction complexes with multiple site A mutants and discussed about the structural influence of amino acidic insertions in such relevant antigenic site of FMDV. Our approach is in agreement with previous ELISA experiments and allows the understanding of how FMDV mutations may alter the interaction with different antibodies, as we can estimate the contribution of each amino acid to the interaction. Overall, our work contributes to the development of specific vaccination strategies for FMD control.

Detección molecular de coinfección con los virus de la diarrea viral bovina (BVDV) en búfalos de agua (Bubalus bubalis) serológicamente negativos / Molecular analyses detect natural coinfection of water buffaloes (Bubalus bubalis) with bovine viral diarrhea viruses (BVDV) in serologically negative animals

La infección de los búfalos de agua (Bubalus bubalis) con los virus de la diarrea viral bovina (BVDV) ha sido confirmada mediante técnicas serológicas y moleculares en trabajos anteriores. Con el fin de determinar la presencia de animales persistentemente infectados y las especies y subtipos circulantes de BVDV en esta especie animal se realizó un estudio sobre una manada de búfalos de producción mixta con ganado bovino (Bossp.). Nuestros resultados serológicos mostraron un alto nivel de positividad frente a BVDV-1 y BVDV-2 dentro de la manada de búfalos. El análisis molecular sobre muestras de sangre de los animales serológicamente negativos reveló la presencia de ácido nucleico viral, lo que confirma la existencia de búfalos persistentemente infectados. El clonado y la secuenciación de la región 5 'UTR de algunas de las muestras obtenidas de búfalo reveló la presencia de coinfección natural con al menos dos subtipos diferentes de BVDV (1a y 1b) y con las especies virales BVDV-1 y BVDV-2

Infection of water buffaloes (Bubalus bubalis) with bovine viral diarrhea viruses (BVDV) has been confirmed in several studies by serological and molecular techniques. In order to determine the presence of persistently infected animals and circulating species and subtypes of BVDV we conducted this study on a buffalo herd, whose habitat was shared with bovine cattle (Bossp.). Our serological results showed a high level of positivity for BVDV-1 and BVDV-2 within the buffalo herd. The molecular analyses of blood samples in serologically negative animals revealed the presence of viral nucleic acid, confirming the existence of persistent infection in the buffaloes. Cloning and sequencing of the 5' UTR of some of these samples revealed the presence of naturally mix-infected buffaloes with at least two different subtypes (1a and 1b), and also with both BVDV species (BVDV-1 and BVDV-2)

Molecular analyses detect natural coinfection of water buffaloes (Bubalus bubalis) with bovine viral diarrhea viruses (BVDV) in serologically negative animals.

Infection of water buffaloes (Bubalus bubalis) with bovine viral diarrhea viruses (BVDV) has been confirmed in several studies by serological and molecular techniques. In order to determine the presence of persistently infected animals and circulating species and subtypes of BVDV we conducted this study on a buffalo herd, whose habitat was shared with bovine cattle (Bossp.). Our serological results showed a high level of positivity for BVDV-1 and BVDV-2 within the buffalo herd. The molecular analyses of blood samples in serologically negative animals revealed the presence of viral nucleic acid, confirming the existence of persistent infection in the buffaloes. Cloning and sequencing of the 5' UTR of some of these samples revealed the presence of naturally mix-infected buffaloes with at least two different subtypes (1a and 1b), and also with both BVDV species (BVDV-1 and BVDV-2).

Identification and molecular characterization of Orf virus in Argentina.

Orf virus (ORFV) is the etiological agent of contagious ecthyma (CE), a pustular dermatitis of sheep and goats. Outbreaks of ORFV have been observed in all geographical regions of the world, including Argentina. The origin and identity of Argentinian ORFVs are unknown, and no comparative or phylogenetic studies of these viruses have been performed. In this study, we described the sequencing and analysis of five ORFV molecular markers: a partial B2L gene (ORF011), VIR (ORF020), an envelope mature protein (ORF109), vIL10 (ORF127), and GIF (ORF117) from two particular Argentinian outbreaks of CE.