Identification of a broad spectrum of mammalian and avian species using the short fragment of the mitochondrially encoded cytochrome b gene

Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach

The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.

Detection of African Swine Fever Virus and Blood Meals of Porcine Origin in Hematophagous Insects Collected Adjacent to a High-Biosecurity Pig Farm in Lithuania; A Smoking Gun?

A seasonal trend of African swine fever (ASF) outbreaks in domestic pig farms has been observed in affected regions of Eastern Europe. Most outbreaks have been observed during the warmer summer months, coinciding with the seasonal activity pattern of blood-feeding insects. These insects may offer a route for introduction of the ASF virus (ASFV) into domestic pig herds. In this study, insects (hematophagous flies) collected outside the buildings of a domestic pig farm, without ASFV-infected pigs, were analyzed for the presence of the virus. Using qPCR, ASFV DNA was detected in six insect pools; in four of these pools, DNA from suid blood was also identified. This detection coincided with ASFV being reported in the wild boar population within a 10 km radius of the pig farm. These findings show that blood from ASFV-infected suids was present within hematophagous flies on the premises of a pig farm without infected animals and support the hypothesis that blood-feeding insects can potentially transport the virus from wild boars into domestic pig farms.

Potential mosquito vector attraction to- and feeding preferences for pigs in Romanian backyard farms

Introduction

Mosquitoes either biologically or mechanically transmit various vector-borne pathogens affecting pigs. Mosquito species display a wide variety of host preference, as well as host attraction and behaviours. Mosquito species attraction rates to- and feeding rates on pigs or other potential hosts, as well as the seasonal abundance of the mosquito species affects their pathogen transmission potential.

Methods

We caught mosquitoes in experimental cages containing pigs situated in Romanian backyard farms. The host species of blood meals were identified with PCR and sequencing.

Results

High feeding preferences for pigs were observed in Aedes vexans (90%), Anopheles maculipennis (80%) and Culiseta annulata (72.7%). However, due to a high abundance in the traps, Culex pipiens/torrentium were responsible for 37.9% of all mosquito bites on pigs in the Romanian backyards, despite low feeding rates on pigs in the cages (18.6%). We also found that other predominantly ornithophilic mosquito species, as well as mosquitoes that are already carrying a blood meal from a different (mammalian) host, were attracted to backyard pigs or their enclosure.

Discussion

These results indicate that viraemic blood carrying, for instance, African swine fever virus, West-Nile virus or Japanese encephalitis virus could be introduced to these backyard pig farms and therefore cause an infection, either through subsequent feeding, via ingestion by the pig or by environmental contamination.

Optimization of polymerase chain reaction for the identification of Roe deer, Saiga, and Siberian stag living in Kazakhstan

Background and Aim:

One of the reasons for the decline in the number of wild species of artiodactyls is poaching and the illegal trading of animal products. Molecular genetic identification of animals from a biological sample effectively proves poaching cases and illegal trade of animal products. This study aimed to develop a polymerase chain reaction (PCR) test that allows for species identification of artiodactyl animals that are most often subject to poaching.

Materials and Methods:

Genomic DNA was extracted from meat and blood samples of animals killed by poachers using commercial kits. Three pairs of primers were designed and used to amplify the cytochrome b gene fragment of Roe deer, Saiga antelope, and Siberian stag.

Results:

The proposed protocol allows amplification of specific PCR products of 542 bp with Roe deer DNA, 587 bp with Saiga DNA, and 525 bp with Siberian stag DNA. Specificity analysis showed no cross activity with DNA from other animal species. The detection limit of PCR ranged from 15.6 pg to 1.9 pg of DNA in 25 mL of the reaction mixture.

Conclusion:

Sequencing the amplified products and subsequent comparison with the corresponding reference sequence showed a similarity ranging from 99.99% to 100%. The PCR based on the developed primers demonstrated high sensitivity and specificity when using DNA from homogeneous and heterogeneous animals.