Detection of rabbit haemorrhagic disease virus isolates and sequence comparison of the N-terminus of the capsid protein gene by the polymerase chain reaction

Advances and insights in the diagnosis of viral infections

Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.

Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.

A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV)

Since the early 1980s, the European rabbit (Oryctolagus cuniculus) has been threatened by the rabbit hemorrhagic disease (RHD). The disease is caused by a lagovirus of the family Caliciviridae, the rabbit hemorrhagic disease virus (RHDV). The need for detection, identification and further characterization of RHDV led to the development of several diagnostic tests. Owing to the lack of an appropriate cell culture system for in vitro propagation of the virus, much of the methods involved in these tests contributed to our current knowledge on RHD and RHDV and to the development of vaccines to contain the disease. Here, we provide a comprehensive review of the RHDV diagnostic tests used since the first RHD outbreak and that include molecular, histological and serological techniques, ranging from simpler tests initially used, such as the hemagglutination test, to the more recent and sophisticated high-throughput sequencing, along with an overview of their potential and their limitations.

Current methods and prospects of coronavirus detection

SARS-COV-2 is a novel coronavirus discovered in Wuhan in December 30, 2019, and is a family of SARS-COV (severe acute respiratory syndrome coronavirus), that is, coronavirus family. After infection with SARS-COV-2, patients often experience fever, cough, gas prostration, dyspnea and other symptoms, which can lead to severe acute respiratory syndrome (SARS), kidney failure and even death. The SARS-COV-2 virus is particularly infectious and has led to a global infection crisis, with an explosion in the number of infections. Therefore, rapid and accurate detection of the virus plays a vital role. At present, many detection methods are limited in their wide application due to their defects such as high preparation cost, poor stability and complex operation process. Moreover, some methods need to be operated by professional medical staff, which can easily lead to infection. In order to overcome these problems, a Surface molecular imprinting technology (SM-MIT) is proposed for the first time to detect SARS-COV-2 virus. For this SM-MIT method, this review provides detailed detection principles and steps. In addition, this method not only has the advantages of low cost, high stability and good specificity, but also can detect whether it is infected at designated points. Therefore, we think SM-MIT may have great potential in the detection of SARS-COV-2 virus.

Rabbit Hemorrhagic Disease Virus Isolated from Diseased Alpine Musk Deer (Moschus sifanicus)

Rabbit hemorrhagic disease virus (RHDV) is the causative agent of rabbit hemorrhagic disease (RHD), and its infection results in mortality of 70-90% in farmed and wild rabbits. RHDV is thought to replicate strictly in rabbits. However, there are also reports showing that gene segments from the RHDV genome or antibodies against RHDV have been detected in other animals. Here, we report the detection and isolation of a RHDV from diseased Alpine musk deer (Moschussifanicus). The clinical manifestations in those deer were sudden death without clinical signs and hemorrhage in the internal organs. To identify the potential causative agents of the disease, we used sequence independent single primer amplification (SISPA) to detect gene segments from viruses in the tissue samples collected from the dead deer. From the obtained sequences, we identified some gene fragments showing very high nucleotide sequence similarity with RHDV genome. Furthermore, we identified caliciviral particles using an electron microscope in the samples. The new virus was designated as RHDV GS/YZ. We then designed primers based on the genome sequence of an RHDV strain CD/China to amplify and sequence the whole genome of the virus. The genome of the virus was determined to be 7437 nucleotides in length, sharing the highest genome sequence identity of 98.7% with a Chinese rabbit strain HB. The virus was assigned to the G2 genotype of RHDVs according to the phylogenetic analyses based on both the full-length genome and VP60 gene sequences. Animal experiments showed that GS/YZ infection in rabbits resulted in the macroscopic and microscopic lesions similar to that caused by the other RHDVs. This is the first report of RHDV isolated from Alpine musk deer, and our findings extended the epidemiology and host range of RHDV.

A novel bivalent Pasteurellosis-RHD vaccine candidate adjuvanted with Montanide ISA70 protects rabbits from lethal challenge

In the present study, a bivalent vaccine against Pasteurella multocida and rabbit hemorrhagic disease virus (RHDV) was formulated with Montanide™ ISA70 oil adjuvant (Seppic, Paris, France). Its efficacy was evaluated and compared to similar monovalent preparations and commercially available monovalent vaccines. White new Zeeland rabbit groups (n = 10) received 2 successive doses of the tested vaccines and were challenged 2 weeks after 2nd dose with Pasteurella multocida and RHDV or either pathogens according to their vaccination schedule. Challenged not-vaccinated group of rabbits (n = 10) was included as a control. The bivalent and monovalent ISA70 preparations were found stable, safe, sterile, pure and of low viscosity. Group 3 (GP3) which received bivalent vaccine showed the highest antibody geometric mean titers against Pasteurella multocida and RHDV evaluated by ELISA and hemagglutination inhibition (HI) respectively. Following virulent challenge; Gp3 rabbits were 90% protected from challenge over other groups that showed 80% protection. Detection of either pathogen in the livers of dead and euthanized rabbits had failed except for non-vaccinated controls. The bivalent vaccine candidate was fully protective. Immunization against both pathogens can be achieved by single vaccination.

Molecular methods in detection and epidemiologic studies of rabbit and hare viruses: a review

Various PCR-based assays for rabbit viruses have gradually replaced traditional virologic assays, such as virus isolation, because they offer high-throughput analysis, better test sensitivity and specificity, and allow vaccine and wild-type virus strains to be fully typed and differentiated. In addition, PCR is irreplaceable in the detection of uncultivable or fastidious rabbit pathogens or those occurring in low quantity in a tested sample. We provide herein an overview of the current state of the art in the molecular detection of lagomorph viral pathogens along with details of their targeted gene or nucleic acid sequence and recommendations for their application. Apart from the nucleic acids-based methods used for identification and comprehensive typing of rabbit viruses, novel methods such as microarray, next-generation sequencing, and mass spectrometry (MALDI-TOF MS) could also be employed given that they offer greater throughput in sample screening for viral pathogens. Molecular methods should be provided with an appropriate set of controls, including an internal amplification control, to confirm the validity of the results obtained.

Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review

Rabbit haemorrhagic disease virus (RHDV) is a calicivirus of the genus Lagovirus that causes rabbit haemorrhagic disease (RHD) in adult European rabbits (Oryctolagus cuniculus). First described in China in 1984, the virus rapidly spread worldwide and is nowadays considered as endemic in several countries. In Australia and New Zealand where rabbits are pests, RHDV was purposely introduced for rabbit biocontrol. Factors that may have precipitated RHD emergence remain unclear, but non-pathogenic strains seem to pre-date the appearance of the pathogenic strains suggesting a key role for the comprehension of the virus origins. All pathogenic strains are classified within one single serotype, but two subtypes are recognised, RHDV and RHDVa. RHD causes high mortality in both domestic and wild adult animals, with individuals succumbing between 48-72 h post-infection. No other species has been reported to be fatally susceptible to RHD. The disease is characterised by acute necrotising hepatitis, but haemorrhages may also be found in other organs, in particular the lungs, heart, and kidneys due to disseminated intravascular coagulation. Resistance to the disease might be explained in part by genetically determined absence or weak expression of attachment factors, but humoral immunity is also important. Disease control in rabbitries relies mainly on vaccination and biosecurity measures. Such measures are difficult to be implemented in wild populations. More recent research has indicated that RHDV might be used as a molecular tool for therapeutic applications. Although the study of RHDV and RHD has been hampered by the lack of an appropriate cell culture system for the virus, several aspects of the replication, epizootology, epidemiology and evolution have been disclosed. This review provides a broad coverage and description of the current knowledge on the disease and the virus.

Persistence of viral RNA in rabbits which overcome an experimental RHDV infection detected by a highly sensitive multiplex real-time RT-PCR

An internally controlled multiplex real-time RT-PCR using TaqMan probes and external standards for absolute RNA quantification was developed as a new diagnostic tool for the detection of rabbit haemorrhagic disease virus (RHDV). The test revealed a specificity of 100%, an analytical sensitivity of 10 copies/well and a linearity over a range from 10(1) to 10(10) copies. The viral loads in organs, leukocytes, sera and excretions of seropositive, convalescent rabbits which were overcoming an experimental infection with RHDV were determined using the validated assay. As a result, viral RNA was demonstrated and quantified for at least 15 weeks. Thus, a persistence of viral RNA after experimental infection of rabbits could be shown for the first time. In contrast, neither antigen nor infectious virus could be detected by antigen-ELISA, immunohistochemistry or experimental transmission. Therefore, further experiments are necessary to prove that the persistence of RNA is linked with the persistence of infectious virus particles.

Response of the North Island brown kiwi, Apteryx australis mantelli and the lesser short-tailed bat, Mystacina tuberculata to a measured dose of rabbit haemorrhagic disease virus

Four North Island brown kiwis and six lesser short-tailed bats were inoculated intramuscularly with 300 000 rabbit lethal doses of rabbit haemorrhagic disease (RHD) virus. No clinical abnormalities were observed in the kiwis and bats throughout the study period. Although no viraemia was detected in any of the kiwis, all four birds produced a serological response to RHD virus above the positive cut-off by 14 days after inoculation, and in two of the birds, antibodies persisted for over 5 months. Two kiwis were killed 48 days after inoculation. Their tissues were examined for lesions, and for the presence of persistent virus by both reverse transcription polymerase chain reaction and by inoculation of tissue suspensions into rabbits. No gross or histological lesions suggestive of a viral infection were detected and tests for detection of virus were negative. The serological response in the kiwis was probably due to the birds responding to viral antigen in the inoculum rather than to multiplication of the virus. None of the bats showed a serological response to RHD virus above the positive cut-off by 14 days after inoculation and the results of the pathological and virological examinations were negative.

Immunocapture-RT-PCR assay for detection and molecular epidemiology studies of Rabbit Haemorrhagic Disease and European Brown Hare Syndrome viruses

Rabbit Haemorrhagic Disease Virus and European Brown Hare Syndrome Virus are two members of the genus Lagovirus in the family Caliciviridae. They are the causative agents of highly contagious and fatal diseases of rabbits and hares respectively. We adjusted one assay for the detection and the genomic characterisation of each virus, based on viral purification by immunocapture and genomic amplification by reverse transcription-polymerase chain reaction (IC-RT-PCR). It is carried out directly with the liver exudate obtained after thawing and suppresses the viral nucleic acid preparation step. This assay combines the advantages of an ELISA test (rapidity) because immunocapture and the RT reaction were carried out in the same microtitre plate, and the advantages of PCR (sensitivity). The procedure described allows the processing of large numbers of samples and is suitable for phylogenetic studies of lagomorphs caliciviruses. In addition, it was compared with sandwich-ELISA used for Rabbit Haemorrhagic Disease or European Brown Hare Syndrome diagnosis. A good correlation was found between ELISA and IC-RT-PCR results for Rabbit Haemorrhagic Disease diagnosis, whereas for European Brown Hare Syndrome diagnosis, the results confirmed the higher sensitivity of the molecular method.

Experimental infections of rabbits with rabbit haemorrhagic disease virus monitored by polymerase chain reaction

Adult and 4-5-week-old rabbits were inoculated subcutaneously with rabbit haemorrhagic disease virus (RHDV). Samples were prepared from various tissues at intervals postinoculation (PI) for the detection of viral RNA and antigens. Using a haemagglutination test (HAT), viral antigens were detected in the liver, bile and spleen of the adult rabbits at and after 36 h PI. The reverse transcription-polymerase chain reaction (RT - PCR) showed that RHDVRNA was present in the liver, bile and spleen as early as 18 hours PI, whereas lung, kidney, thymus, mesenteric lymph node and buffy coat were found to be positive after more than 26 hours PI. In addition, viral RNA in urine and faeces showed a variable positivity at and after 36 hours PI. In the young rabbits, RT - PCR showed that RHDVRNA was present as early as 1 day PI in the liver, bile, spleen and buffy coat; whereas lung, kidney, thymus, mesenteric lymph node and faeces were found to be positive at and after 2 days PI. Bile and spleen were the only samples in which viral RNA was detected throughout the length of the experiment. Virus was not reactivated in six recovered virus-inoculated rabbits treated with dexamethasone or a classical swine fever virus vaccine. Using a haemagglutination inhibition test and an ELISA, antibody titres increased rapidly from one week PI onwards, peaked at approximately three weeks of age, and were maintained throughout the length of the experiment.

Polymerase chain reaction amplification and gene sequence analysis of a calicivirus from a feral rabbit

A reverse transcription-polymerase chain reaction (RT-PCR) amplification assay was used to detect calicivirus gene sequences in a liver tissue derived from a feral rabbit which died of a recent outbreak of rabbit haemorrhagic disease (RHD) in New Zealand. Five pairs of primers were designed to amplify five complementary DNA genomic sequence stretching from nucleotide positions 1594 to 7071, yielding amplified fragments of 361, 340, 805,670 and 386 bp for the primer pairs RC-1/RC-2, RC-3/RC-4, RC-5/RC-6, RC-7/RC-8 and RC-9/RC-10 respectively. The identity of the amplified fragments was confirmed by chemiluminescence Southern blot hybridization and direct cycle sequencing. The nucleotide sequences of the five amplified fragments were determined and comparisons of the nucleotide and deduced amino acid sequences revealed a close genetic relationship of the New Zealand isolate 97-10372 with overseas strains of RHD virus.

Detection and differentiation of rabbit hemorrhagic disease and European brown hare syndrome viruses by amplification of VP60 genomic sequences from fresh and fixed tissue specimens

Two reverse transcription-PCR (RT-PCR) assays have been developed for the detection and differentiation of rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV), two closely related caliciviruses. In order to select highly specific primers, comparative analysis was performed with a large number of RHDV and EBHSV genomic sequences. Regarding these data, primers were selected from similar regions of the VP60 genes to amplify a fragment of 316 nucleotides from the genome of RHDV and a fragment of 265 nucleotides from the genome of EBHSV. In sensitivity studies, as few as 10 copies of cloned viral genomic fragments were detected in each PCR assay, and no cross amplification was observed between the two viruses. The diagnostic value of the assays was confirmed with clinical material by testing fresh and formalin-fixed, paraffin-embedded liver and spleen specimens from a large number of geographically and temporally distant outbreaks. Thus, the two PCR assays provide highly specific and sensitive, novel means of direct detection of the two caliciviruses. In addition, by detecting the viruses in formalin-fixed, paraffin-embedded tissues (PETs), the RT-PCR assays facilitate retrospective virological and epidemiological studies. For example, the identification of EBHSV in PET specimens collected in the 1970s indicates that this virus appeared in the hare populations several years before the first reports of European brown hare syndrome during the 1980s.

Colorimetric detection of lagomorphs' calicivirus genomic sequences by polymerase chain reaction incorporating digoxigenin dUTP

A method of reverse transcription followed by polymerase chain reaction (RT-PCR) has been implemented for the demonstration of the rabbit haemorrhagic disease virus (RHDV) genome in organ suspensions, leukocytes and excretions of infected rabbits. RT-PCR has been tested with 10 RHDV strains isolated at various geographic sites and times using a pair of primers coming from the gene region coding for the capsid protein VP60. The same primers were effective in the amplification of 4 of 5 European brown hare syndrome (EBHS) virus isolates. Non-radioactive labelling of PCR products with digoxigenin during the amplification and a system of colorimetric assessment of hybridization reactions between a biotin-labelled RHDV capture probe and the chains of labelled amplicons (PCR ELISA) were used for specific analyses of nucleic acid synthesis. The sensitivity of the alternative procedure of analysis of the dig-labelled PCR products with PCR ELISA was two logs10 higher than that of conventional electrophoresis in agarose gel stained with ethidium bromide. The results of the hybridization reactions, carried out under various stringency conditions, have confirmed the presumption that the genomic similarity between the amplified and the probed areas of the capsid protein VP60 gene was not uniform within all the tested caliciviruses. A higher degree of heterogeneity was observed between the isolates of EBHSV and RHDV.

The complete nucleotide sequence of rabbit haemorrhagic disease virus (Czech strain V351): use of the polymerase chain reaction to detect replication in Australian vertebrates and analysis of viral population sequence variation

The complete nucleotide sequence of the Czech strain of rabbit haemorrhagic disease virus (RHDV) was determined to be 7437 nucleotides in length with a 5-terminal non-coding region of 9 nucleotides and a 3'-terminal non-coding region of 59 nucleotides. Two open reading frames (ORFs) were found within this sequence coding for polypeptides of 2344 (nucleotides 10-7044) and 117 amino acids (nucleotides 7025-7378). The sequence of this isolate was approximately 1% different from that reported by Meyers et al., having 78 nucleotide changes which resulted in 30 amino acid differences, the majority of these clustering in the N-terminus of the large ORF and the middle of the viral coat protein. Only a single conservative amino acid change was seen in the smaller 3'-terminal ORF. Since the virus cannot at present be propagated in tissue culture, but isolated only after replication in rabbits, the reported sequence must be considered as a consensus sequence from the viral population. To gain some understanding of the possible sequence diversity within this virus population, 97 clones were sequenced from a polymerase chain reaction (PCR) fragment to determine the sequence diversity of the virus population. Four major classes of variant were described with mutations generally in the third base position of codons. A nested reverse transcriptase (RT) PCR (using sequence derived for the coat protein of RHDV) was used to determine the presence or absence of RHDV inoculated into non-host animal species. No replication of the virus was detected in 28 different vertebrate species other than rabbits. PCR tests on both mosquitoes and fleas feeding on RHDV infected rabbits were positive. The RT-PCR test was more sensitive when compared with an antigen capture ELISA to detect the presence of genomic RNA/or virus in infected rabbits.

Diagnosis of rabbit haemorrhagic disease (RHD) and European brown hare syndrome (EBHS) by indirect sandwich polyclonal ELISA

The establishment of two indirect sandwich polyclonal ELISAs for the virological diagnosis of rabbit haemorrhagic disease (RHD) and European brown hare syndrome (EBHS) is described. Each assay uses rabbit and guinea pig antisera raised to RHD or EBHS purified virus particles. The tests are sensitive and specific, but cross-reactions between rabbit haemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are observed. Most rabbit liver homogenates identified as RHDV-positive by ELISA do not haemagglutinate human red blood cells at room temperature.

Preliminary characterization of a non-haemagglutinating strain of rabbit haemorrhagic disease virus from the United Kingdom

A variant strain of rabbit haemorrhagic disease virus, designated "Rainham', originally isolated from a small localized outbreak of the disease in southern England, has been further examined and compared with conventional reference strains. The virus originally failed to haemagglutinate in standard conditions at normal temperature and consistently lacked HA activity after two passages in experimental rabbits. It did haemagglutinate at 4 degrees C. It reacted with hyperimmune sera to normal isolates of RHDV from the UK and Italy, and showed no differential binding activity with a panel of monoclonal antibodies prepared from an Italian reference strain. The Rainham strain appears to be antigenically indistinguishable from other known isolates and this suggests that it may differ by only a few amino acid changes in its capsid protein sequence.

Early stages of rabbit haemorrhagic disease virus infection monitored by polymerase chain reaction

In order to define more accurately the initial events that take place during rabbit haemorrhagic disease virus (RHDV) infection, different organs of experimentally infected rabbits were analysed for the presence of the virus and correlated with histopathological observations. A total of 24 rabbits were intranasally inoculated with a viral suspension, and tissue samples were taken from the liver, spleen, kidney, lung, thymus, lymph node and tonsil at different intervals post-inoculation (2, 4, 6, 12, 18, 24, 30, 36, 48, 50, 51, 70 and 72 h). Histopathological observations revealed the presence of the first significant lesions at 30 h post-inoculation (p.i.) in the liver. Using an ELISA and a haemagglutination test (HAT), the virus was detected in the liver at 36 h p.i. The reverse transcriptase-polymerase chain reaction (RT-PCR) showed that the RHDV RNA was present as early as 18 h p.i. in the liver and spleen, whereas thymus, kidney, tonsil and lymph node were found to be positive after more than 36 h p.i. The lungs presented a variable positivity between 0 and 36 h p.i., but remained positive after this time.