Vaz, P. K. | bioRxiv Science

bioRxiv2026

Virological investigation of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus)

Elephant endotheliotropic herpesviruses (EEHV) pose a significant threat to the conservation of Asian elephants (Elephas maximus) worldwide, with a high mortality rate in young elephants. However, several components of EEHV virology remain underexplored, particularly for EEHV1B. This study describes a fatal case of EEHV1B infection in a nine-year-old Asian elephant from an ex situ conservation herd, examining herd viral dynamics, tissue viral loads and comparative genomics. This elephant succumbed to haemorrhagic disease within three days of developing clinical signs, despite therapeutic intervention. Quantitative PCR (qPCR) was performed on serial trunk washes and whole-blood surveillance samples collected before and after the clinical event, as well as on post-mortem tissues preserved in different storage media (DNA/RNA Shield, RNALater, and viral transport medium). Metagenomic next-generation sequencing of infected tissues was performed to characterise the complete viral genome, analyse variation from other published EEHV genomes and assess for evidence of viral recombination between EEHV subspecies. The affected elephant demonstrated a marked viraemia at onset of clinical disease, with viral load peaking at 5.47 x 106 viral genome equivalents per mL of blood, one day after the onset of clinical signs. Samples stored in viral transport medium yielded the greatest viral and host DNA recovery by qPCR, although tissues stored at -80 {degrees}C without media were still suitable for molecular detection. Whole genome sequencing demonstrated 96.0% pairwise nucleotide identity between the assembled genome (EEHV1B_AUP_01_2023, GenBank accession: PX651398) and the previously reported EEHV1B sequence (KC462164), and a maximum of 90.9% identity to published EEHV1A genomes, with evidence of recombination between the viral subspecies at several genomic regions. Viral recombination between EEHV subspecies may have significant implications for the pathogenesis of EEHV disease, the reliability of molecular diagnostics and the efficacy of vaccinations and anti-viral therapy.

microbiology↗

bioRxiv2023

Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates

Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterised. This study aimed to characterise and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short and long read sequencing methods. The completed genomes encoded a median of 759 open reading frames (min, 743, max 777) and had a median average nucleotide identity (ANI) of 98.2% with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer (HGT) events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction, and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualised using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats. Data summaryAll genome data for this study have been deposited in GenBank under BioProject PRJNA906261. Genome assemblies, as well as Illumina and Oxford Nanopore sequence reads for each isolate, can be found under their respective BioSamples: SAMN32182834 (isolate 047), SAMN32182835 (isolate 219), SAMN32182836 (isolate 329 and associated phage), and SAMN32182837 (isolate 632). The authors confirm all supporting data and protocols have been provided within the article. Impact statementMycoplasma felis is commonly associated with clinical cases of conjunctivitis and feline respiratory disease complex in cats, the leading cause of euthanasia in animal shelters. In the absence of vaccines, infection control is currently limited to the prolonged treatment with antimicrobials. Prior to this study there was only one complete genome assembly of an isolate of M. felis, which had been obtained from a horse. This study has provided the first high quality hybrid assembled genomes of M. felis isolates from cats. This work adds four new genomes from clinical cases, as well as the identification and validation of the presence of a novel phage that utilises the mycoplasma translation code. The genomic data presented here can assist future projects investigating improved diagnostics and development of new treatment options for this significant feline pathogen.

microbiology↗