Observation of high recombination occurrence of porcine reproductive and respiratory syndrome virus in field condition

Recombination in Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a well-documented phenomenon. A high recombination frequency has been reported in experimental conditions both in vitro and in vivo, and its role in driving viral evolution has been postulated by several authors. However field evidences are rare, mainly obtained from large-scale sampling and typically represented by single sequences rather than by groups of circulating \u201crecombinant progenies\u201d. The present work was aimed to investigate the gray area between experimental studies and large-scale epidemiological investigations. The study was performed on ORF5, ORF7 and concatenated sequences obtained in our laboratory or available in GenBank collected between 2009 and 2012 in northern Italy. Six independent recombinant strains out of 66 concatenated sequences ( 3c9%) were found, demonstrating a high recombination frequency respect to previous field studies but comparable to in vitro experiments. In silico analysis let speculate that this new strain displayed physicochemical features diverse enough to potentially alter its immunological properties. Taken altogether, the results of our study support previous experimental evidences that depict PRRSV to be extremely prone to recombination. The limited temporal and geographical spread of recombinant strains however states in favor of a limited fitness of the recombinant progeny compared to parental strains and the marginal role of this phenomenon in PRRSV evolution

Detection of a Novel Chlamydia Species in Invasive Turtles

Trachemys scripta is a turtle species native to Central America. Since the 1950s, pond sliders have been imported worldwide as companion animals, but have often ended up in foreign ecosystems with great ecological consequences. Moreover, both autochthonous and invasive species of turtles can be carriers of pathogens, including Chlamydiaceae. In the present study, pulmonary tissues collected from four Trachemys scripta were tested with a 23S-targeting real-time PCR (rPCR) specific for the Chlamydiaceae family. The turtles were hosted in a rescue center for wild exotic animals located in northeastern Italy, and were found dead after the hibernation period. Two out of four individuals resulted positive in rPCR for the presence of Chlamydiaceae. Further characterization of this positivity was performed by phylogenetic analysis of the 16S rRNA and outer membrane protein A genes. The phylogenetic tree showed that these chlamydial strains are identical to a novel Chlamydia reported in 2017 in Polish freshwater turtles, and closely related to Chlamydia pneumoniae and to other chlamydial strains found in reptiles. This first finding evidences the presence of this Chlamydia strain in Italian turtles, but further studies will be necessary to confirm the presence and the strain pathogenicity and to evaluate its prevalence in the local turtles’ population

Validation and comparison of different end point and real time RT-PCR assays for detection and genotyping of porcine reproductive and respiratory syndrome virus

The accuracy and rapid diagnosis of PRRSV infection is a major prerequisite for every control and/or eradication strategy. In this study two real time RT-PCR based on different chemistry analysis (TaqMan Probes and SYBR Green) have been developed and validated before comparison to an end point two-step RT-PCR validated previously. All assays were aimed at discrimination between PRRSV genotypes. Furthermore, an exogenous internal control (IC) system had also been implemented in qRT-PCR. A rigorous analytical validation, executed on infected cell cultures and serum, demonstrated good sensitivity, specificity and repeatability. In particular RT-PCR was exceptionally sensitive and could detect a viral titre in the order of a magnitude of 1 copies/mu L, 10-fold lower than other qRT-PCR described in this study. Optimal diagnostic performances have been demonstrated analyzing samples retrieved from an experimental infection, with RT-PCR again outperforming real time RT-PCR assays. All tests, showing substantial agreement between them, were able to detect early stages of viraemia (1 DPI) and some animals were classified as positive until the end of the study (76 DPI). Therefore, this supports the assays usefulness in animals with different clinical conditions and in a broad range of epidemiological scenarios. The benefits and disadvantages of different assays were also considered and discussed

International trades, local spread and viral evolution: The case of porcine circovirus type 2 (PCV2) strains heterogeneity in Italy

Porcine circovirus type 2 is one of the most widespread and economically relevant infections of swine. Four genotypes have been recognized, but currently, only three (PCV2a, PCV2b and PCV2d) are effectively circulating. The widespread livestock trade and rapid viral evolution have contributed to determining the high heterogeneity of PCV2 and the dispersal of potentially more virulent strains. Italian swine farming and the related processing industry are relevant in the national economy. Despite the noteworthy losses associated with direct and control measure costs, no data are currently available on the molecular epidemiology of PCV2 in Italy. Our study, which was intended to fill this gap, considered 75 completed genome PCV2 sequences, which were obtained from samples collected from the highly densely populated area of Northern Italy between 2007 and 2014. Phylogenetic analysis and comparison with reference sequences demonstrated the co-circulation, with different prevalences, of PCV2a, PCV2b and PCV2d within the national borders, with PCV2b being the most prevalent. Recombination between different genotypes was also proven to be frequent. Phylogeographic analysis demonstrated that the marked variability of Italian PCV2 strains can be attributable to multiple introduction events. The comparison of the phylogenetic analysis results, the location of different haplotypes and the international commercial routs of live pigs allow the speculation of several links as well as the role of Italy as both an importer and exporter of PCV2 haplotypes, mainly from and to European and Asian countries. A similarly intricate contact network was demonstrated within national borders, with different haplotypes being detected in the same province and different provinces harbouring the same haplotype. Overall, this paper represents the first description of PCV2 in Italy and demonstrates that the high variability of circulating Italian strains is due to multiple introduction events, wide circulation within national boundaries and rapid viral evolution

Persistence of Leptospira borgpetersenii Serovar Hardjo in Refrigerated Raw Milk: A Transmission Risk of Leptospirosis to Humans

Leptospira borgpetersenii serovar Hardjo (LH) is an important infectious agent of reproduction pathologies and lactation decline in cattle, with a possible zoonotic role. To figure out the potential zoonotic risk for human raw-milk consumption, the present study aims at assessing the persistence and viability of LH in refrigerated raw milk over a 10-day period, which is set as the maximum time range for raw-milk domestic consumption. A negative sample of fresh raw milk was contaminated with an LH strain (2 × 108 Leptospires/mL) and analyzed by a rrs (16S) gene targeting real-time PCR (rPCR) protocol for LH DNA at days 1, 2, 3, 6, 7, 9, and 10. Seven aliquots of the same sampling time were inoculated into a semisolid EMJH media for bacterial culture. All aliquots tested positive in both rPCR and culture, which demonstrates that raw milk does not alter the detectability and viability of LH, respectively. The analytical sensitivity (LoD, limit of detection) determined for the rPCR (103 Leptospires/mL) was repeatable during the study, whereas it gradually decreased when it came to the bacterial culture. This study demonstrates that bovine raw milk might be a potential vehicle of infection by LH, even when storage conditions are strictly respected

The impact of porcine reproductive and respiratory syndrome virus genetic heterogeneity on molecular assay performances

The remarkable economic losses due to porcine reproductive and respiratory syndrome (PRRS) have stated the control and eradication of this disease is one of the main issues of swine modern farming. The limited cross-protection of vaccine-induced immunity compelled the adoption of strict biosecurity measures that must be associated with the prompt diagnosis of infection. In our study four RT-PCR methods, a RT-PCR, a SYBR Green I and two hydrolysis probes, were compared to evaluate their respective benefits and disadvantages. One hundred and seventy samples originating from 50 farms located in northern Italy were tested with all assays and performances were evaluated using a Bayesian approach to deal with the absence of a Gold Standard. Sequencing the complete of ORF7, the segment targeted by all methods, allowed a gain of insight into the genetic variability of Italian strains and to investigate the role of mismatches on assay sensitivity. Our study evidenced that methods based only on primers-genome interaction better tolerate PRRSV genetic variability, demonstrating a greater sensitivity (Se): SYBR Green I (Se. = 98.4%) and RT-PCR (Se. = 99%) outperform both in-house (Se. = 71.4%) and commercial (Se. = 91.7%) probe-based methods. On the other hand, probe-based assays allowed an easier genotyping of PRRSV strains and implementation of the internal control system (IC). Phylogenetic analysis allowed demonstration of a presence of two clades circulating continuously in northern Italy since 1996, when their probable ancestors were collecte

IFAT and ELISA phase I/phase II as tools for the identification of Q fever chronic milk shedders in cattle

Q fever is a widespread zoonotic disease caused by Coxiella burnetii. In cattle the bacterial shedding can persist without symptoms for several months and the shedders identification is a critical issue in the control of the infection at herd level. Following the example of the human protocols for the assessment of Q fever infection status, the aim of this study was the evaluation of the antibody response dynamics to phase I and phase II antigens in C. burnetii shedder dairy cows by means of a phase-specific serology, to verify the suitability of the investigated tools in recognising milk shedders. A total of 99 cows were monitored during time and classified on the basis of serological and PCR results in five groups identifying different shedding patterns. The 297 sera collected in three sampling times were tested by means of ELISA IgG for differential phase I and phase II antibodies detection, while a selection of 107 sera were tested by means of phase specific IgM and IgG IFAT. Both ELISA IgG and IFAT IgG highlighted a low reactivity in non-shedder seropositive animals compared to chronic milk shedder animals. ELISA IgG seemed to perform better than IFAT IgG-IgM, showing significant serological differences among groups that allowed recognising specific serological group patterns, in particular for chronic and occasional milk shedders. These results supported the hypothesis that an animal classification based on phase patterns is reasonable, although it needs to be further investigated

IFAT and ELISA phase I/phase II as tools for the identification of Q fever chronic milk shedders in cattle

Q fever is a widespread zoonotic disease caused by Coxiella burnetii. In cattle the bacterial shedding can persist without symptoms for several months and the shedders identification is a critical issue in the control of the infection at herd level. Following the example of the human protocols for the assessment of Q fever infection status, the aim of this study was the evaluation of the antibody response dynamics to phase I and phase II antigens in C. burnetii shedder dairy cows by means of a phase-specific serology, to verify the suitability of the investigated tools in recognising milk shedders. A total of 99 cows were monitored during time and classified on the basis of serological and PCR results in five groups identifying different shedding patterns. The 297 sera collected in three sampling times were tested by means of ELISA IgG for differential phase I and phase II antibodies detection, while a selection of 107 sera were tested by means of phase specific IgM and IgG IFAT. Both ELISA IgG and IFAT IgG highlighted a low reactivity in non-shedder seropositive animals compared to chronic milk shedder animals. ELISA IgG seemed to perform better than IFAT IgG-IgM, showing significant serological differences among groups that allowed recognising specific serological group patterns, in particular for chronic and occasional milk shedders. These results supported the hypothesis that an animal classification based on phase patterns is reasonable, although it needs to be further investigated

Detection of New Leptospira Genotypes Infecting Symptomatic Dogs: Is a New Vaccine Formulation Needed?

Leptospirosis in dogs has been largely described worldwide, and epidemiological studies have been mainly based on serological data. This study aims to detect and genotype leptospires affecting symptomatic dogs in Northeast Italy between 2013 and 2019. Overall, 1631 dogs were tested using real-time PCR, and leptospires from 193 dogs were subjected to Multilocus Sequence Typing and a Multiple Loci Variable-number Tandem Repeat Analysis. Leptospires were successfully isolated from 15 symptomatic dogs. Six distinct Sequence Types (STs) were found for 135 leptospires, with 3 STs characterizing Leptospira interrogans (ST17, ST198 and ST24), 2 STs characterizing Leptospira kirschneri (ST117 and ST289) and 1 ST characterizing Leptospira borgpetersenii (ST155), revealing the circulation of the serogroups Icterohaemorrhagiae, Australis, Sejroe and Pomona. The Multiple Loci Variable-number Tandem Repeat Analysis of 17 samples did not result in any additional discrimination. Genotypes were compared with those of strains present in the historical internal database, and possible transmission chains were identified from rat, mouse, hedgehog and pig. This work highlights the importance of molecular methods in revealing and identifying circulating Leptospira strains, and it also encourages the evaluation of the ability of commercially available vaccines to reduce the disease burden among dogs