Russell, G. C. | Search bioRxiv

bioRxiv2025

Genome sequence and annotation of ovine herpesvirus-1

Ovine herpesvirus 1 (OvHV-1) was first identified over 50 years ago in sheep with ovine pulmonary adenocarcinoma (OPA). An aetiological role in OPA was later ruled out and OvHV-1 was found to be a common infection in sheep in several countries. Here, we report the sequence and annotation of the complete OvHV-1 genome. The virus has a similar genomic architecture to members of the Macavirus genus of the subfamily Gammaherpesvirinae and is most closely related to bovine gammaherpesvirus 6 (BoGHV6). The OvHV-1 genome comprises a 144,637 base pair unique region predicted to encode at least 74 proteins bounded by multiple copies of a 699 base pair GC-rich repetitive terminal repeat. Predicted genes include 61 ORFs conserved among all gammaherpesviruses, and 12 genes present only in macavirus genomes, including a homologue of ovine interleukin-10, previously reported only in ovine gammaherpesvirus-2, and an ornithine decarboxylase, previously described only in BoGHV6. A further gene appears unique to OvHV-1 among macaviruses, encoding a viral-FLIP (FLICE-like inhibitory protein), similar to those found in some other gammaherpesviruses. Notably, several macavirus genes previously predicted in BoGHV6 are defective in OvHV-1. The availability of the genome sequence of OvHV-1 will facilitate studies on its relationship to other macaviruses and its role, if any, in disease.

microbiology↗

bioRxiv2021

Prospective cohort study reveals unexpected aetiologies of livestock abortion in northern Tanzania

Livestock abortion is an important cause of productivity losses worldwide and many infectious causes of abortion are zoonotic pathogens that impact on human health. Little is known about the relative importance of infectious causes of livestock abortion in Africa, including in subsistence farming communities that are critically dependent on livestock for food, income, and wellbeing. We conducted a prospective cohort study of livestock abortion, supported by cross-sectional serosurveillance, to determine aetiologies of livestock abortions in livestock in Tanzania. This approach generated several important findings including detection of a Rift Valley fever virus outbreak in cattle; high prevalence of C. burnetii infection in livestock; and the first report of Neospora caninum, Toxoplasma gondii, and pestiviruses associated with livestock abortion in Tanzania. Our approach provides a model for abortion surveillance in resource-limited settings. Our findings add substantially to current knowledge in sub-Saharan Africa, providing important evidence from which to prioritise disease interventions.

systems biology↗

bioRxiv2020

Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture

Bovine viral diarrhoea (BVD) is an important disease of cattle with significant impacts on animal health and welfare. The wide host range of the causative pestiviruses may lead to formation of virus reservoirs in other ruminant or wildlife species, presenting a concern for the long-term success of BVD eradication campaigns. It is likely that the quasispecies nature of these RNA viruses contributes to their interspecies transmission by providing genetic plasticity. Understanding the spectrum of sequence variants present in BVD persistently infected (PI) animals is therefore essential for studies of virus transmission. To analyse quasispecies diversity without amplification bias, we extracted viral RNA from serum of a PI cow, and from cell culture fluid after three passages of the same virus in culture, to produce cDNA without amplification. Sequencing of this material using Illumina 250bp paired-read technology produced full-length virus consensus sequences from both sources and demonstrated the quasispecies diversity of this Pestivirus A type 1a field strain within serum and after culture. We report the distribution and diversity of over 800 single nucleotide polymorphisms and provide evidence for a loss of diversity after only three passages in cell culture, implying that cultured viruses cannot be used to understand quasispecies diversity and may not provide reliable molecular markers for source tracing or transmission studies. Additionally, both serum and cultured viruses could be sequenced as a set of 25 overlapping PCR amplicons that demonstrated the same consensus sequences and the presence of many of the same quasispecies variants. The observation that aspects of the quasispecies structure revealed by massively parallel sequencing are also detected after PCR and Sanger sequencing suggests that this approach may be useful for small or difficult to analyse samples. Impact statementBovine viral diarrhoea viruses are globally important cattle pathogens, which impact performance due to acute infection and BVD-induced immunosuppression. Eradication of BVD in cattle is widely pursued but is hampered by the production of persistently infected (PI) calves - the offspring of cows infected in early pregnancy - which shed virus constantly and drive BVD spread. Genetic variation in BVD viruses is an important feature of their biology, allowing them to adapt to changing conditions and to infect different hosts. Inaccurate virus replication produces a population of viruses with slightly different sequences, a quasispecies, some of which may grow better in other hosts or in culture. Analysing virus sequence variation may help us understand how the virus evolves within and between its hosts. In this paper we show that a BVD virus strain loses quasispecies diversity quickly when cultured and that these changes can be detected even in small diagnostic samples, implying that cultured viruses do not perfectly represent the field strains they were isolated from and therefore may not provide reliable molecular markers for source tracing or transmission studies. Data SummaryPestivirus A genome sequences used in this article are as follows: O_TBL View this table: org.highwire.dtl.DTLVardef@bb1442org.highwire.dtl.DTLVardef@2f35f3org.highwire.dtl.DTLVardef@17f201corg.highwire.dtl.DTLVardef@11532eforg.highwire.dtl.DTLVardef@c31fd5_HPS_FORMAT_FIGEXP M_TBL C_TBL Sequence data associated with this manuscript has been submitted to the European Nucleotide Archive (www.ebi.ac.uk/ena/) with accession numbers as follows: Consensus genome sequences: MRI103 serum NGS: LR699799 MRI103 culture NGS: LR699800 MRI103 serum Sanger: LR699801 MRI103 culture P3 Sanger: LR699802 MRI103 culture P5 Sanger: LR699803 NGS raw data Serum dataset: ERR3624580 Culture dataset: ERR3624581

evolutionary biology↗