Multiplex Amplification Refractory Mutation System PCR (ARMS-PCR) provides sequencing independent typing of canine parvovirus

Triple-recognition strategy for one-pot detection of single nucleotide variants by aligner-mediated cleavage-triggered exponential amplification

The detection of single nucleotide variants (SNVs) is important for the diagnosis and treatment of cancer. To date, researchers have devised several methods to detect SNVs, but most of them are complex and time-consuming. To improve SNVs detection specificity and sensitivity, we developed a triple-recognition strategy, which facilitates aligner-mediated cleavage-triggered exponential amplification (Trec-AMC-EXPAR) for the rapid, specific, and one-pot detection of SNV. Under optimized conditions, Trec-AMC-EXPAR detected two clinically significant SNVs, PIK3CAH1047R and EGFR L858R within 80 min, with a reliable detection of 0.1% SNV in the wide type, which is lower than that of allele-specific PCR (AS-PCR) for detecting SNV. Finally, by spiking into normal human serum samples, mutants mixed with the wild-type targets in different ratios were analyzed, resulting in the relative standard deviation (RSD) of recovery ratios <3%. The findings suggested the potential application of Trec-AMC-EXPAR in clinical disease diagnosis. In summary, the proposed Trec-AMC-EXPAR technique provides a novel fast and convenient method for one-pot detection of SNV with high sensitivity and specificity.

Antioxidant supplementation during treatment of outpatient dogs with parvovirus enteritis ameliorates oxidative stress and attenuates intestinal injury: A randomized controlled trial

A prospective randomized controlled clinical study was conducted to determine whether antioxidant supplementation as an adjunct therapy alters hemogram, oxidative stress, serum intestinal fatty acid binding protein-2 (IFABP-2) level, fecal viral load, clinical score (CS) and survivability in outpatient canine parvovirus enteritis (CPVE) dogs. The dogs with CPVE were randomized to one of the five treatment groups: supportive treatment (ST) alone, ST with N-acetylcysteine (ST+NAC), resveratrol (ST+RES), coenzyme Q10 (ST+CoQ10) or ascorbic acid (ST+AA). The primary outcome measures were reduction of CS and fecal HA titre, and enhancement of survivability. Secondary outcome measures were reduction of oxidative stress indices and IFABP-2 level from day 0 to day 7. The mean CS and HA titre were significantly (P < 0.05) decreased from day 0 to 7 in ST and all antioxidant groups. The supplementations of NAC, RES and AA along with ST markedly (P < 0.05) reduced the concentrations of malondialdehyde, nitric oxide and IFABP-2 on day 7 as compared to ST alone. Additionally, NAC and RES supplementations markedly (P < 0.05) improved the total leukocyte count and neutrophil count in CPVE-affected dogs. NAC and RES could serve as better antioxidants for the amelioration of oxidative stress in CPVE but, the antioxidants did not confer any additional benefits in reduction of CS, fecal HA tire, or survivability when compared with ST alone.

Prognostic Potential of Thrombocyte Indices, Acute Phase Proteins, Electrolytes and Acid-Base Markers in Canine Parvovirus Infected Dogs With Systemic Inflammatory Response Syndrome

Dogs with canine parvovirus enteritis (CPVE) that develop systemic inflammatory response syndrome (SIRS) frequently have a poor prognosis. The aim of the study was to assess the prognostic potential of thrombocyte indices, acute phase proteins, electrolytes, and acid-base markers in CPVE puppies with SIRS (CPVE-SIRS+) at admission. A case-controlled, prospective, and observational study was performed on 36 CPVE puppies. Mean concentrations of C-reactive protein (CRP), albumin, thrombocyte count, mean platelet volume (MPV), platelet distribution width (PDW), sodium (Na+), potassium (K+), chloride (Cl-) and ionized calcium (iCa) were measured and strong ion difference 3 (SID3), ATOT-albumin and ATOT-total protein were determined in CPVE-SIRS+ survivors and nonsurvivors. A prognostic cut-off value for predicting the disease outcome was determined by receiver operating characteristic (ROC) curve analysis. The mean values of MPV, PDW and CRP were significantly higher and the mean values of albumin, Cl- and ATOT-albumin were significantly lower in CPVE-SIRS+ nonsurvivor than CPVE-SIRS+ survivor puppies on the day of admission, but the thrombocyte count, Na+, K+, iCa, SID3 and ATOT- total protein values did not differ significantly. The positive predictive values (PPVs) for survival using cut-off value of MPV (≤15.08 fL), PDW (≤14.85%), CRP (≤180.7 mg/L), albumin (≥1.795 g/dL), Cl- (≥96.00 mmol/L), and ATOT-albumin (≥7.539) were determined as 100%, 100%, 100%, 80%, 100%, and 80%, respectively with better area under ROC curve and sensitivity. Based on sensitivity, specificity, and PPVs from ROC analysis, it is concluded that the determination of Cl- concentration and MPV at admission followed by CRP will serve as the most appropriate biomarkers in predicting the disease outcome of CPVE puppies that develop SIRS.

A comprehensive molecular survey of viral pathogens associated with canine gastroenteritis

Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been conducted. In this study, 475 rectal swabs collected over three years (2018-2021) from clinical canine gastroenteritis cases were screened for the presence of six major enteric viruses - canine parvovirus 2 (CPV-2), canine distemper virus (CDV), canine adenovirus 2 (CAdV-2), canine coronavirus (CCoV), canine astrovirus (CaAstV), and canine rotavirus (CRV) - by real-time PCR. The most frequently detected virus was CPV-2, which was present in 64.8% of the samples (subtype 2a, 21.1%; 2b, 77.4%; 2c, 1.5%), followed by CDV (8%), CaAstV (7.2%), CCoV (5.9%), and CAdV-2 (4.6%). Two to four of these viruses in different combinations were found in 16.8% of the samples, and CRV was not detected. The complete genome sequences of Indian isolates of CDV, CCoV, and CaAstV were determined for the first time, and phylogenetic analysis was performed. This study highlights the need for routine prophylactic vaccination with the appropriate vaccines. Notably, 70.3% of animals vaccinated with DHPPiL were found to be positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial for addressing vaccination failures.

Site-specific insertion of endonuclease recognition sites into amplicons to improve post-PCR analysis sensitivity of gene mutation

Precise detection of low-frequency gene mutations surrounded by excess wild-type DNA is important in many aspects of medical fields. Most hybridization-based methods for high-resolution mutant allele analysis are hindered by competition of the complementary strand with single-strand probes for the target strand. Here, we demonstrate that site-specific insertion of endonuclease recognition sites into amplicons allows post-PCR generation of short dsDNA or ssDNA, whereby improves the sensitivity of both melting temperature analysis (MTA) and end-point detection following up. Using a three-staged PCR protocol, enrichment of target gene and incorporation of specific restriction sites in amplicons were ensued with hardly any loss in amplification efficiency and specificity. It enables simultaneous discrimination among a panel of totally 11 EGFR 19 exon deletion mutations via MTA after post-PCR digestion by either FokI only or cooperated with CRISPR-Cas12a, using SYBR green I. By replacement of one double-strand cleavage site with a nickase binding domain post-PCR generation of ssDNA of interest via strand displacement amplification (termed as iSDA) is realized. Our preliminary investigation shows that iSDA permits analysis of single nucleotide variants down to 0.1% allelic-frequency using end-point detection. Given the good compatibility with the majority of mutant-enrich PCR methods, we envision it would advance the current gene profiling technologies to a large extent.

Canine parvovirus-2: An Emerging Threat to Young Pets

Canine parvovirus-2 (CPV-2) is a highly contagious and key enteropathogen affecting the canine population around the globe by causing canine parvoviral enteritis (CPVE) and vomition. CPVE is one of the the leading causes of morbidity and mortality in puppies and young dogs. Over the years, five distinct antigenic variants of CPV-2, namely CPV-2a, CPV-2b, new CPV-2a, new CPV-2b, and CPV-2c, have emerged throughout the world. CPV-2 infects a diverse range of wild animals, and the newer variants of CPV-2 have expanded their host range to include felines. Despite the availability of highly specific diagnostics and efficacious vaccines, CPV-2 outbreaks have been reported globally due to the emergence of newer antigenic variants, expansion of the viral host range, and vaccination failures. The present chapter describes the latest information pertaining to virus properties and replication, disease manifestations in animals, and an additional recent updates on diagnostic, prevention and control strategies of CPV-2.

Canine parvovirology - A brief updated review on structural biology, occurrence, pathogenesis, clinical diagnosis, treatment and prevention

Canine parvovirus (CPV) is a major cause of hemorrhagic diarrhea and mortality in puppies worldwide. There are 2 types of Parvovirus which affects canines: Canine parvovirus 2 (CPV-2) and Canine parvovirus 1 (CPV-1) or the Minute Virus of Canine (MVC). CPV-2 originated from Feline panleukopenia virus and has undergone genetic variation to give rise to its three variants (CPV-2a, CPV-2b and CPV-2c). Amino acid substitutions in VP2 capsid protein have led virus to adapt new host range. The original CPV-2 was known to be dominant in Japan, Belgium, Australia as well as USA and later circulated throughout the world. Clinically, CPV-2 infection is characterized by anorexia, lethargy, depression, vomiting, leukopenia and severe hemorrhagic diarrhea. Several diagnostic tests have been developed to detect parvoviral infections which are categorized into immunological tests (latex agglutination test, SIT-SAT and ELISA etc.) and molecular based tests (PCR, mPCR and RT-PCR etc.). To control and manage the disease several treatments like fluid therapies, antibiotics, and adjunctive treatments are available and some are in various stages of development. Apart from this, many vaccines are also commercially available and some are in developmental stages. The present review contains detailed information regarding structural biology, occurrence, pathogenesis, clinical diagnosis, treatments and prevention in order to understand the need and the growing importance of CPV-2.

Isolation and genetic characterization of canine adenovirus type 2 from a domestic dog showing neurological symptoms

Canine adenoviruses (CAVs) are of two types: canine adenovirus type 1 (CAV-1), which causes infectious canine hepatitis, and canine adenovirus type 2 (CAV-2), which is mainly associated with the respiratory type of disease in dogs. Due to the widespread use of modified live vaccines to control canine adenoviral infections and subsequently reduced disease incidence, CAVs are often neglected by clinicians. Although a number of studies are available about CAV-1 prevalence in India, only meagre information is available about CAV-2. This study reports the CAV-2 infection in a vaccinated dog with neurological and respiratory symptoms which was found negative for other canine pathogens like canine distemper virus and canine parvovirus. The virus was successfully isolated from rectal swab in MDCK cells and characterized by immunofluorescence assay and virus neutralization test. On phylogenetic analysis of partial E3 region, the Indian CAV-2 grouped in a separate clade different from established subgroups. An insertion of "G" nucleotide was reported at nucleotide (nt.) position 1077 in the E3 gene of Indian CAV-2 isolates which led to a frameshift in the coding region of E3 gene thereby imparting additional eleven amino acids to its C-terminal end in comparison to isolates from other parts of the world. This may have an implication on the functional role of E3 protein inside the cell. This study reinforces the unique signature insertion in the E3 gene of Indian CAV-2 and is the second study in the world to report the association of CAV-2 with neurological disease in dogs.

Identification and characterization of DNA aptamers specific to VP2 protein of canine parvovirus

Abstract

Canine parvovirus‐2 (CPV‐2) is ubiquitously distributed in dog population worldwide causing a severe and often fatal gastroenteritis. Owing to its highly contagious nature, rapid detection of CPV is crucial in effective control of the disease. Aptamers have emerged as potential alternative to antibodies as affinity reagents in diagnostic field. Present study was aimed to select and validate ssDNA aptamers specific to CPV. Systematic evolution of ligands through exponential enrichment (SELEX) method was employed for selection of CPV structural protein (VP2) specific DNA aptamers. SELEX was performed using a pool of ssDNA library comprising 30 random nucleotide region. A total of seven rounds of SELEX were performed using VP2 protein as target antigen which yielded ten aptamers (1A-10A) with distinct sequences. Target binding of all ten aptamers was assessed by dot blot and enzyme-linked oligonucleotide assay (ELONA) which revealed that 5A, 6A, 9A, and 10A were superior binders. In silico analysis of the aptamers revealed the existence of binding site on VP2 protein, and binding pattern was similar to in vitro findings. The affinity (K_D) of all these four binders against CPV was evaluated by ELONA indicating relatively higher affinity of 6A and 10A than remaining two DNA sequences. Out of which, aptamer 6A displayed cross-reactivity with canine distemper virus and canine corona virus. Hence, aptamer 10A was considered as better binding sequence having high specificity and affinity for CPV. The study confirms the future utility of selected aptamers in development of a reliable diagnostic for rapid detection of CPV.

Key points

• Canine parvovirus-specific ssDNA aptamers were identified with nanomolar affinity (100–150 nM).

• Three aptamers displayed negligible cross-reactivity with other related viruses.

• Aptamer 10A displayed high binding affinity and specificity to CPV.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11651-x.

A novel one-step amplification refractory mutation system PCR (ARMS-PCR) for differentiation of canine parvovirus-2 variants

Enteritis caused by CPV-2 antigenic variants (CPV-2a, 2b, and 2c) is frequently reported in dogs worldwide leading to significant morbidity and mortality. Here, we describe about a simple, single-step, ARMS-PCR strategy targeting the mutant 426 amino acid of VP2 to differentiate CPV-2 antigenic types. A total of 150 fecal samples were subjected to ARMS-PCR of which 18 were typed as CPV-2a, 79 were typed as CPV-2b, and 6 were typed as CPV-2c. The ARMS-PCR results were validated by randomly sequencing partial VP2 gene of 14 samples. Phylogenetic analysis of partial VP2 gene sequencing of each of the CPV-2 variants revealed that CPV-2a and CPV-2b isolates formed a separate clade of Indian lineage, while CPV-2c shared common evolutionary origin with Asian lineage. The developed technique is first of its kind, one-step, rapid, sequencing independent method for typing of CPV-2 antigenic variants.

First report of canine parvovirus molecular detection in Bangladesh

Background and Aim:

Canine parvovirus (CPV) is the most important cause of mortality in dogs in many parts of the world. Clinical cases exhibit characteristic signs, including foul-smelling bloody diarrhea, vomiting, fever, and dehydration. This study assessed field and vaccine variants of parvovirus in the Chattogram metropolitan area, Bangladesh. The investigation also aimed to identify risk factors for this disease. This research is the first to identify the presence of CPV in Bangladesh through molecular examination.

Materials and Methods:

From October to December 2019, a total of 100 dogs were included in the study. Rectal swabs were taken from all dogs. Twenty dogs showed clinical signs of parvovirus. All clinically affected animals along with 20 randomly selected healthy dogs were tested using amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR) to identify variants from the samples. Logistic regression model analysis was performed to determine the possible risk factors for CPV.

Results:

ARMS-PCR showed the presence of all three variants, CPV2a, CPV2b, and CPV2c, in clinically ill dogs, and vaccines available in the study area showed either CPV2a or CPV2b strain. The CPV2c variants showed a higher incidence than the other variants. All apparently healthy animals tested were molecularly negative. Multivariable logistic regression model (generalized linear mixed model) indicated that exotic breeds were 3.83 times more likely to be infected by CPV than local breeds. Furthermore, dogs reared in semi-intensive and extensive management systems were 3.64 and 3.79 times more likely to be infected, respectively, than those reared in an intensive management system.

Conclusion:

These findings provide practitioners and pet owners information on the occurrence of different variants and help design effective prevention strategies for CPV infection.

Application of Duplex Fluorescence Melting Curve Analysis (FMCA) to Identify Canine Parvovirus Type 2 Variants

Canine parvovirus (CPV-2) is an enteric virus causing morbidity and mortality in dogs worldwide. Since CPV-2 emerged as canine pathogen, the original CPV-2 strain has constantly evolved, and its primary variants (CPV-2a, CPV-2b, and CPV-2c) co-circulate to varying extents in canine populations worldwide. Thus, rapid and accurate laboratory diagnoses of CPV-2 variants are crucial to monitor CPV-2 evolution. Conventional methods for CPV-2 genotyping are laborious, time consuming, and determining the genotype of a CPV-2 variant often requires two or more reaction tubes. The present study developed a probe-based fluorescence melting curve analysis (FMCA) for genotyping six different CPV-2 variants (original CPV-2, CPV-2a, CPV-2b, CPV-2c, and vaccine strains of CPVpf and CPVint) in a single reaction tube using only two TaqMan probes. One of the TaqMan probes (FAM labeled) was designed to perfectly match with the target sequence of CPV-2a, this probe allows a 1-bp mismatched hybridization with the CPV-2b VP2 gene region (A4062G), and a 2-bp mismatched hybridization for CPV-2c (A4062G and T4064A); Another TaqMan probe (HEX labeled) was produced to perfectly match with the target sequence of original CPV-2, this probe enables 1-bp mismatched hybridization with the other CPV-2 variants (A3045T). Using the two TaqMan probes, all six CPV-2 variants were readily distinguished by their respective melting temperature values in a single reaction tube. The detection limits of this assay were 1–10 copies per reaction for six CPV-2 construction plasmids and no cross reactions were observed with several other common canine viruses. In this assay, co-infected samples were also directly identified via probe-based FMCA without using a mixing control; only a pure control is required. The clinical evaluation of this assay was demonstrated by analyzing 83 clinical fecal samples, among which 41 (49.39%), 8 (9.63%), and 14 (16.87%) samples were found to be positive for CPV-2a, CPV-2b, and CPV-2c, respectively. The concordance rate between probe-based FMCA and Sanger sequencing was 100%. Thus, the duplex FMCA is effective, rapid, simple, high-throughput, and straightforward for genotyping CPV-2 variants, and is useful to effectively diagnose and monitor CPV-2 epidemiology.

Multiplex amplification refractory mutation system PCR (ARMS-PCR) provides convenient method for differentiation of canine parvovirus vaccine and field strains

Vaccination with canine parvovirus-2 (CPV-2) modified live attenuated vaccine remains an effective control strategy for preventing parvovirus induced enteritis in dogs. Virus shedding is a common phenomenon few days after vaccination, possessing a diagnostic dilemma for accurate differentiation of CPV-2 vaccine and wild type field strains. Though several molecular approaches are available for differentiation, the present study focuses on a simple, rapid, cost-effective differentiating infected from vaccinated animals strategy employing ARMS-PCR for differentiation of CPV-2 vaccine and wild type field strains. The ARMS-PCR was initially validated using positive controls of recombinant plasmids, further used for screening six commercial CPV-2 vaccines and 24 archived CPV-2 positive field samples as well as to check fecal shedding of vaccine virus for 10 days post-vaccination in three vaccinated dogs. Sequencing of randomly selected CPV-2 commercial vaccine strains and archived field samples confirmed authenticity of the developed ARMS-PCR assay.

Determination of immune status in dogs against CPV-2 by recombinant protein based latex agglutination test

Canine parvoviral enteritis is a highly contagious viral illness caused by canine parvovirus-2 (CPV-2) which affects puppies of mainly 6-20 weeks of age. Vaccination is pivotal in preventing and controlling CPV-2 infection. Determination of antibody status is a critical determinant for successful vaccination. The hemagglutination inhibition (HI) test is 'gold standard' test for quantification of antibodies specific to CPV-2, although the execution of this test is not feasible under field conditions. The present study was undertaken to develop a point of care testing to determine immune status prior to CPV-2 vaccination or to detect seroconversion in immunized dogs by latex agglutination test (LAT) using recombinant antigen. Truncated portion of VP2 protein (tVP2) of CPV-2 was selected on the basis of antigenic indices, overexpressed the recombinant protein in E. coli system and was subsequently used in development of LAT. A total of 59 serum samples obtained from vaccinated (n = 54) and healthy unvaccinated (n = 5) dogs were tested. The positivity was observed in 85% (46/54) of these dogs with varying agglutination pattern. The overall sensitivity and specificity of latex agglutination test in comparison to HI test was recorded as 90% and 88% respectively with an agreement value of 90% (CI = 95%).