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Abstract
The genomic characteristics of human cytomegalovirus (HCMV) strains sequenced directly from clinical pathology samples were investigated, focusing on variation, multiple-strain infection, recombination, and gene loss. A total of 207 datasets generated in this and previous studies using target enrichment and high-throughput sequencing were analyzed, in the process enabling the determination of genome sequences for 91 strains. Key findings were that (i) it is important to monitor the quality of sequencing libraries in investigating variation; (ii) many recombinant strains have been transmitted during HCMV evolution, and some have apparently survived for thousands of years without further recombination; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for long periods and can cause congenital infection and resulting clinical sequelae; and (iv) intrahost variation in single-strain infections is much less than that in multiple-strain infections. Future population-based studies are likely to continue illuminating the evolution, epidemiology, and pathogenesis of HCMV.
Highlights
Human cytomegalovirus (HCMV) poses a risk, to people with immature or compromised immune systems, and can have serious outcomes in congenitally infected children, transplant recipients, and people with human immunodeficiency virus/AIDS
Mounting evidence of the existence of multiple-strain infections and the propensity of human cytomegalovirus (HCMV) to mutate during cell culture [6,7,8, 14, 15] added impetus to sequencing genomes directly from clinical material to define natural populations
Another utilizes an oligonucleotide bait library representing known HCMV diversity to select target sequences from random DNA fragments. This target enrichment technology originated in commercial kits for cellular exome sequencing, and was subsequently applied to various pathogens [17, 18], including HCMV [19,20,21]. We have applied it to HCMV since 2012 and have systematically released via GenBank many genome sequences that have proved pivotal in other studies [11, 12, 19,20,21]
Summary
Human cytomegalovirus (HCMV) poses a risk, to people with immature or compromised immune systems, and can have serious outcomes in congenitally infected children, transplant recipients, and people with human immunodeficiency virus/AIDS. Mounting evidence of the existence of multiple-strain infections and the propensity of HCMV to mutate during cell culture [6,7,8, 14, 15] added impetus to sequencing genomes directly from clinical material to define natural populations One strategy for this involves sequencing overlapping PCR amplicons [7, 16]. The HCMV genome exhibits several evolutionary phenomena, including variation, multiple-strain infection, recombination, and gene loss, all of which were discovered prior to high-throughput sequencing and have since been illuminated by this technology (early references are [22,23,24,25,26]) We explore these and other key genomic features of HCMV, with an emphasis on the strains present in clinical material
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