The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus

Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship.

A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus

Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus evolution. We identify Atlas virus - an intact retrovirus-like EVE in the human hookworm Ancylostoma ceylanicum, with an envelope protein genetically related to GN-GC glycoproteins from phleboviruses. A cryo-EM structure of Atlas GC reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas GC has the structural hallmarks of an active fusogen. Atlas GC trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas GC has cell-cell fusion activity. RNA-Seq data analysis detected transcripts mapping to Atlas virus at different stages of hookworm development. With its preserved biological activities, Atlas GC has the potential to acquire a cellular function. Our work reveals structural plasticity in reverse-transcribing RNA viruses.

640 Stem-like CD4 T cells in cancer

BackgroundCD4 T cells can differentiate into multiple effector subsets that can mediate variable functions. In this work we aim to understand how CD4 T cells differentiate in response to tumor antigens and their respective function in the anti-tumor response.MethodsTumor tissue was collected from patients undergoing surgery at Emory University Hospital. Activated PD1+ CD45RA- tumor infiltrating CD4 T cells were sent for 10X single cell RNA-seq. Tumor samples were also processed for flow cytometry and ex vivo functional analyses. For in vivo studies, prostate cancer mouse model expressing the LCMV glycoprotein (TRAMPC1-GP) was used, as well as LCMV Armstrong infection.ResultsTo characterize the heterogeneity of CD4 T cells infiltrating kidney tumors, we performed single cell RNAseq. We found three distinct activated (PD1+ CD45RA-) CD4 T cell populations. Two effector clusters consisting of Th1-like (EOMES+) and Treg (FOXP3+) cells, and a third cluster expressing TCF1, and genes associated with stemness and survival that did not fit defined CD4 effector lineages. We further confirmed these data by flow cytometry and found the same tumor infiltrating CD4 subsets in 100 kidney cancer patients. When placed in culture under different polarization conditions, tumor TCF1+ CD4 T cells proliferated and differentiated into the Th1-like and Treg effector populations found in the tumor, in addition to other effector lineages (Th1, Tfh) given the appropriate conditions, while the Th1-like and Treg cells underwent no proliferation or phenotype changes. These data suggests that the TCF1+ CD4s act as activated unpolarized precursors to the effector subsets in the tumor. To further test this hypothesis in vivo, we adoptively transferred tumor specific (SMARTA) CD4 T cells into mice followed by TRAMPC1-GP tumor inoculation. Transferred SMARTAs activated and first acquired a TCF1+ phenotype in the TDLN prior to predominantly differentiating into Tregs in the tumor. Given their plasticity in vitro, we asked whether TCF1+ SMARTAs primed in tumors were destined to differentiate into Tregs. To test this, we transferred 4-week activated TCF1+ SMARTAs from TDLNs of TRAMPC1-GP mice into naïve mice that were immediately infected with LCMV Armstrong. We found that the transferred SMARTAs differentiated into Th1 and Tfh cells in response to the virus, similar to the endogenous virus specific CD4 T cells.ConclusionsOverall, this work shows that CD4 T cells remain in an activated phenotype in the tumor with the capacity to differentiate into non-suppressive effector lineages given the appropriate conditions that may benefit the anti-tumor response.

Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

Hybridization and environmental stress trigger genome shock that perturbs patterns of gene expression leading to phenotypic changes. In extreme examples it is associated to transposon mobilization and genome rearrangement. Here we discover a novel alternative mechanism in interspecific Solanum hybrids in which changes to gene expression were associated with DCL2-mediated small (s)RNAs derived from endogenous (para)retroviruses (EPRVs). Correspondingly, the altered patterns of gene expression overlapped with the effects of dcl2 mutation and the changes to sRNA profiles involved 22nt species produced in the DCL2 biogenesis pathway. These findings implicate hybridization-induced genome shock leading to EPRV activation and sRNA silencing as causing changes in gene expression. Such hybridization-induced variation in gene expression could increase the range of traits available for selection in natural evolution or in breeding for agriculture.

Concerns regarding vaccination as a management strategy against koala retrovirus

Koalas are of great cultural, ecological and economic significance to Australia. However, they are in steep decline throughout much of their geographic range, with the recently endogenized koala retrovirus (KoRV) presumed to be a contributing factor. Olagoke, et al. have proposed vaccination against KoRV as a suitable control mechanism to reduce the severity of KoRV infections and suggest that their recombinant vaccine is effective at invoking a neutralising immune response and significantly reducing viral loads. Here, we report the findings of our own attempts to detect antibodies specific to the KoRV envelope protein (Env) in infected animals. Antibodies against Env were undetectable in all animals, as would be expected in the case of an endogenous virus antigen which should proceed towards a pathway of self-tolerance. This finding calls into question the results of Olagoke, et al., and prior work by this team. Following a critical review of this work, we have identified a number of assay inaccuracies and possible over interpretations of the data and conclude that further work to develop and test a vaccine against KoRV in koalas is not supported by evidence.

Endogenization of ssDNA fragment from an infectious virus in the genome of the Chaetoceros tenuissimus

One of the smallest diatoms, Chaetoceros tenuissimus, maintains their population despite coexisting with infectious viruses during blooms. To further understand this relationship, here, we sequenced the C. tenuissimus NIES-3715 genome. A gene fragment of a replication-associated gene from its own infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated in a total of 41 Mbp of both haploid assemblies. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. A target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study used genome information provides further insights into the diatom-virus evolutionary relationship.

Specific properties of shRNA-mediated CCR5 downregulation that enhance the inhibition of HIV-1 infection in combination with shRNA targeting HIV-1 rev

Treatment with RNAi against HIV-1 transcripts efficiently inhibits viral replication but induces selection of escape mutants; therefore, the CCR5 coreceptor was suggested as an additional target. Blocking viral and host transcripts improved the antiviral effect. We have used short hairpin RNA (shRNA) targeting the human CCR5 (shCCR5) or the HIV-1 rev (shRev) transcripts to demonstrate distinctive properties of anti-CCR5 shRNA: shCCR5 induced more sustained protection than shRev; partial reduction in CCR5 expression substantially decreased HIV-1 infection, and shCCR5 performed better than shRev in the mixed shRNA-treated and untreated cultures. These observations indicate that CCR5 inhibitors should be conveniently included in HIV-1 gene silencing treatment schedules when only a certain cell fraction is protected to further reduce endogenous virus in a properly ART-treated HIV-1 infected individual.

Contemporary Distribution, Estimated Age, and Prehistoric Migrations of Old World Monkey Retroviruses

Old World monkeys (OWM), simians inhabiting Africa and Asia, are currently affected by at least four infectious retroviruses, namely, simian foamy virus (SFV), simian immunodeficiency virus (SIV), simian T-lymphotropic virus (STLV), and simian type D retrovirus (SRV). OWM also show chromosomal evidence of having been infected in the past with four more retroviral species, baboon endogenous virus (BaEV), Papio cynocephalus endogenous virus (PcEV), simian endogenous retrovirus (SERV), and Rhesus endogenous retrovirus-K (RhERV-K/SERV-K1). For some of the viruses, transmission to other primates still occurs, resulting, for instance, in the HIV pandemic. Retroviruses are intimately connected with their host as they are normally spread by close contact. In this review, an attempt to reconstruct the distribution and history of OWM retroviruses will be made. A literature overview of the species infected by any of the eight retroviruses as well as an age estimation of the pathogens will be given. In addition, primate genomes from databases have been re-analyzed for the presence of endogenous retrovirus integrations. Results suggest that some of the oldest retroviruses, SERV and PcEV, have travelled with their hosts to Asia during the Miocene, when a higher global temperature allowed simian expansions. In contrast, younger viruses, such as SIV and SRV, probably due to the lack of a primate continuum between the continents in later times, have been restricted to Africa and Asia, respectively.

Isolation and Identification of Subgroup J Avian Leukosis Virus Inducing Multiple Systemic Tumors in Parental Meat-Type Chickens

Avian leukosis virus (ALV) continues evolving to obtain new genomic characters to enhance its pathogenicity. In the present study, an ALV-J strain LH20180301 was isolated from broiler breeder chickens that reached the speak of paralyzation before 20-week-old. The necropsy chickens showed subcutaneous and muscular hemorrhage, and developed tumors in multiple organs including bone, liver, spleen, and kidney. The complete provirus was then cloned and sequenced to investigate the molecular characteristics and oncogenicity etiology of this virus associated with the outbreak of disease. The genomic structure of the reported ALV-J strain LH20180301 was highly conservative with other ALVs. Recombination events between the virus with endogenous virus were identified in the viral genome. Compared with the ALV-J original HPRS-103 strain, the major recombination sites of the viral genome with ev-1 were located in 5′ UTR-gag and 3′ UTR regions. Phylogenetic analysis of group specific antigen gp85 encoding protein showed that the LH20180301 branched with ALV-J prevalent in “yellow chickens” of local breeds in South China. Nine amino acids (N58, D60, K70, A71, K108, N112, N113, N121, R272) in the gp85 were highly conserved among ALV-J isolates before 2012, but various mutations were found in the late isolates including LH20180301. In addition, the LH20180301 strain also had the same deletion pattern of 3′ UTR with them. Therefore, LH20180301 might derive from the same ancestor with those viruses and may be the trend of ALV-J evolution in China. The defined new genomic characters in the gp85 and 3′ UTR region of ALV-J might provide the molecular basis for its enhanced oncogenicity.