Unbiased optical mapping of telomere-integrated endogenous human herpesvirus 6.

Next-generation sequencing technologies allowed sequencing of thousands of genomes. However, there are genomic regions that remain difficult to characterize, including telomeres, centromeres, and other low-complexity regions, as well as transposable elements and endogenous viruses. Human herpesvirus 6A and 6B (HHV-6A and HHV-6B) are closely related viruses that infect most humans and can integrate their genomes into the telomeres of infected cells. Integration also occurs in germ cells, meaning that the virus can be inherited and result in individuals harboring the virus in every cell of their body. The integrated virus can reactivate and cause disease in humans. While it is well established that the virus resides in the telomere region, the integration locus is poorly defined due to the low sequence complexity (TTAGGG)n of telomeres that cannot be easily resolved through sequencing. We therefore employed genome imaging of the integrated HHV-6A and HHV-6B genomes using whole-genome optical site mapping technology. Using this technology, we identified which chromosome arm harbors the virus genome and obtained a high-resolution map of the integration loci of multiple patients. Surprisingly, this revealed long telomere sequences at the virus-subtelomere junction that were previously missed using PCR-based approaches. Contrary to what was previously thought, our technique revealed that the telomere lengths of chromosomes harboring the integrated virus genome were comparable to the other chromosomes. Taken together, our data shed light on the genetic structure of the HHV-6A and HHV-6B integration locus, demonstrating the utility of optical mapping for the analysis of genomic regions that are difficult to sequence.

Endogenization and excision of human herpesvirus 6 in human genomes.

Sequences homologous to human herpesvirus 6 (HHV-6) are integrated within the nuclear genome of about 1% of humans, but it is not clear how this came about. It is also uncertain whether integrated HHV-6 can reactivate into an infectious virus. HHV-6 integrates into telomeres, and this has recently been associated with polymorphisms affecting MOV10L1. MOV10L1 is located on the subtelomere of chromosome 22q (chr22q) and is required to make PIWI-interacting RNAs (piRNAs). As piRNAs block germline integration of transposons, piRNA-mediated repression of HHV-6 integration has been proposed to explain this association. In vitro, recombination of the HHV-6 genome along its terminal direct repeats (DRs) leads to excision from the telomere and viral reactivation, but the expected "solo-DR scar" has not been described in vivo. Here we screened for integrated HHV-6 in 7,485 Japanese subjects using whole-genome sequencing (WGS). Integrated HHV-6 was associated with polymorphisms on chr22q. However, in contrast to prior work, we find that the reported MOV10L1 polymorphism is physically linked to an ancient endogenous HHV-6A variant integrated into the telomere of chr22q in East Asians. Unexpectedly, an HHV-6B variant has also endogenized in chr22q; two endogenous HHV-6 variants at this locus thus account for 72% of all integrated HHV-6 in Japan. We also report human genomes carrying only one portion of the HHV-6B genome, a solo-DR, supporting in vivo excision and possible viral reactivation. Together these results explain the recently-reported association between integrated HHV-6 and MOV10L1/piRNAs, suggest potential exaptation of HHV-6 in its coevolution with human chr22q, and clarify the evolution and risk of reactivation of the only intact (non-retro)viral genome known to be present in human germlines.

Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa.

Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) if they still occur, and 3) whether circulating virus strains differ from integrated ones. Here, we used next-generation sequencing and mining of public human genome data sets to generate the largest and most diverse collection of circulating and integrated HHV-6 genomes studied to date. In genomes of geographically dispersed, only distantly related people, we identified clades of integrated viruses that originated from a single ancestral event, confirming this with fluorescent in situ hybridization to directly observe the integration locus. In contrast to HHV-6B, circulating and integrated HHV-6A sequences form distinct clades, arguing against ongoing integration of circulating HHV-6A or "reactivation" of integrated HHV-6A. Taken together, our study provides the first comprehensive picture of the evolution of HHV-6, and reveals that integration of heritable HHV-6 has occurred since the time of, if not before, human migrations out of Africa.

Marek's Disease Virus Requires Both Copies of the Inverted Repeat Regions for Efficient In Vivo Replication and Pathogenesis.

Marek's disease virus (MDV) is an oncogenic alphaherpesvirus of chickens. The MDV genome consists of two unique regions that are both flanked by inverted repeat regions. These repeats harbor several genes involved in virus replication and pathogenesis, but it remains unclear why MDV and other herpesviruses harbor these large sequence duplications. In this study, we set to determine if both copies of these repeat regions are required for MDV replication and pathogenesis. Our results demonstrate that MDV mutants lacking the entire internal repeat region (ΔIRLS) efficiently replicate and spread from cell-to-cell in vitro However, ΔIRLS replication was severely impaired in infected chickens and the virus caused significantly less frequent disease and tumors compared to the controls. In addition, we also generated recombinant viruses that harbor a deletion of most of the internal repeat region, leaving only short terminal sequences behind (ΔIRLS-HR). These remaining homologous sequences facilitated rapid restoration of the deleted repeat region, resulting in a virus that caused disease and tumors comparable to the wild type. Therefore, ΔIRLS-HR represents an excellent platform for rapid genetic manipulation of the virus genome in the repeat regions. Taken together, our study demonstrates that MDV requires both copies of the repeats for efficient replication and pathogenesis in its natural host.IMPORTANCE Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that infects chickens and causes losses in the poultry industry of up to $2 billion per year. The virus is also widely used as a model to study alphaherpesvirus pathogenesis and virus-induced tumor development in a natural host. MDV and most other herpesviruses harbor direct or inverted repeats regions in their genome. However, the role of these sequence duplications in MDV remains elusive and has never been investigated in a natural virus-host model for any herpesvirus. Here, we demonstrate that both copies of the repeats are needed for efficient MDV replication and pathogenesis in vivo, while replication was not affected in cell culture. With this, we further dissect herpesvirus genome biology and the role of repeat regions in Marek's disease virus replication and pathogenesis.

Cell-Derived Viral Genes Evolve under Stronger Purifying Selection in Rhadinoviruses.

Like many other large double-stranded DNA (dsDNA) viruses, herpesviruses are known to capture host genes to evade host defenses. Little is known about the detailed natural history of such genes, nor do we fully understand their evolutionary dynamics. A major obstacle is that they are often highly divergent, maintaining very low sequence similarity to host homologs. Here we use the herpesvirus genus Rhadinovirus as a model system to develop an analytical approach that combines complementary evolutionary and bioinformatic techniques, offering results that are both detailed and robust for a range of genes. Using a systematic phylogenetic strategy, we identify the original host lineage of viral genes with high confidence. We show that although host immunomodulatory genes evolve rapidly compared to other host genes, they undergo a clear increase in purifying selection once captured by a virus. To characterize this shift in detail, we developed a novel technique to identify changes in selection pressure that can be attributable to particular domains. These findings will inform us on how viruses develop strategies to evade the immune system, and our synthesis of techniques can be reapplied to other viruses or biological systems with similar analytical challenges.IMPORTANCE Viruses and hosts have been shown to capture genes from one another as part of the evolutionary arms race. Such genes offer a natural experiment on the effects of evolutionary pressure, since the same gene exists in vastly different selective environments. However, sequences of viral homologs often bear little similarity to the original sequence, complicating the reconstruction of their shared evolutionary history with host counterparts. In this study, we use a genus of herpesviruses as a model system to comprehensively investigate the evolution of host-derived viral genes, using a synthesis of genomics, phylogenetics, selection analysis, and nucleotide and amino acid modeling.

A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets.

Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases.

The first endogenous herpesvirus, identified in the tarsier genome, and novel sequences from primate rhadinoviruses and lymphocryptoviruses.

Herpesviridae is a diverse family of large and complex pathogens whose genomes are extremely difficult to sequence. This is particularly true for clinical samples, and if the virus, host, or both genomes are being sequenced for the first time. Although herpesviruses are known to occasionally integrate in host genomes, and can also be inherited in a Mendelian fashion, they are notably absent from the genomic fossil record comprised of endogenous viral elements (EVEs). Here, we combine paleovirological and metagenomic approaches to both explore the constituent viral diversity of mammalian genomes and search for endogenous herpesviruses. We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi's sarcoma-associated virus. We also identify 58 genes of Pan paniscus lymphocryptovirus 1, the bonobo equivalent of human Epstein-Barr virus. For each of the viruses, we postulate gene function via comparative analysis to known viral relatives. Most notably, the evidence from gene content and phylogenetics suggests that the aye-aye sequences represent the most basal known rhadinovirus, and indicates that tumorigenic herpesviruses have been infecting primates since their emergence in the late Cretaceous. Overall, these data show that a genomic fossil record of herpesviruses exists despite their extremely large genomes, and expands the known diversity of Herpesviridae, which will aid the characterization of pathogenesis. Our analytical approach illustrates the benefit of intersecting evolutionary approaches with metagenomics, genetics and paleovirology.

The origins of giant viruses, virophages and their relatives in host genomes.

Giant viruses have revealed a number of surprises that challenge conventions on what constitutes a virus. The Samba virus newly isolated in Brazil expands the known distribution of giant mimiviruses to a near-global scale. These viruses, together with the transposon-related virophages that infect them, pose a number of questions about their evolutionary origins that need to be considered in the light of the complex entanglement between host, virus and virophage genomes.

Current understanding of human herpesvirus 6 (HHV-6) chromosomal integration.

Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are members of the genus Roseolovirus in the Betaherpesvirinae subfamily. HHV-6B infects humans in the first years of life, has a seroprevalence of more than 90% and causes Roseola Infantum, but less is known about HHV-6A. While most other herpesviruses maintain their latent genome as a circular episome, HHV-6A and HHV-6B (HHV-6A/B) have been shown to integrate their genome into the telomeres of infected cells. HHV-6A/B can also integrate into the chromosomes of germ cells, resulting in individuals carrying a copy of the virus genome in every nucleated cell of their bodies. This review highlights our current understanding of HHV-6A/B integration and reactivation as well as aspects that should be addressed in the future of this relatively young research area. It forms part of an online symposium on the prevention and therapy of DNA virus infections, dedicated to the memory of Mark Prichard.

Interferon-Inducible Protein 16 (IFI16) Has a Broad-Spectrum Binding Ability Against ssDNA Targets: An Evolutionary Hypothesis for Antiretroviral Checkpoint.

Human endogenous retroviruses (HERVs) are under genomic and epigenetic control but can be expressed in normal tissues, producing RNA transcripts some of which are translated. While it has not been demonstrated experimentally in modern humans, cDNA copies from HERV RNA (namely HERV-K HML-2 or HK2) were produced after the human-chimp split and until at least 250,000 years ago. We were interested in determining if such cDNA could be a ligand for pattern recognition receptors (PRRs) of the innate immune response. The AIM-2-like receptors for DNA, interferon-γ-inducible protein 16 (IFI16) and Cyclic GMP-AMP synthase (cGAS) were candidate PRRs. IFI16 can detect cDNA produced during HIV-1 replication, causing increased T cell death. While HIV-1 has emerged relatively recently as a human pathogen, the cDNA functionality of IFI16 could have been selected for during the course of human evolution. Here we present a novel hypothesis that the products of reverse transcription of HK2, which has been proliferating in the genome of human ancestors for 30 million years, could interact with IFI16. In support of our hypothesis, we provide preliminary data showing that IFI16 (but not cGAS) interacts with synthetic single-stranded HK2 oligos corresponding to the first product of reverse transcription. Further, we show that ssDNA detection by IFI16 has variability with respect to sequence features but is not dependent on strong secondary structures mimicking dsDNA. Among the HK2 oligos, IFI16 interacts more intensely with those derived from LTRs, suggesting these oligos have undetermined structural features that allow IFI16 to bind with greater affinity. Further, cells with stem cell features that naturally allow HK2 expression were found to express many components of the innate immune system including cGAS but not IFI16. Based on the presented preliminary data we further postulate another hypothesis: that the IFI16 functionality in human cells has been acting as "second-line" defense to control abnormal HK2 replication in somatic tissues. The absence of this protein in stem cells and a stem cell line could permit these cells to express HERVs which contribute to stem cell identity. Finally, we also comment on potential studies that could support or refute our hypothesis.

A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.

Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.

Disentangling the origins of virophages and polintons.

Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.

Evolution: Endogenous Viruses Provide Shortcuts in Antiviral Immunity.

Endogenous viruses are occasionally co-opted by their hosts to combat other viruses. The discovery of the widespread recruitment of endogenous viruses as regulatory elements for immune genes points to a systematic evolutionary process in their co-option for host immunity.

Optical Profile Following High Hyperopia Correction With a 500-Hz Excimer Laser System.

PURPOSE: To evaluate corneal higher order aberrations after LASIK for the correction of high hyperopia using a 500-Hz excimer laser and optimized ablation profile. METHODS: Retrospective consecutive study including 51 eyes of 28 patients (age range: 21 to 54 years) with high hyperopia or hyperopic astigmatism (sphere ≥ 5.00 diopters). All cases underwent LASIK using the sixth generation Amaris excimer laser (SCHWIND eye-tech-solutions, Kleinostheim, Germany) and a femtosecond laser platform for flap creation. Postoperative changes in corneal higher order aberrations for the 4-, 5-, and 6-mm pupil diameters and corneal asphericity for 4.5 and 8 mm were represented at the end of the 6-month follow-up. RESULTS: A significant increase in corneal root mean square higher order, spherical, and coma aberrations was observed 6 months after surgery (P < .01). Corneal asphericity for the 4.5-mm (Q45) and 8-mm (Q8) corneal diameter also changed significantly during the postoperative period (P < .01). Strehl ratio change was not statistically significant (P = .77). CONCLUSIONS: Correction of high hyperopia with LASIK significantly induces corneal higher order aberrations regardless of the physiologic level of photopic and mesopic pupil conditions.

Convergent capture of retroviral superantigens by mammalian herpesviruses.

Horizontal gene transfer from retroviruses to mammals is well documented and extensive, but is rare between unrelated viruses with distinct genome types. Three herpesviruses encode a gene with similarity to a retroviral superantigen gene (sag) of the unrelated mouse mammary tumour virus (MMTV). We uncover ancient retroviral sags in over 20 mammals to reconstruct their shared history with herpesviral sags, revealing that the acquisition is a convergent evolutionary event. A retrovirus circulating in South American primates over 10 million years ago was the source of sag in two monkey herpesviruses, and a different retrovirus was the source of sag in a Peruvian rodent herpesvirus. We further show through a timescaled phylogenetic analysis that a cross-species transmission of monkey herpesviruses occurred after the acquisition of sag. These results reveal that a diverse range of ancient sag-containing retroviruses independently donated sag twice from two separate lineages that are distinct from MMTV.

Refractive lens exchange.

Advances in small incision surgery have enabled cataract surgery to evolve from being concerned primarily with the safe removal of the opaque crystalline lens to a procedure refined to yield the best possible postoperative refractive result. As the outcomes of cataract surgery have improved, the use of lens surgery as a refractive modality in patients without cataracts (clear lens extraction) has increased in popularity. The removal of the crystalline lens for refractive purposes, or so-called refractive lens exchange (RLE), offers distinct advantages over corneal refractive surgery in selected cases. Nevertheless, in some middle-aged patients with high refractive errors, corneal refractive surgery can be a safe and effective treatment. In addition, the use of multifocal lenses offers an alternative for the correction of presbyopia. A further advantage of RLE is that it simultaneously eliminates the need for cataract surgery in the future. The keys for success in RLE are effectiveness and consistency in the refractive outcome, providing at the same time surgical and postoperative safety. To achieve these goals, adequate indications following strict risk/benefit criteria and refractive precision based on accurate preoperative protocols for IOL calculation and selection are mandatory, together with an appropriate choice of surgical procedure based on the surgeon's skills, minimizing complications.

Laser-assisted in situ keratomileusis in high mixed astigmatism with optimized, fast-repetition and cyclotorsion control excimer laser.

PURPOSE: To evaluate the visual refractive and aberrometric outcomes of laser-assisted in situ keratomileusis (LASIK) surgery for the correction of high mixed astigmatism using a new-generation excimer laser and optimized aspherical profiles. DESIGN: Retrospective interventional case series. METHODS: Fifty-two eyes of 36 patients (21-53 years) with primary mixed astigmatism over 3.0 diopters (D) were included. All cases underwent LASIK surgery using the sixth-generation excimer laser Amaris with cyclotorsion control and a femtosecond platform for flap creation. Visual, refractive, corneal topographic, and aberrometric outcomes were evaluated during a 3-month follow-up. Refractive astigmatic changes were analyzed by Alpins method. RESULTS: A significant reduction of refractive sphere and cylinder was observed 3 months postoperatively (P = .001), with an associated improvement of uncorrected distance visual acuity (P = .001). Best-corrected distance visual acuity (CDVA) remained unchanged in 31 eyes (59.6%), while 3 eyes (5.76%) lost 2 lines of CDVA. Fourteen eyes (26.9%) had spherical equivalent (SE) within ±0.5 D of emmetropia and 34 (65.3%) had SE within ±1.0 D of emmetropia. No significant difference was observed when comparing surgically induced and target astigmatism. A significant induction of higher-order aberration attributable to increase of spherical aberration was found (P = .003). Seven eyes (13.4%) required retreatment. CONCLUSIONS: LASIK for primary high mixed astigmatism using optimized aspherical profiles and a fast-repetition-rate excimer laser with cyclotorsion control is a safe, effective, and predictable procedure. Induction of higher-order aberrations is still present in the correction of the refraction error of the magnitude included in this study.

Laser in situ keratomileusis for high hyperopia (>5.0 diopters) using optimized aspheric profiles: efficacy and safety.

PURPOSE: To evaluate the clinical outcomes of laser in situ keratomileusis (LASIK) for high hyperopia using an excimer laser and optimized aspheric profiles. SETTING: Vissum Corporation and Miguel Hernández University, Alicante, Spain, and Research Institute of Ophthalmology, Giza, Egypt. DESIGN: Case series. METHODS: Eyes of patients with high hyperopia or hyperopic astigmatism (spherical equivalent [SE] ≥ 5.64 diopters [D]) had uneventful LASIK with an aspheric optimized ablation profile centered on the corneal vertex using an Amaris 500 kHz excimer laser and a femtosecond platform for flap creation with a temporal hinge. RESULTS: There was a significant improvement in uncorrected distance visual acuity 3 months postoperatively (P<.01), with no significant changes afterward (P=.72). At 6 months, the corrected distance visual acuity (CDVA) remained unchanged or improved in 90.48% of eyes; 2 eyes (9.52%) lost 2 lines of logMAR CDVA. The postoperative SE was within ± 0.50 D of emmetropia in 70.37% of eyes. The LASIK enhancement rate at the end of the follow-up was 29.4%. Significant induction of corneal primary spherical aberration and coma was found with 6.0 mm pupils (P<.01). The safety index was 0.94 and the efficacy index, 0.85. CONCLUSION: Laser in situ keratomileusis for high hyperopia using optimized aspheric profiles requires further improvement in terms of safety but was still an effective and a predictable procedure.

Intraocular optical quality of phakic intraocular lenses: comparison of angle-supported, iris-fixated, and posterior chamber lenses.

PURPOSE: To evaluate internal aberrometric profiles following phakic intraocular lens (PIOL) implantation. DESIGN: Retrospective and consecutive case series. METHODS: One hundred and five eyes of 65 patients were included. The optical aberrations were measured with the Topcon KR-1W aberrometer. Comparisons of internal aberrations for different models were made. Comparisons at 4 and 6 mm were made also within the same model for all the lenses. Comparisons regarding the implantation site were also performed: angle-supported (AS) anterior chamber (AC) (n = 47), iris-fixated (IF) (n = 27), and posterior chamber (PC) (n = 31). RESULTS: Root mean square (RMS) of internal optical higher-order aberrations (HOAs) changed significantly to higher values from 4-6 mm aperture diameter in each PIOL, as should be expected. However, this significant change was not detected in spherical aberration for Kelman Duet (P = .753) and in trefoil for Acrysoft (P = .059). Kelman lens showed significantly lower values of spherical aberration compared to Acrysoft at 4 mm (P = .022) and at 6 mm (P = .042). Acrysoft showed the lowest values at central zone for trefoil (P = .043) and tetrafoil (P = .002) in AC group. In the IF group, Artisan and Artiflex showed similar results for all internal aberrations. In the comparison between Visian Implantable Collamer Lens (ICL; STAAR Surgical Co, Monrovia, California, USA) and phakic refractive lens (PRL), both for posterior chamber, significantly lower values of coma were observed for ICL (P = .033). IF lenses showed clinical evidence, but not significant, of better centering capability than AS lenses (P = .096). CONCLUSIONS: The study of intraocular aberrations is an adequate method to identify the clinical optical behavior and could help the surgeon to identify the most frequent problems related with each model.