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Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with the nuclear speckle.

Viruses rely on host cellular machinery for replication. After entering the nucleus, the HIV genome accumulates in nuclear niches where it undergoes reverse transcription and integrates into neighboring chromatin, promoting high transcription rates and new virus progeny. Despite antiretroviral treatment, viral genomes can persist in these nuclear niches and reactivate upon treatment interruption, raising the possibility that they could play a role in the establishment of viral reservoirs. The post-nuclear entry dynamics of HIV remain unclear, and understanding these steps is critical for revealing how viral reservoirs are established. In this study, we elucidate the formation of HIV-induced CPSF6 puncta and the domains of CPSF6 essential for this process. We also explore the roles of nuclear speckle scaffold factors, SON and SRRM2, in the biogenesis of these puncta. Through genetic manipulation and depletion experiments, we demonstrate the key role of the intrinsically disordered region of SRRM2 in enlarging nuclear speckles in the presence of the HIV capsid. We identify the FG domain of CPSF6 as essential for both puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 puncta. While the low-complexity regions (LCRs) modulate CPSF6 binding to the viral capsid, they do not contribute to puncta formation, nor do the disordered mixed charge domains (MCDs) of CPSF6. Interestingly, the FG peptide facilitates viral replication. These results demonstrate how HIV evolved to hijack host nuclear factors, enabling its persistence in the host. Of note, this study provides new insights into the underlying interactions between host factors and viral components, advancing our understanding of HIV nuclear dynamics and offering potential therapeutic targets for preventing viral persistence.

Journal Article

Boreal and subarctic freshwaters harbour a diversity of jumbophages.

Bacteriophages (phages) are major drivers of microbial evolution and ecology, yet their diversity and functional roles remain poorly characterized in many natural environments, such as in freshwater systems. In boreal and subarctic freshwater habitats, where bacteria are typically slow-growing and nutrient-limited, phages are predicted to have a critical role in host regulation and horizontal gene exchange. However, only a few isolates have been obtained from such environments, leaving the genetic and functional diversity of these phages largely unexplored. Here, we present a collection of 40 bacteriophages isolated from boreal lakes and rivers using a set of diverse freshwater bacterial hosts. Despite using conventional isolation methods, eight of the isolates possess genomes larger than 200 kilobases and are classified as jumbophages. All jumbophages exhibited myovirus morphology and comparatively slow infection dynamics. These jumbophages include the first known representatives infecting members of Janthinobacterium and Herbaspirillum. Comparative genomic and phylogenetic analyses show that nearly all genomes are distinct from previously described phages, indicating substantial novelty. Diverse auxiliary metabolic and anti-defence systems were identified, including putative NAD+ salvage and acyl carrier protein modules, along with predicted Anti-Thoeris and Anti-CBASS elements. The Pseudomonas-infecting jumbophage Ahti encoded homologues of all 21 core genes that define the nucleus-forming family Chimalliviridae. Additionally, Ahti displayed compartmentalization of DNA during infection, establishing it as the first freshwater nucleus-forming phage. These findings expand our understanding of the ecological, genomic, and functional diversity of phages in boreal environments and highlight the role of freshwater ecosystems as significant reservoirs of novel viral lineages.

anti-defence systems

[Nosogeography of viral hepatitis in the Ukraine over the last 25 years (1952-1976)].

For 25 years of observation the morbidity rate of viral hepatitis in the Ukraine was irregular. In individual regions the morbidity level fluctuated within 2 to 3-fold range. Regions with invariably high or low morbidity levels for viral hepatitis were distributed over the territory of the republic not chaotically, but in zones: a zone with invariably high morbidity rate (western), a zone with morbidity rate corresponding to the average level for the republic (south-western), and a zone with an invariably low morbidity rate (north-eastern). The expediency of dividing the territory into epidemiological areas in respect of viral hepatitis on a regional or republican level is discussed.

Disease Reservoirs

Serological evidence of H1 influenza virus infection among Japanese hogs.

Classical H1 influenza firus infection among Japanese hogs was confirmed in 1978 by serological examination. Of 820 swine sera collected from July 1977 to February 1979 in Miyagi Prefecture, northern Japan, six sera were found to contain haemagglutination inhibition (HI) antibodies to the A/FM/1/47 (H1N1) strain. Of the six sera, one showed a significant high HI antibody titre, which was classified as IgM, to the FM1 strain, but not the other H1N1 variants. These results strongly suggest that hogs may carry an old type of H1 influenza virus. The possible role of pigs as a reservoir of human pandemic influenza strains is discussed.

Animals

In vivo genome editing of central nervous system SIV reservoirs in ART-suppressed rhesus macaques.

Latent human immunodeficiency virus type 1 (HIV-1) reservoirs in the central nervous system (CNS) may sustain viral persistence and neuroinflammation contributing to HIV-associated neurocognitive disorders (HAND) despite suppressive ART. AAV9-delivered CRISPR has successfully edited SIV proviral DNA in peripheral tissues with acceptable safety profiles, but the extent of in vivo genome editing in the brain remains unclear. Using SIV-infected rhesus macaques, we mapped intact proviral DNA across CNS regions and tested systemic AAV9-CRISPR-Cas9 targeting conserved sites within Ψ packaging signal and Gag region. Ten adult rhesus macaques were infected with genetically barcoded SIVmac239, suppressed with ART, then randomized to receive intravenous AAV9-SaCas9 with dual gRNAs (Ψ + Gag) or a Cas9-only control. At necropsy after viral rebound, SIV genomes were detected in multiple brain regions as well as lymphoid tissues, confirming the CNS as a persistent reservoir during ART. Barcode analysis revealed region-specific patterns consistent with compartmentalized CNS persistence. In CRISPR-treated animals, proviral editing was measurable across anatomically distinct CNS sites. These findings demonstrate that intact and potentially replication-competent virus persists in the primate brain under ART and that systemic AAV9-CRISPR can reach and edit proviral DNA in this sanctuary, supporting genome editing as a strategy toward durable remission of CNS reservoirs.

ART

Psittacosis: the reservoir persists.

During a one-year period, 101 parakeets and parrots were submitted for laboratory examination. The birds were sick, dead, or from premises where morbidity had been observed. Tissue specimens from these birds were tested for the presence of Chlamydiapsittaci by two methods. A tissue culture system using McCoy cells treated with 5-iodo-2-deoxyuridine was found to be more sensitive than intraperitoneal inoculation of mice for isolation of the chlamydiae. Chlamydiae were recovered from 21 (34%) of 61 parakeets and 16 (40%) of 40 parrots tested. This high rate of infection persists despite the availability of effective chemotherapeutic regimens for control of chlamydial infection in psittacines. The origins of some of the infected birds were traced to aviaries where subsequent treatment with chlortetracycline was successful in eradication of the chlamydial infection. Other infected birds had been imported recently and could be traced back to quarantine centers where (by law) the birds received chemoprophylaxis for chlamydial infection. Our results suggest that this program is an administrative failure.

Animals

[Relations between human and animal influenza viruses].

The following more important problems are dealth with in the present paper:--antigenic relationships between human and animal influenza viruses;--recombination of human and animal influenza viruses;--epidemiological relationships between human and animal influenza viruses;--the theory of cyclical evolution of influenza viruses.

Animals

Expression of intron-containing HIV-1 RNA induces NLRP1 inflammasome activation in myeloid cells.

Despite the success of antiretroviral therapy in suppressing plasma viremia in people living with human immunodeficiency virus type-1 (HIV-1), persistent viral RNA expression in tissue reservoirs is observed and can contribute to HIV-1-induced immunopathology and comorbidities. Infection of long-lived innate immune cells, such as tissue-resident macrophages and microglia may contribute to persistent viral RNA production and chronic inflammation. We recently reported that de novo cytoplasmic expression of HIV-1 intron-containing RNA (icRNA) in macrophages and microglia leads to MDA5 and MAVS-dependent innate immune sensing and induction of type I IFN responses, demonstrating that HIV icRNA is a pathogen-associated molecular pattern (PAMP). In this report, we show that cytoplasmic expression of HIV-1 icRNA also induces NLRP1 inflammasome activation and IL-1β secretion in macrophages and microglia in an RLR- and endosomal TLR-independent manner. Infection of both macrophages and microglia with either replication-competent or single-cycle HIV-1 induced IL-1β secretion, which was attenuated when cytoplasmic expression of viral icRNA was prevented. While IL-1β secretion was blocked by treatment with caspase-1 inhibitors or knockdown of NLRP1 or caspase-1 expression in HIV-infected macrophages, overexpression of NLRP1 significantly enhanced IL-1β secretion in an HIV-icRNA-dependent manner. Immunoprecipitation analysis revealed interaction of HIV-1 icRNA, but not multiply-spliced HIV-1 RNA, with NLRP1, suggesting that HIV-1 icRNA sensing by NLRP1 is sufficient to trigger inflammasome activation. Together, these findings reveal a pathway of NLRP1 inflammasome activation induced by de novo expressed HIV icRNA in HIV-infected myeloid cells.

HIV-1

[Nature and significance of persistent infections (author's transl)].

The "persistent" viral infections, besides "subclinical" infections, pertain to the vast group of "clinically inapparent" infections. They differ from subclinical infections by a temporally unlimited "co-existence" with the pathogen. Pathogenetically, three forms of development are possible: 1. latent infections, 2. tolerated infections, 3. occult infections. Persistent viral infections are the inexhaustible reservoir for many viruses. To the organism affected they may be of benefit (infection immunity, interference, paraimmunity) or of disadvantage (activation of the infection with conversion into a disease, cause of many chronic, slowly developing disease processes, immunopathogenic consequences), the disadvantages prevailing. To the environment, persistent infections are invisible sources of danger as they produce carriers and chronic carriers.

Carrier State

Morphology and morphogenesis of arenaviruses.

Arenaviruses have unique structural characteristics; they are pleomorphic, have a mean diameter of 110-130 nm, and consist of a membranous envelope with surface projections surrounding an interior containing ribosomes and filaments. Virus particles bud from plasma membranes of infected cells and in many cases large intracytoplasmic inclusion bodies are formed. These characteristics allow generic identification, but not differentiation of individual viruses. Ultrastructural identification of virus particles and pathological processes in infected tissues of man and experimental animals is important in understanding the nature of arenaviral pathogenesis Such identification also contributes to our understanding of the mechanisms of viral shedding and transmission in reservoir host species.

Animals

Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024.

SARS-CoV-2 continues to transmit and evolve in humans and animals. White-tailed deer (Odocoileus virginianus) have been previously identified as a zoonotic reservoir for SARS-CoV-2 with high rates of infection and probable spillback into humans. Here we report sampling 1,127 white-tailed deer (WTD) in Pennsylvania, and a genomic analysis of viral dynamics spanning 1,017 days between April 2021 and January 2024. To assess viral load and genotypes, RNA was isolated from retropharyngeal lymph nodes and analyzed using RT-qPCR and viral whole genome sequencing. Samples showed a 14.64% positivity rate by RT-qPCR. Analysis showed no association of SARS-CoV-2 prevalence with age, sex, or diagnosis with Chronic Wasting Disease. From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. The viral variants identified included 17 Alpha, 11 Delta, and 14 Omicron. Alpha largely stopped circulating in humans around September 2021, but persisted in WTD as recently as March of 2023. Phylodynamic analysis of pooled genomic data from Pennsylvania documents at least 12 SARS-CoV-2 spillovers from humans into WTD, including a recent series of Omicron spillovers. Prevalence was higher in WTD in regions with crop coverage rather than forest, suggesting an association with proximity to humans. Analysis of seasonality showed increased prevalence in winter and spring. Multiple examples of recurrent mutations were identified associated with transmissions, suggesting WTD-specific evolutionary pressures. These data document ongoing infections in white-tailed deer, probable onward transmission in deer, and a remarkable rate of new spillovers from humans.

Animals

Sex Differences in Human Immunodeficiency Virus Persistence and Reservoir Size During Aging.

BACKGROUND: Sex differences in human immunodeficiency virus (HIV) reservoir dynamics remain underexplored. METHODS: Longitudinal samples from virally suppressed midlife women (n = 59, median age 45 years) and age-matched men (n&#x2005;=&#x2005;31) were analyzed retrospectively. At each time point, we measured sex hormones (by means of enzyme-linked immunosorbent assay) and cellular HIV DNA and RNA (by means of digital droplet polymerase chain reaction). Number of inducible HIV RNA+ cells, which provides an upper estimate of the replication-competent reservoir, was quantified longitudinally in a different subset of 14 women, across well-defined reproductive stages. Mixed-effects models included normalized reservoir outcomes and sex, time since antiretroviral therapy (ART) initiation, and the sex-by-time interaction as predictors. RESULTS: At ART initiation, women and men had median (interquartile range [IQR]) CD4+ T-cell counts of 204/&#x3bc;L (83-306/&#x3bc;L) versus 238/&#x3bc;L (120-284/&#x3bc;L), respectively; median ages of 45 (42-48) versus 47 (43-51) years; and median follow-up times of 79.2/&#x3bc;L (60.5-121.1/&#x3bc;L) versus 66.2/&#x3bc;L (43.2-80.6/&#x3bc;L) months. We observed a significant decline of total HIV DNA over time in both men and women (P&#x2005;<&#x2005;.01). However, the rates of change differed significantly between the sexes (P&#x2005;<&#x2005;.01), with women having a significantly slower rate of decline than men, more pronounced with age. By contrast, the levels of inducible HIV RNA increased incrementally over time in women during reproductive aging (P&#x2005;<&#x2005;.01). CONCLUSIONS: In contrast to men, in whom the HIV reservoir steadily declines with aging, the HIV reservoir in women is more dynamic. Total HIV DNA (including intact and defective genomes) declines more slowly in women than in men, while the inducible HIV RNA+ reservoir, which is highly enriched in replication-competent virus, increases in women after menopause.

Aging

Water-bone transmission of influenza A viruses?

The isolation of influenza A viruses from unconcentrated lake water and from fecal samples on the shore of these lakes is reported for the first time. Influenza A viruses, representative of most of the major antigenic subtypes, co-circulate in ducks on the lakes.

Animals