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Recently published near full-length KSHV genomes from a Cameroon Kaposi sarcoma case-control study showed strong evidence of viral recombination and mixed infections, but no sequence variations associated with disease. Using the same methodology, an additional 102 KSHV genomes from 76 individuals with KSHV-associated diseases have been sequenced. Diagnoses comprise all KSHV-associated diseases (KAD): Kaposi sarcoma (KS), primary effusion lymphoma (PEL), KSHV-associated large cell lymphoma (KSHV-LCL), a type of multicentric Castleman disease (KSHV-MCD), and KSHV inflammatory cytokine syndrome (KICS). Participants originated from 22 different countries, providing the opportunity to obtain new near full-length sequences of a wide diversity of KSHV genomes. These include near full-length sequence of genomes with KSHV K1 subtypes A, B, C, and F as well as subtype E, for which no full sequence was previously available. High levels of recombination were observed. Fourteen individuals (18%) showed evidence of infection with multiple KSHV variants (from two to four unique genomes). Twenty-six comparisons of sequences, obtained from various sampling sites including PBMC, tissue biopsies, oral fluids, and effusions in the same participants, identified near complete genome conservation between different biological compartments. Polymorphisms were identified in coding and non-coding regions, including indels in the K3 and K15 genes and sequence inversions here reported for the first time. One such polymorphism in KSHV ORF46, specific to the KSHV K1 subtype E2, encoded a mutation in the leucine loop extension of the uracil DNA glycosylase that results in alteration of biochemical functions of this protein. This confirms that KSHV sequence variations can have functional consequences warranting further investigation. This study represents the largest and most diverse analysis of KSHV genome sequences to date among individuals with KAD and provides important new information on global KSHV genomics. Author summary: The prevalence of KSHV infection, one of eight viruses associated with human cancer, differs geographically as does the incidence of Kaposi sarcoma and other KSHV-associated diseases. Distribution of KSHV subtypes, defined solely by the sequence of the K1 gene, also differs by region. One hundred and two near full-length KSHV genomes from people with associated diseases from a wide variety of countries were sequenced, substantially increasing the number and diversity of KSHV genomes publicly available, thereby allowing the analysis of variance across geographical regions, potential contributions of viral genetics to the risk of disease, and viral evolution. Our data demonstrate that viral recombination is common, as previously published, and that infections with multiple KSHV genomes may also be frequent, which has not been widely reported. We did not find evidence of an association between viral subtypes and disease nor indications that different sampling sites from the same individual, including tumor specimens, harbored substantially different KSHV genomes. Our data significantly inform the current efforts to study epidemiology and the prevention of KSHV infection, including vaccine development, as well as the pathogenesis of associated diseases. [ABSTRACT FROM AUTHOR]

Kaposi sarcoma herpesvirus (KSHV) is the etiological agent of three malignancies, Kaposi sarcoma (KS), primary effusion lymphoma (PEL) and KSHV-associated multicentric Castelman disease. KSHV infected patients may also have an interleukin six-related KSHV-associated inflammatory cytokine syndrome. KSHV-associated diseases occur in only a minority of chronically KSHV-infected individuals and often in the setting of immunosuppression. Mechanisms by which KSHV genomic variations and systemic co-infections may affect the pathogenic pathways potentially leading to these diseases have not been well characterized in vivo. To date, the majority of comparative genetic analyses of KSHV have been focused on a few regions scattered across the viral genome. We used next-generation sequencing techniques to investigate the taxonomic groupings of viruses from malignant effusion samples from fourteen participants with advanced KSHV-related malignancies, including twelve with PEL and two with KS and elevated KSHV viral load in effusions. The genomic diversity and evolutionary characteristics of nine isolated, near full-length KSHV genomes revealed extensive evidence of mosaic patterns across all these genomes. Further, our comprehensive NGS analysis allowed the identification of two distinct KSHV genome sequences in one individual, consistent with a dual infection. Overall, our results provide significant evidence for the contribution of KSHV phylogenomics to the origin of KSHV subtypes. This report points to a wider scope of studies to establish genome-wide patterns of sequence diversity and define the possible pathogenic role of sequence variations in KSHV-infected individuals. [ABSTRACT FROM AUTHOR]

The article traces the history of the 340B Drug Pricing Program (340B Program) in the U.S. Topics discussed include growth of the 340B Program under the Affordable Care Act, the legal clashes between the Health and Human Services (HHS) and Pharmaceutical Research and Manufacturers of America over the orphan drug rule and standards used by the courts to determine that HHS has limited authority to issue binding guidance over the program.