Mardivirus meleagridalpha1 (MeAHV1), commonly known as herpesvirus of turkeys (HVT), was developed as a vaccine against Marek's disease (MD). Beyond its role as an MD vaccine, HVT has been successfully used as a recombinant vaccine vector to protect poultry from various viral, bacterial, and parasitic diseases. To study the process of viral genome concatemerization during HVT replication, the full-length genome of the HVT Fc126 strain was cloned into a bacterial artificial chromosome (BAC) by inserting a mini-F cassette. Full-length sequencing of three recombinant HVT-BAC clones was performed using long-read next-generation sequencing. The resulting genomic sequences were compared to the published HVT reference genome. HVT-BAC#1 and HVT-BAC#2 showed 95.8 % and 95.6 % identity, respectively, while HVT-BAC#3 had a 99.4 % identity. Further analysis revealed that HVT-BAC#1 and HVT-BAC#2 contained an inverted unique short (US) subgenomic region, classifying them as the Inverted short (IS) isomer, whereas HVT-BAC#3 had a prototype (P) genome arrangement. In silico inversion of the US region in HVT-BACs #1 and HVT-BAC#2 increased their sequence identity to the reference to 99.4 % and 99.5 %, respectively. In addition, all three HVT-BACs constructed in this study contained deletions encompassing the HVT071 ORF and the 5′ end of the HVT070 ORF. The IS and P genomes of HVT-BAC were re-isolated from the DNA of HVT-BAC#1 reconstituted viruses infected cells. Regardless of the variable genomic structure of HVT-BAC clones, the protective efficacy of the two HVT-BAC-derived viruses was slightly better than that of the parental HVT in Rep2, but it was not significantly different from that of the parental HVT in Rep1 against virulent Marek’s disease virus challenge. These data have confirmed the variability of the MeAHV1 genome in isomerization during replication.
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