A novel alphaherpesvirus associated with fatal diseases in banded Penguins

Abstract

A novel avian alphaherpesvirus, preliminarily designated sphenicid alphaherpesvirus 1 (SpAHV-1), has been independently isolated from juvenile Humboldt and African penguins (Spheniscus humboldti and Spheniscus demersus) kept in German zoos suffering from diphtheroid oropharyngitis/laryngotracheitis and necrotizing enteritis (collectively designated as penguin-diphtheria-like disease). High-throughput sequencing was used to determine the complete genome sequences of the first two SpAHV-1 isolates. SpAHV-1 comprises a class D genome with a length of about 164 kbp, a G+C content of 45.6 mol% and encodes 86 predicted ORFs. Taxonomic association of SpAHV-1 to the genus Mardivirus was supported by gene content clustering and phylogenetic analysis of herpesvirus core genes. The presented results imply that SpAHV-1 could be the primary causative agent of penguin-diphtheria-like fatal diseases in banded penguins. These results may serve as a basis for the development of diagnostic tools in order to investigate similar cases of penguin diphtheria in wild and captive penguins.

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

“…The sample processing workflow as depicted in Fig. 2 and described in detail in Supplementary File 1 , is applicable with RNA or DNA as input and has been proven with respect to diagnostic metagenomics in veterinary medicine 4 , 5 , 21 – 27 . Here, the workflow was further tested for different sample types and pathogens as described below.…”

“…Examples of new animal RNA viruses are Schmallenberg virus 5 and novel bovine and ovine astroviruses that caused different neurological symptoms including unusual behaviour and encephalitis 22 , 23 . A new Alphaherpesvirus of penguins, the most likely causative agent of diphtheria-like disease of banded penguins, represents the group of the DNA viruses that were detected and characterized using the presented workflow 21 . The protocol was also successfully applied to human samples and with the variegated squirrel bornavirus 1 (VSBV-1), a novel zoonotic bornavirus was identified 4 .…”

Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2

“…This procedure ensures that the resulting sequencing data reflect the original sample composition in the best way [2]. This generic HTS approach is a powerful tool and led to the detection of novel viruses in many cases [19][20][21][22], although the initial presence of the virus can be low in some cases [19,22,23]. Indeed, samples with very low pathogen (virus) content represent a typical diagnostic setting.…”

Full genome sequence of bovine alphaherpesvirus 2 (BoHV-2)

“…For Riems 8/85 a single scaffold contained the non-redundant viral genome sequence, as shown by sequence comparison to HHV-1 and leporid alphaherpesvirus 4 (LeHV-4), and was further used as a guide for the construction of the genome sequence of strain C1Z FZR. Additional mapping and assembly steps were carried out using Newbler (version 3.0) in order to identify and resolve misassemblies of repeats and duplications within the scaffolds of the initial de novo assembly, as described previously [13]. Remaining gaps were subsequently closed using PCR and Sanger sequencing.…”

“…The bar represents amino acid substitutions per site, and an asterisk indicates bootstrap support of 100%, while italic numbers indicate lower bootstrap support. Herpesviruses that are currently not classified at the species level by the ICTV are indicated by a hash symbol simplexviruses with primate hosts [13], it may represent a specific adaptation to primates.…”