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 reactive 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 describedin 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

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 harbor ing 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

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, similar to 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

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

Paleovirology and the evolution of virus-host gene exchange

Paleovirology is the study of viruses at large evolutionary timescales through the investigation of endogenous viral elements (EVEs) that are found in host genomes. EVEs are the result of a heritable, genomic integration of a viral genome in a host germline cell. The presence of retroviral sequences in animal genomes has been recognized since the 1970âs, but discoveries made in the last five years have revealed that viruses of all genome types can endogenise. Moreover, although most EVEs are non-functional relics, there are a number of examples of functional EVEs that are co-opted to benefit the host. There remain some methodological challenges in the identification and analysis of EVEs, and we have yet to fully understand the evolutionary processes involved in the rare instances of co-option. In this thesis, I develop novel techniques to identify and characterize large herpesviruses, which lead to the discovery of the first endogenous herpesvirus in the genome of the Philippine tarsier. The same methods were redeployed to identify a new family of dsDNA virus in the genome data of their hosts. Among the 15 different new species of virus, at least four viruses in four different host fish exhibit characteristic features of EVEs such as non-sense mutations and the accumulation of transposable elements. Moreover, more than half of the predicted genes in a full-length salmon virus have no detectable similarity to known genes. The second investigative theme of this thesis explored the idea that EVEs can sometimes be the result of adaptive gene transfer, and that this is the conceptual equivalent of viral genes that are host-derived. Considering a subset of rare, functional EVEs that act as antiviral genes, I developed an evolutionary framework to understand such gene transfers as a biological strategy within the evolutionary arms race between viruses and hosts. In viruses, I conducted a systematic genome-wide evolutionary analysis of host-derived genes, which revealed a consistent shift towards higher purifying selection when switching from host to virus genome. Finally, this thesis also considered the evolution of gene transfer between viruses, by investigating the intriguing history of a retroviral superantigen gene with similarity to genes in unrelated herpesviruses. Through the evolutionary reconstruction of a large group of mammalian EVEs, I was able to prove the independent horizontal gene transfer of superantigens from retroviruses to herpesviruses from two different donor lineages. This shows that viral gene capture can occur in an evolutionary manner, and demonstrates the utility of paleovirological methods in understanding the evolution of pathogenicity. Altogether, this thesis highlights the results of synthesizing methods from paleovirology with metagenomic techniques, demonstrating that genomic databases are themselves rich with novel viral biodiversity that hold key insights for virology, genomics and evolution.</p

Aberraciones de la superficie corneal anterior y aberraciones intraoculares después del tratamientode errores refractivos altos con lasik y lentes intraoculares fáquicas

Es una práctica común considerar el cambio de lente refractiva fáquica o implante de lente intraocular para la corrección de altos niveles de ametropía en el rango de entre - 12D - 18D para corregir la miopía, +5,5 D y +8,5 D para la hipermetropía y +3 D para el astigmatismo, ya que existe una preocupación por la inducción de aberraciones corneales anteriores, la previsibilidad y la pérdida de líneas de CDVA en correcciones de errores refractivos altos mediante LASIK según algunos ensayos anteriores. En esta tesis, se demuestra que la corrección LASIK utilizando una plataforma láser excimer 500Hz disminuye el riesgo de la inducción de aberraciones, mejora la previsibilidad y las líneas perdidas de CDVA, lo cual nos motiva a considerarlo como un plan de tratamiento alternativo para altos niveles de ametropía, el cual a su vez, conlleva complicaciones menos graves, teniendo en cuenta que es una operación extraocular. Sin embargo, aún quedan futuros retos por resolver en relación con la corrección de niveles elevados de ametropía mediante láser excimer. Todavía estamos trabajando en la consecución del ojo ópticamente perfecto, y hoy en día seguimos sin entender cabalmente si la corrección total de las aberraciones existentes o la no-corrección total sería la mejor manera de llegar hasta tal fin, o incluso si existe un grado óptimo absoluto. Aunque la investigación sigue avanzando en la dirección correcta, todavía queda un largo camino por recorrer de la imagen que vemos hasta la percepción que el cerebro hace de ella. El estudio de las ópticas intraoculares es un excelente método para identificar el comportamiento óptico clínico de lentes intraoculares fáquicas

Ten species simulation (simulation C)

Gene trees reconstructed from simulated sequences. Forty loci are interleaved

Phylogenetic and genomic analysis of the <i>Daubentonia madagascariensis</i> rhadinovirus.

<p>Panel A is a maximum likelihood amino acid phylogeny of DNA polymerase, indicating the subfamily placement of the DmadHVL sequence as a gammaherpesvirus. Numbers at each node represent bootstrap support and only those above 50% are shown. Lineages other than those leading to DmadHVL are collapsed for clarity. In Panel B, the tree shown is a maximum likelihood phylogeny estimated using a concatenated alignment of 6 core genes (terminase, large tegument, uracil-DNA glycosylase, kinase, capsid and helicase). Coloured clades represent the different genera within gamma-2 herpesviruses, and bootstrap support is shown for each node. Panel C shows DmadHVL sequences mapped to <i>Saimiriine herpesvirus 2</i> (SaHV2) as a guide, and major repeat blocks as well as noteworthy genomic differences and genes discussed in the main text are highlighted in coloured boxes. The green blocks are the FGAM synthase coding sequences, which are found at the termini. The red box annotated as glycoprotein H is presumed to be an assembly error. Pink boxes are discussed genes present in SaHV2, while the yellow ORFs are those found in different viruses. The blue lines indicate the different sequences that are a composite of multiple wgs contigs, the number of which is indicated above each sequence. The composite DmadHVL sequences discussed in the main text are numbered from 1–16 in a left-right direction. The DmadHVL virus genome appears to have a slightly larger region spanning herpes core block (HCB) 3 and HCB4, and so contig 11 is drawn to represent this. The scale of the schematic is approximate. Abbreviations for Panel B are porc2/3: OvHV2: <i>Ovine herpesvirus 2</i>, AlHV1: <i>Alcelaphine herpesvirus 1</i>, <i>Porcine lymphotropic herpesvirus 2/3</i>, EqHV2: <i>Equine herpesvirus 2</i>, RodHV: <i>Rodent herpesvirus peru</i>, MuHV4: <i>Murid herpesvirus 4</i>, AtHV3: <i>Ateline herpesvirus 3</i>, SaHV2: <i>Saimiriine herpesvirus 2</i>, BoHV4: <i>Bovine herpesvirus 4</i>, HHV8: <i>human herpesvirus 8</i>, MaHV5: <i>Macacine herpesvirus 5</i>.</p

Phylogenetic and genomic analysis of the tarsier endogenous herpesvirus.

<p>Panel A: DNA polymerase tree showing the placement of the TsyrHVL sequence within the <i>Betaherpesvirinae</i>. Only the lineage leading to the node including TsyrHVL is shown and the rest are collapsed for clarity, and the size of the collapsed clade is arbitrary. Panel B represents the phylogeny reconstructed from a concatenated amino acid alignment of 6 core genes (terminase, large tegument, uracil-DNA glycosylase, kinase, capsid protein and helicase). Unclassified betaherpesviruses are shown as black branches, whereas those belonging to defined genera are indicated in colour. The rooting at <i>Proboscivirus</i> was determined according to the phylogeny in panel A. Numbers at each node in both Panel A and B represent bootstrap support. Panel C shows a schematic of the tarsier sequences mapped to HHV6 as a reference. Orange lines indicate wgs contigs obtained from NCBI and GenBank IDs are annotated. Contig ABRT02391417.1 is represented on both sides, since it consists entirely of the DR region, although it aligns with ABRT02259801.1 with only 5 differences, and both placements are plausible. Blue box indicates the virus' terminal direct repeat (DR) regions. Yellow boxes represent the major internal repeat regions. Because the genomes are so large, it is not feasible to represent the complete coding content. Instead major herpesvirus core blocks (HCB) are indicated (as in reference <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004332#pgen.1004332-Fields1" target="_blank">[5]</a>), and genes that are relevant to discussion points in the main text are also annotated. Abbreviations for Panel A and B are THEVE: Tarsier Herpesvirus Endogenous Viral Element, HHV6A/6B/7/5: <i>human herpesvirus 6A/6B/7/5</i>, MuHV1/2/8: <i>Murid herpesvirus 1/2/8</i>, AoHV1: <i>Aotine herpesvirus 1</i>, SaHV3: <i>Saimiriine herpesvirus 3</i>, PaHV2: <i>Panine herpesvirus 2</i>, CeHV5: <i>Cercopithecine herpesvirus 5</i>, TuHV1, PoCMV: <i>Porcine cytomegalovirus</i>.</p

Genomes containing Herpesvirus-like sequences.

<p>Details of the genome records that were investigated for viral sequences. Information was obtained from the NCBI assembly website: <a href="http://www.ncbi.nlm.nih.gov/assembly/" target="_blank">http://www.ncbi.nlm.nih.gov/assembly/</a>. N50 is the contig length at which all contigs of that length or longer represent 50% of the total of the lengths of all contigs.</p