Primers design for the detection and genotyping of the Canine Distemper Virus

Canine Distemper Virus (CDV) has potential hosts, all carnivores, including wild animals. The associated disease, called canine distemper (CD) has a high prevalence and is highly contagious, being one of the main causes of death in domestic and wild canids. Although it is a monotypic virus, that is, with little genetic preference, the H gene has a high genetic variation, which would produce different strains of the virus, some more virulent than others and with different tropism. It is because of this specific specification that patients still get sick, despite being vaccinated, since the eightfold vaccine protects against one strain of the virus: America-1.
Thus, any carnivore susceptible to the virus that is confronted with a strain against which it has not been vaccinated is as likely to become ill as an animal that has simply never been vaccinated against this viral disease. To face this situation, it is essential to know the characteristics of the genotypes of the virus present in the country. Through previous studies, it is known that in Chile there are at least two of the fourteen VDC lineages, but this does not imply that they are the only ones in the country, which is why it is proposed to propose a prior Polymerase Chain Reaction protocol. Reverse transcription using both matches for the N gene and for the H gene (lineages: America-1 and European) to shed light on the genotype found in the samples, which may not even belong to either of the two lineages described above in the country.
For the generation of an RT-PCR protocol capable of detecting VDC, the use of the Genbank® genomic database in conjunction with the in silico design of primers is very interesting, indicating whether it corresponds to the American-1 or European lineage.