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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Publications at this Location » Publication #411428
Research Project: Elucidation of Molecular Determinants of Avian Herpesviruses Virulence and Evolution to Inform the Development of Safe and Effective Vaccines

Location: Endemic Poultry Viral Diseases Research

Title: Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation

Author
item ORTIGAS-VASQUEZ, ALEJANDRO - Pennsylvania State University
item PANDEY, UTSAV - Pennsylvania State University
item RENNER, DANIEL - Pennsylvania State University
item BOWEN, CHRIS - Pennsylvania State University
item BAIGENT, SUSAN - The Pirbright Institute
item Dunn, John
item Cheng, Hans
item YAO, YONGXIU - The Pirbright Institute
item READ, ANDREW - Pennsylvania State University
item NAIR, VENUGOPAL - The Pirbright Institute
item KENNEDY, DAVE - Pennsylvania State University
item SZPARA, MORIAH - Pennsylvania State University

Submitted to: Virus Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Marek's disease (MD) is a serious problem to the poultry industry as Marek's disease virus (MDV), the causative agent, induces tumors and immunosuppression in susceptible birds. Identifying the molecular basis for why a virus is virulent or can act as a vaccine depends on having consistent reagents. In this study, deep DNA sequencing of viral genomes demonstrated that there can be considerable differences even within strains with the same name. This information is important to the scientific community to ensure that proper comparisons and interpretation of results are made. Ultimately, US consumers should benefit from the knowledge gain with more precise experiments using well-characterized MDV strains.

Technical Abstract: Current strategies to understand the molecular basis of Marek’s disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988-GenBank diverged from CVI988-UK and CVI988-USDA. Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988-GenBank that were not present in either CVI988-UK or CVI988-USDA. Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988-GenBank. Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.