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.

Clinical Virology Unit Department of Clinical Microbiology and Infectious Diseases Hadassah University Hospital Jerusalem Israel

Department of Clinical Surgical Diagnostic and Pediatric Sciences University of Pavia Italy

Department of Medical Microbiology Motol University Hospital Prague Czech Republic Israel

Departments of Obstetrics and Gynecology Fondazione IRCCS Policlinico San Matteo Pavia Italy

Division of Infection and Immunity School of Medicine Cardiff University United Kingdom

German Center for Infection Research Hannover Braunschweig site United Kingdom

Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tuebingen Germany

Institute of Virology Hannover Medical School United Kingdom

Laboratory of Genetics Transplantology and Cardiovascular Diseases Italy

Medical Research Council University of Glasgow Centre for Virus Research United Kingdom

Molecular Virology Unit Microbiology and Virology Department Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo Italy

Pathogen Molecular Biology Department London School of Hygiene and Tropical Medicine United Kingdom

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