Gene Segments Research Articles

Severe fever with thrombocytopenia syndrome virus genotype B in Thailand.

Severe fever with thrombocytopenia syndrome virus (SFTSV) has been reported in many countries in Southeast Asia, which expands the original geographic range of China, Korea, and Japan. Here, we report the complete genome sequences of two Thai SFTSV strains previously identified in patients with undifferentiated febrile illness in 2020. Phylogenetically, both clustered with SFTSV genotype B strains and were most closely related to those previously reported in central China (≥99.0% nucleotide sequence identity) in the L, M, and S gene segments. Nine amino acid residues encoded by one or more Thai SFTSV genomes differed from those found in global strains. Interestingly, the observed differences in numerous residues between the Thai strains suggest possible separate introductions of different variants into the region.

Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response.

The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of 'cryptic' viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.

Hantavirus: an overview and advancements in therapeutic approaches for infection.

Hantaviruses are a significant and emerging global public health threat, impacting more than 200,000 individuals worldwide each year. The single-stranded RNA viruses belong to the Hantaviridae family and are responsible for causing two acute febrile diseases in humans: Hantavirus pulmonary syndrome (HPS) and hemorrhagic fever with renal syndrome (HFRS). Currently, there are no licensed treatments or vaccines available globally for HTNV infection. Various candidate drugs have shown efficacy in increasing survival rates during the early stages of HTNV infection. Some of these drugs include lactoferrin, ribavirin, ETAR, favipiravir and vandetanib. Immunotherapy utilizing neutralizing antibodies (NAbs) generated from Hantavirus convalescent patients show efficacy against HTNV. Monoclonal antibodies such as MIB22 and JL16 have demonstrated effectiveness in protecting against HTNV infection. The development of vaccines and antivirals, used independently and/or in combination, is critical for elucidating hantaviral infections and the impact on public health. RNA interference (RNAi) arised as an emerging antiviral therapy, is a highly specific degrades RNA, with post-transcriptional mechanism using eukaryotic cells platform. That has demonstrated efficacy against a wide range of viruses, both in vitro and in vivo. Recent antiviral methods involve using small interfering RNA (siRNA) and other, immune-based therapies to target specific gene segments (S, M, or L) of the Hantavirus. This therapeutic approach enhances viral RNA clearance through the RNA interference process in Vero E6 cells or human lung microvascular endothelial cells. However, the use of siRNAs faces challenges due to their low biological stability and limited in vivo targeting ability. Despite their successful inhibition of Hantavirus replication in host cells, their antiviral efficacy may be hindered. In the current review, we focus on advances in therapeutic strategies, as antiviral medications, immune-based therapies and vaccine candidates aimed at enhancing the body's ability to control the progression of Hantavirus infections, with the potential to reduce the risk of severe disease.

Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution.

Spliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second 'minor' spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes' greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing's persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.

STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review.

X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.

Natural recombination of the torque teno canis virus within the ORF1, -2, and -3 genes and the untranslated region

The torque teno canis virus (TTCaV) was first reported in 2001 and it shares similarities with the known Torque teno virus (TTV) in terms of genomic organization and putative transcriptional features. It is a single-stranded DNA virus characterized by high rates of recombination and nucleotide substitution, like RNA viruses. Studies reported recombination events in torque teno virus; however, there is limited reporting of TTCaV reorganization events. This study screened fecal samples from domestic dogs in Henan Province. There was a positivity rate of 16.5% (19/115) for TTCaV. Four nearly complete TTCaV genomes, namely Canine/HeNan/4, 5, 6, and 13/2019, were obtained from the 19 positive fecal samples, whose genome sequence was obtained using gap-filling PCR. Sequence analysis revealed two unique amino acid mutation sites in the TTCaV strains, K278Q (compared with the first isolate Cf-TTV10 in Japan) and V/L268I (compared with the TTCaV strain from southern China). Subsequently, 17 near full-length TTCaV genome sequences were subjected to phylogenetic and recombination detection program analyzes. We obtained evidence supporting recombination events in the Chinese TTCaV strains. These findings suggest that mutation and recombination occurred in the three individual gene segments (ORF1, ORF2, ORF3) and the untranslated region, an area of major recombination in the Chinese TTCaV strain GX265 genome. Interestingly, the TTCaV strain (Canine/HeNan/6/2019) was a major parent involved in the genetic recombination of the GX265 strain. This study provides insights into the genetic variability and evolution of TTCaV.

Molecular Characterization of Fungal Isolates of Locally Processed Rice from Five Agro-Ecological Zones of Nigeria

The purpose of this study was to characterize fungal isolates contaminating locally processed rice in Nigeria and to assess the genetic similarity in the fungi isolates. Fungal species were characterized by amplification of a segment of the β-tubulin gene using Bt2aF (5’-GGTAACCAAATCGGTGCTGCTTTC-3’) and Bt2bR (5’ACCCTCAGTGT GT GACCCTTGGC-3’) primers and phylogenetic relationship established using the Maximum Likelihood method. Amplification of between 450 and 550bp of the β-tubulin region of the genomic DNA of the fungal isolates was obtained from thirty-eight samples (89%). Members of Aspergillus section flavi and section nigri groups were differentiated as A. flavus, A. parasiticus, A. tubigensis, A. sydowii and A. niger respectively. Molecular method identified Paecilomycesformosus with 99% similarity index while all the morphologically identified Penicillium species were identified to genus level as P. formosus, P. steckii and P. citrinum with a percentage similarity ranging from 95%-100%. Collectotrichum fruticola and Talaromyces flavus from SGS and NGS zone respectively were documented for the first time in the locally processed rice with 100% and 89% similarity index respectively. All the Aspergillus species were closely related to one another and narrowly diverged from the Penicillium species. Aspergilla and Penicillia were the predominant genera identified and the isolates were genetically similar irrespective of their agroecological zones.

Xenopus Ssbp2 is required for embryonic pronephros morphogenesis and terminal differentiation

The nephron, functional unit of the vertebrate kidney, is specialized in metabolic wastes excretion and body fluids osmoregulation. Given the high evolutionary conservation of gene expression and segmentation patterning between mammalian and amphibian nephrons, the Xenopus laevis pronephric kidney offers a simplified model for studying nephrogenesis. The Lhx1 transcription factor plays several roles during embryogenesis, regulating target genes expression by forming multiprotein complexes with LIM binding protein 1 (Ldb1). However, few Lhx1-Ldb1 cofactors have been identified for kidney organogenesis. By tandem- affinity purification from kidney-induced Xenopus animal caps, we identified single-stranded DNA binding protein 2 (Ssbp2) interacts with the Ldb1–Lhx1 complex. Ssbp2 is expressed in the Xenopus pronephros, and knockdown prevents normal morphogenesis and differentiation of the glomus and the convoluted renal tubules. We demonstrate a role for a member of the Ssbp family in kidney organogenesis and provide evidence of a fundamental function for the Ldb1–Lhx1-Ssbp transcriptional complexes in embryonic development.

The emergence of poultry-adapted H9 subtype avian influenza viruses. Proceeding of The First International Avian Influenza Summit, University of Arkansas- October 16-17, 2023"

Avian influenza is a highly contagious disease that severely affects poultry production and food security. Several countries have developed vaccination programs to prevent and control avian influenza. Unlike currently available vaccines, modified live virus (MLV) vaccines have the potential to be easily mass-applied. Concerns of reversion, recombination, and unintended transmission have slowed the development of MLVs against avian influenza for use in poultry. To address these concerns, we generated reassortment-impaired, non-transmissible, safe, immunogenic, and protective MLVs based on the rearrangement of internal gene segments and additional modifications of the surface gene segments HA and NA. The HA was produced to carry the unique DRPAVIAN peptide marker, whereas NA was modified as a chimera encoding the chicken interleukin-18 (ckIL18) gene (MLV-IL). As a proof of principle and given its economic importance and widespread geographic distribution, we tested the MLV and MLV-IL approaches in chickens against a prototypic H9N2 low pathogenic avian influenza virus (MLV-H9N2 and MLV-H9N2-IL, respectively). \textit{In-vitro}, the MLV-H9N2 and MLV-H9N2-IL candidates were stable and achieved yields similar to the wild-type H9N2 strain. Co-infection studies with a wild-type H9N2 virus showed that the altered HA segment in the MLV-H9N2 and MLV-H9N2-IL candidates has a fitness disadvantage and did not reassort. Likewise, the modified NA segment in the MLV-H9N2-IL candidate was impaired in reassortment. \textit{In-vivo}, the MLV-H9N2 and MLV-H9N2-IL candidates did not transmit chicken-to-chicken via direct contact. MLV-H9N2- and MLV-H9N2-IL-vaccinated chickens showed no clinical signs upon intranasal vaccination, and all were seroconverted. More importantly, including ckIL18 in the MLV-H9N2-IL vaccine enhanced the generation of neutralizing antibodies, suggesting a role in the host immune response. A significant decrease in viral loads post-challenge demonstrated the protective effect of the MLVs. The MLV-H9N2-IL vaccine administered via drinking water was immunogenic in chickens in a dose-dependent manner and generated levels of neutralizing antibodies after prime and boost predictive of protection, which was later confirmed upon aggressive homologous virus challenge. In summary, this work provides the basis for novel and safe MLVs against avian influenza amenable for mass vaccination.

Prevalence and Genomic Characterization of Rotavirus A from Domestic Pigs in Zambia: Evidence for Possible Porcine-Human Interspecies Transmission.

Rotavirus is a major cause of diarrhea globally in animals and young children under 5 years old. Here, molecular detection and genetic characterization of porcine rotavirus in smallholder and commercial pig farms in the Lusaka Province of Zambia were conducted. Screening of 148 stool samples by RT-PCR targeting the VP6 gene revealed a prevalence of 22.9% (34/148). Further testing of VP6-positive samples with VP7-specific primers produced 12 positives, which were then Sanger-sequenced. BLASTn of the VP7 positives showed sequence similarity to porcine and human rotavirus strains with identities ranging from 87.5% to 97.1%. By next-generation sequencing, the full-length genetic constellation of the representative strains RVA/pig-wt/ZMB/LSK0137 and RVA/pig-wt/ZMB/LSK0147 were determined. Genotyping of these strains revealed a known Wa-like genetic backbone, and their genetic constellations were G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1, respectively. Phylogenetic analysis revealed that these two viruses might have their ancestral origin from pigs, though some of their gene segments were related to human strains. The study shows evidence of reassortment and possible interspecies transmission between pigs and humans in Zambia. Therefore, the "One Health" surveillance approach for rotavirus A in animals and humans is recommended to inform the design of effective control measures.

The complete mitochondrial genome of parasitoid wasp Pseudoligosita yasumatsui (Hymenoptera: Trichogrammatidae) and its phylogenetic implications

Pseudoligosita yasumatsui (Viggiani and Rao, 1978) (Hymenoptera: Trichogrammatidae) is an egg parasitoid wasp that preys on rice planthoppers, one of the most significant pests in Asian rice-growing regions. An enriched mitochondrial genome database of rice planthopper egg parasitoids is the basis for phylogenetic analysis. Therefore, the complete mitochondrial genome of P. yasumatsui was sequenced using NGS sequencing. The total length of the mitochondrial genome of P. yasumatsui is 16,036 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR). The mitochondrial genome showed a negative AT skew (-0.09) and a positive GC skew (0.19). Thirteen PCGs all started with ATN codons and ended with TAA. All 22 tRNAs have a typical cloverleaf structure. A comparison with the presumed arthropod ancestral mitochondrial genome using CREx web serve observed a large number of tRNAs as well as PCGs inversions, rearrangements, and inversion reversals of large gene segments (trnE-rrnL). Based on the Bayesian inference (BI) and maximum likelihood (ML) phylogenetic tree of P. yasumatsui and other 14 mitochondrial genomes from the Chalcidoidea superfamily, the phylogenetic relationship of P. yasumatsui within the Trichogrammatidae family was found to be ((Pseudoligosita + Megaphragma) + Trichogamma), and the phylogenetic relationship of five families was (Mymaridae + (Trichogrammatidae + (Aphelinidae + (Eulophidae + Pteromalidae)))). The close relationship between Pseudoligosita and Megaphragma as sister groups was suggested, and the data provide support for the monophyly of Oligositini.

IDENTIFICATION OF ‘TONGKOL’ FISH IN KEDONGANAN FISH MARKET, KUTA, BADUNG DISTRICT, BALI

‘Tongkol’ fishes are species in the family Scombridae. There are many types of ‘tongkol’ fishes, namely longtail tuna, eastern little tuna, frigate tuna and bullet tuna. Morphologically, ‘tongkol’ species are similar to one another. This can result in errors in recording the production of ‘tongkol’ species. The purpose of this study was to identify ‘tongkol’ species collected from Kedonganan Market, Badung, Bali using the COI (Cytochrome C Oxidase Subunit I) gene. Two species of ‘tongkol’ fish were purchased from Kedonganan Market, Badung, Bali. DNA isolation was carried out from fish fins using chelex, followed by amplification of the COI gene segment. The PCR products were then electrophoresed and sequenced. DNA sequences were matched to the database using the Basic Local Alignment Search Tool (BLAST) found in NCBI. Extraction yielded DNA with a concentration of 5.91 ng/ml with a ratio of A260/A280 = 1.3 for sample 1, while for sample 2 the concentration of DNA was 6.27 ng/ml with a ratio of A260/A280 = 1.33. The resulting PCR product is about 700bp in size. The results of the COI gene sequences had a gene size length of 682 bp for both fish species. BLAST analysis yielded a percent identity of 99.84-100% with eastern little tuna (Euthynnus affinis) and bullet tuna (Auxis rochei).

Genome-wide identification, expression analysis, and potential roles under low-temperature stress of bHLH gene family in Prunus sibirica.

The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in Prunus sibirica have not been reported to date. In this study, 104 PsbHLHs were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. PsbHLHs of the same subfamily usually share similar motif compositions and exon-intron structures. PsbHLHs contain multiple stress-responsive elements. PsbHLHs exhibit functional diversity by interacting and coordinating with other members. Twenty PsbHLHs showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in -4°C. The majority of PsbHLHs were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed PsbHLH42 have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of Prunus sibirica.

Fitness Determinants of Influenza A Viruses.

Influenza A (IAV) is a major human respiratory pathogen that causes illness, hospitalizations, and mortality annually worldwide. IAV is also a zoonotic pathogen with a multitude of hosts, allowing for interspecies transmission, reassortment events, and the emergence of novel pandemics, as was seen in 2009 with the emergence of a swine-origin H1N1 (pdmH1N1) virus into humans, causing the first influenza pandemic of the 21st century. While the 2009 pandemic was considered to have high morbidity and low mortality, studies have linked the pdmH1N1 virus and its gene segments to increased disease in humans and animal models. Genetic components of the pdmH1N1 virus currently circulate in the swine population, reassorting with endemic swine viruses that co-circulate and occasionally spillover into humans. This is evidenced by the regular detection of variant swine IAVs in humans associated with state fairs and other intersections of humans and swine. Defining genetic changes that support species adaptation, virulence, and cross-species transmission, as well as mutations that enhance or attenuate these features, will improve our understanding of influenza biology. It aids in surveillance and virus risk assessment and guides the establishment of counter measures for emerging viruses. Here, we review the current understanding of the determinants of specific IAV phenotypes, focusing on the fitness, transmission, and virulence determinants that have been identified in swine IAVs and/or in relation to the 2009 pdmH1N1 virus.

Effects of low-dose ionizing radiation on genomic instability in interventional radiology workers

Interventional radiologists are chronically exposed to low-dose ionizing radiation (IR), which may represent a health risk. The aim of the present study was to evaluate genomic instability by analyzing chromosomal aberrations, micronuclei, and 53BP1 DNA repair foci in peripheral blood lymphocytes of radiologists. Based on the IAEA guidelines on biodosimetry using dicentrics, the average protracted whole-body dose in radiologists were estimated. Since preleukemic fusion genes (PFG) are the primary events leading to leukemia, we also studied their presence by RT-qPCR and FISH. No significant difference in 53BP1 foci and incidence of PFG (MLL-AF4, MLL-AF9, AML1-ETO, BCR-ABL p190) was found in cells of interventional radiologists in comparison to controls. However, our results showed an increased frequency of micronuclei and various types of chromosomal aberrations including dicentrics in interventional radiologists. The average protracted whole body estimated dose was defined at 452.63 mGy. We also found a significantly higher amplification of the MLL gene segment and increased RNA expression in cells of interventional radiologists in comparison to controls. In conclusion, our results showed that long-term low-dose IR induces genomic instability in interventional radiologists.

Exploring spatial and temporal patterns of viral infection across populations of the Melissa blue butterfly

Abstract Identifying patterns of pathogen infection in natural systems is crucial to understanding mechanisms of host–pathogen interactions. In this study, we explored how Junonia coenia densovirus (JcDV) infection varies over space and time in populations of the Melissa blue butterfly (Lycaeides melissa: Lycaenidae) using two different host plants. Collections of L. melissa adults from multiple populations and years, along with host plant tissue and community samples of arthropods found on host plants, were screened to determine JcDV prevalence and load. Additionally, we sampled at multiple time points within a single L. melissa flight season to investigate intra‐annual variation in infection patterns. We found population‐specific variation in viral prevalence of L. melissa across collection years, with historical samples potentially having higher viral prevalence than contemporary samples, although host plant diet was not informative for these patterns. Patterns of infection across multiple generations within a flight season showed that late‐season samples had a higher proportion of JcDV‐positive individuals, suggesting an accumulation of virus over the season. Sequence data from a segment of the JcDV capsid gene showed a lack of viral genetic diversity between L. melissa collected from different localities, and little to no viral particles were found in the surrounding environment. Our discovery of temporal variation in infection suggests that multiple sampling efforts must be made when describing pathogen prevalence in multivoltine hosts. Our findings represent an important first step towards further exploration of the ecological factors mediating disease prevalence and host‐specific variability of infection in wild insect populations.

Molecular Mechanisms of DNA Sequence Selectivity in V(D)J Recombination.

Antigen receptor (AgR) diversity is central to the ability of adaptive immunity in jawed vertebrates to protect against pathogenic agents. The production of highly diverse AgR repertoires is initiated during B and T cell lymphopoiesis by V(D)J recombination, which assembles the receptor genes from component gene segments in a cut-and-paste recombination reaction. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank AgR gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence, and the molecular mechanism for semiselective V(D)J recombination specificity is unknown. The modulation of chromatin structure during V(D)J recombination is essential in the formation of diverse AgRs in adaptive immunity while also reducing the likelihood for off-target recombination events that can result in chromosomal aberrations and genomic instability. Here we review what is presently known regarding mechanisms that facilitate assembly of RAG1/2 with RSSs, the ensuing conformational changes required for DNA cleavage activity, and how the readout of the RSS sequence affects reaction efficiency.

Genome-informed investigation of the molecular evolution and genetic reassortment of severe fever with thrombocytopenia syndrome virus.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a viral pathogen causing significant clinical signs from mild fever with thrombocytopenia to severe hemorrhages. World Health Organization has paid special attention to the dramatic increase in human SFTS cases in China, Japan, and South Korea since the 2010s. The present study investigated the molecular evolution and genetic reassortment of SFTSVs using complete genomic sequences. We collected the complete genome sequences of SFTSVs globally isolated until 2019 (L segment, n = 307; M segment, n = 326; and S segment, n = 564) and evaluated the evolutionary profiles of SFTSVs based on phylogenetic and molecular selection pressure analyses. By employing a time-scaled Bayesian inference method, we found the geographical heterogeneity of dominant SFTSV genotypes in China, Japan, and South Korea around several centuries before and locally spread by tick-born spillover with infrequent long-distance transmission. Purifying selection predominated the molecular evolution of SFTSVs with limited gene reassortment and fixed substitution, but almost all three gene segments appeared to harbor at least one amino acid residue under positive selection. Specifically, the nonstructural protein and glycoprotein (Gn/Gc) genes were preferential selective targets, and the Gn region retained the highest number of positively selected residues. Here, the large-scale genomic analyses of SFTSVs improved prior knowledge of how this virus emerged and evolved in China, Japan, and South Korea. Our results highlight the importance of SFTSV surveillance in both human and non-human reservoirs at the molecular level to fight against fatal human infection with the virus.

Abstract PO-082: Antigen presentation and inflammatory effects on immune surveillance: Window of opportunity metformin monotherapy trial for squamous cell carcinoma of the head and neck (HNSCC)

Abstract Introduction: The tumor microenvironment frequently displays dysregulated cellular metabolism, which contributes to aggressive behavior of the tumor. Though the mechanism of effect is unclear, clinical data suggest an association between metformin and improved outcomes in head and neck squamous cell carcinoma (HNSCC). The aim of this study is to investigate post-metformin treatment effects on the tumor microenvironment (TME) of HNSCC by using spatial RNA sequencing data from a metformin monotherapy window-of-opportunity clinical trial. Methods: This was a single-center prospective clinical trial of metformin in patients with HNSCC and a plan for definitive surgical resection. Primary lesions were biopsied prior to treatment and compared to matched post-treatment surgical specimens. Following biopsy-proven HNSCC diagnosis, metformin was initiated at 500 mg/day and increased to 1,000 mg twice daily by day 6. Spatial RNA sequencing of 18,000+ genes in CD45, CD163, and PanCK segments was conducted using Nanostring’s GeoMx digital spatial profiling (DSP). Sequencing data was analyzed by using unbiased gene set enrichment analysis (GSEA) and reported as a rank in gene list from 18,000+ total genes for post- vs pre-treatment analyses. Results: In all HPV positive, post-treatment samples in all three segments, GSEA demonstrated enrichment of antigen presenting cell types including NK cells, monocytes, and dendritic cells (q< 0.001). Inflammatory and metabolism signatures (IFN-y, IFN-a, oxidative phosphorylation) were enriched after metformin monotherapy in HPV+ samples within the PanCK positive segment (q< 0.001). Epithelial mesenchymal transition (EMT) was noted to be positively enriched while plasma cell signatures were negatively enriched within in HPV- post-treatment samples in the CD163 segment (q< 0.001). Within the CD45 positive segment, enriched expression of mRNAs for ribosomal-protein subsets were noted in T-cell gene sets and not in B-cell gene sets; in the CD45 segment, cytoplasmic ribosomal proteins is the second-most enriched gene set from C2 canonical pathways gene sets. Conclusion: Antigen presentation, inflammation, and ribosomal protein encoding genes were enriched with metformin monotherapy in the window of opportunity setting for HNSCC. Ribosomal proteins may also play a role in antigen presentation and immune surveillance in the post-treatment setting. Further research is required to describe the TME effects of metformin monotherapy and its effects on treatment response. Citation Format: Derek S. Mann, Sruti Tekumalla, Amiti Jain, Jacob Riordan, Alban Linnenbach, Diana Menezes, Ubaldo Martinez-Outschoorn, Joseph M. Curry. Antigen presentation and inflammatory effects on immune surveillance: Window of opportunity metformin monotherapy trial for squamous cell carcinoma of the head and neck (HNSCC) [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-082.

Characterization of novel recombinant mycobacteriophages derived from homologous recombination between two temperate phages.

Comparative analyses of mycobacteriophage genomes reveals extensive genetic diversity in genome organization and gene content, contributing to widespread mosaicism. We previously reported that the prophage of mycobacteriophage Butters (cluster N) provides defense against infection by Island3 (subcluster I1). To explore the anti-Island3 defense mechanism, we attempted to isolate Island3 defense escape mutants on a Butters lysogen, but only uncovered phages with recombinant genomes comprised of regions of Butters and Island3 arranged from left arm to right arm as Butters-Island3-Butters (BIBs). Recombination occurs within two distinct homologous regions that encompass lysin A, lysin B, and holin genes in one segment, and RecE and RecT genes in the other. Structural genes of mosaic BIB genomes are contributed by Butters while the immunity cassette is derived from Island3. Consequently, BIBs are morphologically identical to Butters (as shown by transmission electron microscopy) but are homoimmune with Island3. Recombinant phages overcome antiphage defense and silencing of the lytic cycle. We leverage this observation to propose a stratagem to generate novel phages for potential therapeutic use.