Castillo-Aliaga, C. | Search bioRxiv

bioRxiv2025

Cross-species Transmission and Host Adaptation of Feline Leukaemia Virus between Domestic Cats and the Wild Felid Leopardus guigna.

2.Feline leukaemia virus (FeLV) is widespread in domestic cats and frequently spills over into wild felid populations, causing severe outbreaks in non-domestic felid populations. Domestic cats carry both endogenous FeLV (enFeLV) and exogenous variants of FeLV (exFeLV), which can recombine to generate novel variants with alternate receptor usage. In contrast, most non-domestic felids, including the guigna are lack enFeLV This study applied amplification of the FeLV envelope gene combined with Illumina sequencing to characterise FeLV envelope gene diversity and transmission dynamics in guignas (Leopardus guigna), a small wild felid native to Chile and Argentina. Seven PCR amplicons from five free ranging guignas were sequenced. Illumina contigs demonstrated that infections originated from Chilean domestic cats; however, a distinct guigna-specific cluster with unique sequence variations was identified, suggesting that FeLV transmission also occurs among guignas independent of domestic cats. Phylogenetic analysis showed that all guigna sequences formed a Chile-specific FeLV clade, closely related to domestic cat viruses but clearly separated from international FeLV-A strains.

microbiology↗

bioRxiv2023

COMPARISON BETWEEN SANGER, ILLUMINA AND NANOPORE SEQUENCING EVIDENCING INTRA-HOST VARIATION OF FELINE LEUKEMIA VIRUS THAT INFECTS DOMESTIC CATS.

Knowledge of Feline Leukemia Virus (FeLV) sequence variation has mainly been developed using Sanger sequencing methods. However, advances in next generation sequencing methods and their broad use in laboratories has been changing our understanding of viral genetics. FeLV sequencing has specific complications with the presence of both exogenous (exFeLV) and endogenous (enFeLV) virus with frequent recombination between them, limiting sequencing approaches. Here we report an FeLV-A and FeLV-B amplicon-based comparison between Sanger, Illumina, and Oxford Nanopore sequencing methods in Chilean domestic cats. We analysed the hypervariable envelope gene, where a higher number of variants as well as recombination with endogenous strains occurs. We detected multiple variants and viral quasispecies infecting the cats. We compared these three methods to evaluate the advantages and disadvantages between them. Although the Sanger method is highly reliable, it showed a high fail rate (many amplicons did not produce useable sequence) and the sequences obtained showed artificial sequence clustering when compared with the NGS methods. Illumina sequencing showed a lower error rate but could not discriminate between exogenous and endogenous viruses. Finally, Oxford Nanopore (MinION) sequencing could successfully detect low-abundance sequences and discriminate between FeLV-A and FeLV-B sequences, although its higher error-rate requires caution in interpretation of the results. Our results indicate advantages and disadvantages for each method, with the purpose of sequencing needing to be considered in the choice of method. Results of large viral phylogenetic trees combing sequences derived from mixed sequencing methods, such as those combining historical and contemporary sequencing need to be considered with some caution as artificial clustering by sequencing method may occur.

microbiology↗