Development of methods for detection and quantification of avian influenza and Newcastle disease viruses in compost by real-time reverse transcription polymerase chain reaction and virus isolation

Pathogenicity and Full Genome Sequencing of the Avian Influenza H9N2 Moroccan Isolate 2016

In Morocco in early 2016, a low pathogenic avian influenza virus serotype H9N2 caused large economic losses to the poultry industry, with specific clinical symptoms and high mortality rates on infected farms. Subsequent to the H9N2 outbreak, the causal agent was successfully isolated from chicken flocks with high morbidity and mortality rates, propagated on embryonated eggs, and fully sequenced. The phylogenetic analysis suggested that the Moroccan isolate could have derived from the Middle East isolate A/chicken/Dubai/D2506.A/2015. This study was designed to assess the pathogenicity of the Moroccan isolate H9N2 in experimentally infected broiler and specific-pathogen-free (SPF) chickens. At 22 days of age, one broiler and two SPF chicken groups were inoculated by dropping 0.2 ml of the H9N2 isolate (10^7.5 EID₅₀/ml) in both nostrils and eyes. Clinically inoculated chickens with H9N2 displayed mild lesions, low mortality rates, and an absence of clinical signs. The H9N2 virus was more pathogenic in broiler chickens and produced more severe tissue lesions compared to SPF chickens. The viral shedding was detected up to 6 days postinoculation (pi) in oropharyngeal and cloacal swabs in infected birds with a maximum shedding in the oropharynges of the broiler group. All experimental chickens seroconverted and registered high hemagglutination inhibition titers as early as day 7 pi. The present study indicates that the H9N2 virus isolated from a natural outbreak was of low pathogenicity under experimental conditions. However, under field conditions infection with other pathogens might have aggravated the disease.

A review on emerging diagnostic assay for viral detection: the case of avian influenza virus

Biotechnology-based detection systems and sensors are in use for a wide range of applications in biomedicine, including the diagnostics of viral pathogens. In this review, emerging detection systems and their applicability for diagnostics of viruses, exemplified by the case of avian influenza virus, are discussed. In particular, nano-diagnostic assays presently under development or available as prototype and their potentials for sensitive and rapid virus detection are highlighted.

Inactivation of Aleutian mink disease virus through high temperature exposure in vitro and under field-based composting conditions

Disposal of manure contaminated with Aleutian mink disease virus (AMDV) is a significant concern to the mink industry. Inactivation of AMDV under field conditions has received limited attention in the scientific literature. We evaluated the thermal inactivation of AMDV in vitro and during composting of mink manure. Spleen homogenate containing AMDV was heated under controlled conditions at 45°C, 55°C, and 65°C for 3 days. Results of the in vitro study identified complete absence of viral replication in mink at 65°C only. Next, manure-mixed AMDV packed in polyester pouches was inserted in different layers of three replicate mink manure compost piles. The virus was retrieved after the compost piles had undergone a heating period and subsequently returned to ambient temperatures. Temperature regimes in the compost piles were categorized as ≥65°C, ≥60-64°C, and ≥55-59°C. Initially, layer-wise composite virus samples were assayed for virus replication in mink. Twenty-one-day post-inoculation (p.i.) plasma tested for AMDV and antibodies indicated infection in 40%, 80%, and 100% of mink inoculated from samples originating from the top, center and bottom layers of the piles, respectively. Subsequently, the virus was extracted from individual pouches in compost layers achieving thermal activity ≥65°C and was tested in mink. No antibodies or virus was detected in plasma taken weekly up to day 21 p.i. PCR data of bone marrow and lymph nodes collected on day 21 p.i. also showed no AMDV. However, mink that received virus from positive control manure indicated infection in their plasma as early as 1 week p.i.

Field scale evaluation of volatile organic compound production inside biosecure swine mortality composts

Emergency mortality composting associated with a disease outbreak has special requirements to reduce the risks of pathogen survival and disease transmission. The most important requirements are to cover mortalities with biosecure barriers and avoid turning compost piles until the pathogens are inactivated. Temperature is the most commonly used parameter for assessing success of a biosecure composting process, but a decline in compost core temperature does not necessarily signify completion of the degradation process. In this study, gas concentrations of volatile organic compounds (VOCs) produced inside biosecure swine mortality composting units filled with six different cover/plant materials were monitored to test the state and completion of the process. Among the 55 compounds identified, dimethyl disulfide, dimethyl trisulfide, and pyrimidine were found to be marker compounds of the process. Temperature at the end of eight weeks was not found as an indicator of swine carcass degradation. However, gas concentrations of the marker compounds at the end of eight weeks were found to be related to carcass degradation. The highest gas concentrations of the marker compounds were measured for the test units with the lowest degradation (highest respiration rates). Dimethyl disulfide was found to be the most robust marker compound as it was detected from all composting units in the eighth week of the trial. Concentration of dimethyl disulfide decreased from a range of 290-4340 ppmv to 6-160 ppbv. Dimethyl trisulfide concentrations decreased to a range of below detection limit to 430 ppbv while pyrimidine concentrations decreased to a range of below detection limit to 13 ppbv.

Use of quantitative and conventional PCR to assess biodegradation of bovine and plant DNA during cattle mortality composting

Understanding mortality composting requires assessing the biodegradation efficacy of carcasses and other materials of animal and plant origin. Biosecure (plastic-wrapped) compost structures were built containing 16 cattle carcasses placed on 40 cm straw and covered with 160-cm of feedlot manure. Compost was collected from depths of 80 and 160 cm (P80, P160) and DNA degradation assessed over 147 days of static composting, and during 180 days of active composting. Residual soft tissues from carcasses were collected on day 147. At P80, copies of a 171-bp bovine mitochondrial DNA (Mt171) and 138-bp plant Rubisco gene fragment (Rub138) were reduced compared to initial copy numbers (CN) by 79% and 99% after 147 days, respectively. At P160, Mt171, and Rub138 decreased compared to initial CN by 20% and 99% by day 147, respectively. After 327 days, degradation of Mt171 increased to 91% compared to initial CN. Compared to fresh tissues, residual tissues at day 147 had a 99% reduction in genomic DNA yield. Yield of DNA was related to copies of a 760-bp bovine mitochondrial fragment (Mt760) which were > 93% reduced at both P80 and P160 after 147 day. Secondary composting improved decomposition of bovine tissues and Mt760 was not detectable after 207 days. A 99% reduction in genomic DNA of composted tissue and > 93% reduction of Mt760 suggests almost complete decomposition of carcass soft tissue after 147 days.

A biosecure composting system for disposal of cattle carcasses and manure following infectious disease outbreak

During outbreaks of infectious animal diseases, composting may be an effective method of disposing of mortalities and potentially contaminated manure. Duplicate biosecure structures containing 16 cattle (Bos taurus) mortalities (343 kg average weight) were constructed with carcasses placed on a 40-cm straw layer and overlaid with 160 cm of feedlot manure. At a depth of 80 cm (P80), compost heated rapidly, exceeding 55 degrees C after 8 d and maintained temperatures of 55 to 65 degrees C for > 35 d. Temperatures at 160 cm (P160) failed to exceed 55 degrees C, but remained above 40 degrees C for >4 mo. To investigate rates of microbial inactivation, Escherichia coli O157:H7, Campylobacter jejuni, and Newcastle disease virus (NDV) were inoculated in manure (E. coli O157:H7 and C. jejuni approximately 10(8) CFU g(-1); NDV, approximately 10(6) EID(50) g(-1)), embedded at P80 and P160 and retrieved at intervals during composting. Escherichia coli O157:H7 and NDV were undetectable after 7 d at both depths. The C. jejuni DNA was detected up to 84 d at P80 and >147 d at P160. To estimate degradation of recalcitrant substrates, bovine brain, hoof, and rib bones were also embedded at P80 and P160 and retrieved at intervals. Residues of soft tissues remained in carcasses after opening at 147 d and bovine tissue decomposition ranked as brain > hoof > bone. More than 90% dry matter (DM) of brain disappeared after 7 d and 80% DM of hoof decomposed after 56 d. High degradation of cattle carcasses, rapid suppression of E. coli O157:H7 and NDV and reduction in viable cell densities of >6 logs for C. jejuni demonstrates that the biosecure composting system can dispose of cattle carcasses and manure in an infectious disease outbreak.

Comparison and evaluation of RNA quantification methods using viral, prokaryotic, and eukaryotic RNA over a 10(4) concentration range

Quantification of RNA is essential for various molecular biology studies. In this work, three quantification methods were evaluated: ultraviolet (UV) absorbance, microcapillary electrophoresis (MCE), and fluorescence-based quantification. Viral, bacterial, and eukaryotic RNA were measured in the 500 to 0.05-ng microl(-1) range via an ND-1000 spectrophotometer (UV), Agilent RNA 6000 kits (MCE), and Quant-iT RiboGreen assay (fluorescence). The precision and accuracy of each method were assessed and compared with a concentration derived independently using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Cost, operator time and skill, and required sample volumes were also considered in the evaluation. Results indicate an ideal concentration range for each quantification technique to optimize accuracy and precision. The ND-1000 spectrophotometer exhibits high precision and accurately quantifies a 1-microl sample in the 500 to 5-ng microl(-1) range. The Quant-iT RiboGreen assay demonstrates high precision in the 1 to 0.05-ng microl(-1) range but is limited to lower RNA concentrations and is more costly than the ND-1000 spectrophotometer. The Agilent kits exhibit less precision than the ND-1000 spectrophotometer and Quant-iT RiboGreen assays in the 500 to 0.05-ng microl(-1) range. However, the Agilent kits require 1 microl of sample and can determine the integrity of the RNA, a useful feature for verifying whether the isolation process was successful.