bluuebunny/crossref_metadata_2025 huggingface dataset:
Flavivirus–Host Interaction Landscape Visualized through Genome-Wide CRISPR Screens
Authors: Kanojia Aditi , Sharma Mansi , Shiraz Rishad , Tripathi Shashank
Published: October 2022

Flaviviruses comprise several important human pathogens which cause significant morbidity and mortality worldwide. Like any other virus, they are obligate intracellular parasites. Therefore, studying the host cellular factors that promote or restrict their replication and pathogenesis becomes vital. Since inhibiting the host dependency factors or activating the host restriction factors can suppress the viral replication and propagation in the cell, identifying them reveals potential targets for antiviral therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR) technology has provided an effective means of producing customizable genetic modifications and performing forward genetic screens in a broad spectrum of cell types and organisms. The ease, rapidity, and high reproducibility of CRISPR technology have made it an excellent tool for carrying out genome-wide screens to identify and characterize viral host dependency factors systematically. Here, we review the insights from various Genome-wide CRISPR screens that have advanced our understanding of Flavivirus-Host interactions.
Detection of New H5N1 High Pathogenicity Avian Influenza Viruses in Winter 2021–2022 in the Far East, Which Are Genetically Close to Those in Europe
Authors: Isoda Norikazu , Onuma Manabu , Hiono Takahiro , Sobolev Ivan , Lim Hew , Nabeshima Kei , Honjyo Hisako , Yokoyama Misako , Shestopalov Alexander , Sakoda Yoshihiro
Published: October 2022

Many high pathogenicity avian influenza (HPAI) cases in wild birds due to H5N1 HPAI virus (HPAIV) infection were reported in northern Japan in the winter of 2021–2022. To investigate the epidemiology of HPAIVs brought to Japan from surrounding areas, a genetic analysis of H5 HPAIVs isolated in northern Japan was performed, and the pathogenicity of the HPAIV in chickens was assessed by experimental infection. Based on the genetic analysis of the hemagglutinin gene, pathogenic viruses detected in northern Japan as well as one in Sakhalin, the eastern part of Russia, were classified into the same subgroup as viruses prevalent in Europe in the same season but distinct from those circulating in Asia in winter 2020–2021. High identities of all eight segment sequences of A/crow/Hokkaido/0103B065/2022 (H5N1) (Crow/Hok), the representative isolates in northern Japan in 2022, to European isolates in the same season could also certify the unlikeliness of causing gene reassortment between H5 HPAIVs and viruses locally circulating in Asia. According to intranasal challenge results in six-week-old chickens, 50% of the chicken-lethal dose of Crow/Hok was calculated as 104.5 times of the 50% egg-infectious dose. These results demonstrated that the currently prevalent H5 HPAIVs could spread widely from certain origins throughout the Eurasian continent, including Europe and the Far East, and implied a possibility that contagious viruses are gathered in lakes in the northern territory via bird migration. Active monitoring of wild birds at the global level is essential to estimate the geographical source and spread dynamics of HPAIVs.
The P3N-PIPO Protein Encoded by Wheat Yellow Mosaic Virus Is a Pathogenicity Determinant and Promotes Its Pathogenicity through Interaction with NbRLK6 in Nicotiana benthamiana
Authors: Miao Runpu , Ye Zhuangxin , MacFarlane Stuart , Li Yanjun , Mao Qianzhuo , Tian Yanzhen , Deng Zhiping , Sun Zongtao , Yang Jian , Li Junmin , Yan Fei , Chen Jianping , Yu Chulang
Published: October 2022

Similarly to other potyvirids, the bymovirus wheat yellow mosaic virus (WYMV) encodes a P3N-PIPO protein that is expressed by frameshifting occurring within the open reading frame of the P3 protein. P3N-PIPO is known to be essential for the cell-to-cell movement of several potyviruses, but this has not yet been confirmed for the WYMV. Here, we show that the WYMV P3N-PIPO protein influences disease symptom formation. Infection of Nicotiana benthamiana plants with a potato virus X (PVX)-based vector carrying the WYMV P3N-PIPO gene induced more severe disease symptoms and resulted in higher virus accumulation levels than did infection with PVX lacking the P3N-PIPO gene. N. benthamiana P3N-PIPO-interacting proteins were identified through co-immunoprecipitation (Co-IP) coupled with LC-MS/MS (mass spectrometry), and the interaction between P3N-PIPO and the N. benthamiana receptor-like kinase NbRLK6 was further verified by Co-IP and bimolecular fluorescence complementation (BiFC) of transiently-expressed proteins. Furthermore, our investigation showed that the disease symptom severity and accumulation level of PVX-P3N-PIPO were decreased in N. benthamiana plants when NbRLK6 expression was reduced by tobacco rattle virus-induced gene silencing.
Exploiting V-Gene Bias for Rapid, High-Throughput Monoclonal Antibody Isolation from Horses
Authors: Wibmer Constantinos Kurt , Mashilo Poppy
Published: October 2022

Horses and humans share a close relationship that includes both species’ viromes. Many emerging infectious diseases can be transmitted between horses and humans and can exhibit mortality rates as high as 90% in both populations. Antibody biologics represents an emerging field of rapidly discoverable and potent antiviral therapeutics. These biologics can be used to provide passive immunity, as well as blueprints for the rational design of novel active vaccine antigens. Here, we exploit the limited diversity of immunoglobulin variable genes used by horses to develop a rapid, high-throughput monoclonal antibody discovery pipeline. The antibodies isolated from two horses in this study were developed with near exclusivity from a few highly related germline genes within a single IgHV and IgλV gene family and could be recovered for cloning with just three primer pairs. This variable gene pairing was compatible with both horse and human immunoglobulin G isotypes, confirming the suitability of an equine antibody discovery pipeline for developing novel therapeutics to meet the One Health approach to infectious diseases.
RNA Viruses, Pandemics and Anticipatory Preparedness
Authors: Garcia-Blanco Mariano A. , Ooi Eng Eong , Sessions October M.
Published: October 2022

RNA viruses are likely to cause future pandemics and therefore we must create and organize a deep knowledge of these viruses to prevent and manage this risk. Assuming prevention will fail, at least once, we must be prepared to manage a future pandemic using all resources available. We emphasize the importance of having safe vaccine candidates and safe broad-spectrum antivirals ready for rapid clinical translation. Additionally, we must have similar tools to be ready for outbreaks of RNA viruses among animals and plants. Finally, similar coordination should be accomplished for other pathogens with pandemic potential.
Envelope-Fusion-Syncytium Formation in Microplitis bicoloratus bracovirus Maturation
Authors: Dai Ming-Wu , Luo Kai-Jun
Published: October 2022

The viral envelope is essential for virus maturation. Virus-mediated syncytium formations are induced by viral envelope proteins that cause membrane fusion of the infected cells. Polydnaviridae (Polydnavirus) are enveloped viruses with multiple nucleocapsids, and virions mature in symbiotic parasitoid wasp ovaries. However, the mechanism governing the envelope packaging of multiple nucleocapsids remains unclear. In this study, we used transmission electron microscopy to examine the process whereby multiple nucleocapsids of Microplitis bicoloratus bracovirus are packaged into an envelope and observed envelope-fusion-syncytium formation in symbiotic wasp calyx cells during virus maturation. The virus maturation process in calyx cells comprised four stages: pre-virogenic stroma, virogenic stroma, assembly, and fusion. Each virus contained a single envelope with one nucleocapsid in the assembly stage; multiple envelopes then fused to form a viral envelope with multiple nucleocapsids (i.e., the envelope-fusion-syncytium) around the envelope fusion core in the fusion stage. The envelope-fusion-syncytium then stabilized the virions that were released into the lumen of the ovary across the calyx epithelial layer. The phagocytic calyx epithelial cells on the border of the calyx and ovary lumen cleared the majority of non-enveloped nucleocapsids. In contrast, non-phagocytic calyx epithelial cells with microvilli and a cuticular line between the ovary wall and the lumen remained intact in the ovary lumen. These results indicate that envelope-fusion-syncytium formation is important for packaging multiple nucleocapsids in bracovirus maturation.
Cromileptes altivelis microRNA Transcriptome Analysis upon Nervous Necrosis Virus (NNV) Infection and the Effect of cal-miR-155 on Cells Apoptosis and Virus Replication
Authors: Du Hehe , Cao Zhenjie , Liu Zhiru , Wang Guotao , Wu Ying , Du Xiangyu , Wei Caoying , Sun Yun , Zhou Yongcan
Published: October 2022

MicroRNAs (miRNAs) could regulate various biological processes. Nervous necrosis virus (NNV) is one of the primary germs of the Humpback grouper (Cromileptes altivelis), a commercial fish of great importance for Asian aquaculture. However, there is limited available information on the host-virus interactions of C. altivelis. miRNAs have been shown to play key roles in the host response to infection by a variety of pathogens. To better understand the regulatory mechanism of miRNAs, we constructed miRNA transcriptomes and identified immune-related miRNAs of C. altivelis spleen in response to NNV infection. Reads from the three libraries were mapped onto the Danio rerio reference genome. As a result, a total of 942 mature miRNAs were determined, with 266 known miRNAs and 676 novel miRNAs. Among them, thirty-two differentially expressed miRNAs (DEmiRs) were identified compared to the PBS control. These DEmiRs were targeted on 895 genes, respectively, by using miRanda v3.3a. Then, 14 DEmiRs were validated by qRT-PCR and showed consistency with those obtained from high-throughput sequencing. In order to study the relationship between viral infection and host miRNA, a cell line from C. altivelis brain (CAB) was used to examine the expressions of five known DEmiRs (miR-132-3p, miR-194a, miR-155, miR-203b-5p, and miR-146) during NNV infection. The results showed that one miRNA, cal-miRNA-155, displayed significantly increased expression in response to the virus infection. Subsequently, it was proved that overexpression of cal-miR-155 enhanced cell apoptosis with or without NNV infection and inhibited virus replication in CAB cells. Oppositely, the cal-miRNA-155 inhibitor markedly suppressed apoptosis in CAB cells. The results of the apoptosis-related genes mRNA expression also showed the regulation of cal-miR-155 on the apoptosis process in CAB cells. These findings verify that miR-155 might exert a function as a pro-apoptotic factor in reply to NNV stimulation in CAB cells and help us further study the molecular mechanisms of the pathogenesis of NNV in C. altivelis.
Investigating the Role of African Horse Sickness Virus VP7 Protein Crystalline Particles on Virus Replication and Release
Authors: Bekker Shani , Potgieter Christiaan A. , van Staden Vida , Theron Jacques
Published: October 2022

African horse sickness is a deadly and highly infectious disease of equids, caused by African horse sickness virus (AHSV). AHSV is one of the most economically important members of the Orbivirus genus. AHSV is transmitted by the biting midge, Culicoides, and therefore replicates in both insect and mammalian cell types. Structural protein VP7 is a highly conserved major core protein of orbiviruses. Unlike any other orbivirus VP7, AHSV VP7 is highly insoluble and forms flat hexagonal crystalline particles of unknown function in AHSV-infected cells and when expressed in mammalian or insect cells. To examine the role of AHSV VP7 in virus replication, a plasmid-based reverse genetics system was used to generate a recombinant AHSV that does not form crystalline particles. We characterised the role of VP7 crystalline particle formation in AHSV replication in vitro and found that soluble VP7 interacted with viral proteins VP2 and NS2 similarly to wild-type VP7 during infection. Interestingly, soluble VP7 was found to form uncharacteristic tubule-like structures in infected cells which were confirmed to be as a result of unique VP7-NS1 colocalisation. Furthermore, it was found that VP7 crystalline particles play a role in AHSV release and yield. This work provides insight into the role of VP7 aggregation in AHSV cellular pathogenesis and contributes toward the understanding of the possible effects of viral protein aggregation in other human virus-borne diseases.
Comparison of Quantitative Real-Time PCR and Digital PCR to Detect the Polyomavirus in Merkel Cell Carcinoma
Authors: Barchitta Martina , Maugeri Andrea , Campisi Elisabetta , Magnano San Lio Roberta , Favara Giuliana , Soto Parra Hector Jose , Salvatorelli Lucia , Magro Gaetano , Basile Guido , Agodi Antonella
Published: October 2022

Merkel cell polyomavirus (MCPyV) prevalence in Merkel cell carcinoma (MCC) cases is controversial. The detection and quantification of MCPyV DNA is mainly performed by PCR techniques using formalin-fixed, paraffin-embedded (FFPE) tissues. The aim of this study is to compare the performance of two different molecular techniques, specifically the quantitative Real-Time PCR (qPCR) and digital PCR (dPCR). Samples from 31 cases of MCC excisional surgical biopsies were analyzed. DNA extraction and purification from clinical samples were performed using the QIAcube Qiagen automated nucleic acid extractor. After the extraction, MCPyV was detected by qPCR and dPCR using specially designed primers and probes. Of the 31 MCC samples under study, the MCPyV genome was detected in 11 samples (35%) by qPCR compared with 20 samples (65%) detected by dPCR. Notably, 65% of primary tumors were positive for MCPyV (15/23). The viral genome was detected in 75% of tumors located at UV-exposed sites (6/8), 55% of tumors at partially UV-protected sites (5/9), and 67% of tumors at UV-protected sites (4/6). Our results showed a better sensitivity of dPCR in detecting the MCPyV genome in MCC samples compared with traditional qPCR techniques.
The Performances of Three Commercially Available Assays for the Detection of SARS-CoV-2 Antibodies at Different Time Points Following SARS-CoV-2 Infection
Authors: Syre Heidi , Obreque Marius Eduardo Brå , Dalen Ingvild , Riis Åse Garløv , Berg Åse , Löhr Iren Høyland , Sundal Jon , Kleppe Lars Kåre , Vadla May Sissel , Lenning Ole Bernt , Olofsson Jan Stefan , Mohn Kristin Greve-Isdahl , Tøndel Camilla , Blomberg Bjørn , Trieu Mai Chi , Langeland Nina , Cox Rebecca Jane
Published: October 2022

The aim of this study was to evaluate the performances of three commercially available antibody assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies at different time points following SARS-CoV-2 infection. Sera from 536 cases, including 207 SARS-CoV-2 PCR positive, were tested for SARS-CoV-2 antibodies with the Wantai receptor binding domain (RBD) total antibody assay, Liaison S1/S2 IgG assay and Alinity i nucleocapsid IgG assay and compared to a two-step reference ELISA (SARS-CoV-2 RBD IgG and SARS-CoV-2 spike IgG). Diagnostic sensitivity, specificity, predictive values and Cohen’s kappa were calculated for the commercial assays. The assay’s sensitivities varied greatly, from 68.7% to 95.3%, but the specificities remained high (96.9–99.1%). The three tests showed good performances in sera sampled 31 to 60 days after PCR positivity compared to the reference ELISA. The total antibody test performed better than the IgG tests the first 30 days and the nucleocapsid IgG test showed reduced sensitivity two months or more after PCR positivity. Hence, the test performances at different time points should be taken into consideration in clinical practice and epidemiological studies. Spike or RBD IgG tests are preferable in sera sampled more than two months following SARS-CoV-2 infection.
Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies
Authors: Ramaswamy Kavitha , Rashid Mariya , Ramasamy Selvarajan , Jayavelu Tamilselvan , Venkataraman Sangita
Published: October 2022

RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
Assessment of the Impact of a Toll-like Receptor 2 Agonist Synthetic Lipopeptide on Macrophage Susceptibility and Responses to African Swine Fever Virus Infection
Authors: Franzoni Giulia , Zinellu Susanna , Razzuoli Elisabetta , Mura Lorena , De Ciucis Chiara G. , De Paolis Livia , Carta Tania , Anfossi Antonio G. , Graham Simon P. , Chessa Bernardo , Dei Giudici Silvia , Oggiano Annalisa
Published: October 2022

Toll-like receptor 2 (TLR2) ligands are attracting attention as prophylactic and immunopotentiator agents against pathogens, including viruses. We previously reported that a synthetic diacylated lipopeptide (Mag-Pam2Cys_P48) polarized porcine macrophages towards a proinflammatory antimicrobial phenotype. Here, we investigated its role in modulating monocyte-derived macrophage (moMΦ) responses against African swine fever virus (ASFV), the etiological agent of one of the greatest threats to the global pig industry. Two ASFV isolates were compared: the attenuated NH/P68 and the virulent 26544/OG10. No effect on virus infection nor the modulation of surface markers’ expression (MHC I, MHC II DR, CD14, CD16, and CD163) were observed when Mag-Pam2Cys_P48 treated moMΦ were infected using a multiplicity of infection (MOI) of 1. Mag-Pam2Cys_P48 treated moMΦ released higher levels of IL-1α, IL-1β, IL-1Ra, and IL-18 in response to infection with NH/P68 ASFV compared to 26544/OG10-infected and mock-infected controls. Surprisingly, when infected using a MOI of 0.01, the virulent ASFV 26544/OG10 isolate replicated even slightly more efficiently in Mag-Pam2Cys_P48 treated moMΦ. These effects also extended to the treatment of moMΦ with two other lipopeptides: Mag-Pam2Cys_P80 and Mag-Pam2Cys_Mag1000. Our data suggested limited applicability of TLR2 agonists as prophylactic or immunopotentiator agents against virulent ASFV but highlighted the ability of the virulent 26544/OG10 to impair macrophage defenses.
The Japanese Encephalitis Antigenic Complex Viruses: From Structure to Immunity
Authors: Khare Baldeep , Kuhn Richard J.
Published: October 2022

In the last three decades, several flaviviruses of concern that belong to different antigenic groups have expanded geographically. This has resulted in the presence of often more than one virus from a single antigenic group in some areas, while in Europe, Africa and Australia, additionally, multiple viruses belonging to the Japanese encephalitis (JE) serogroup co-circulate. Morphological heterogeneity of flaviviruses dictates antibody recognition and affects virus neutralization, which influences infection control. The latter is further impacted by sequential infections involving diverse flaviviruses co-circulating within a region and their cross-reactivity. The ensuing complex molecular virus–host interplay leads to either cross-protection or disease enhancement; however, the molecular determinants and mechanisms driving these outcomes are unclear. In this review, we provide an overview of the epidemiology of four JE serocomplex viruses, parameters affecting flaviviral heterogeneity and antibody recognition, host immune responses and the current knowledge of the cross-reactivity involving JE serocomplex flaviviruses that leads to differential clinical outcomes, which may inform future preventative and therapeutic interventions.
Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function
Authors: Lokareddy Ravi K. , Hou Chun-Feng David , Li Fenglin , Yang Ruoyu , Cingolani Gino
Published: October 2022

The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions.
Phylodynamics of Highly Pathogenic Avian Influenza A(H5N1) Virus Circulating in Indonesian Poultry
Authors: Karo-karo Desniwaty , Bodewes Rogier , Restuadi Restuadi , Bossers Alex , Agustiningsih Agustiningsih , Stegeman Jan Arend , Koch Guus , Muljono David Handojo
Published: October 2022

After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis sampling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the divergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and diverged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.
A Review of Bioactive Compounds against Porcine Enteric Coronaviruses
Authors: Duan Cong , Luo Yufeng , Liang Xianming , Wang Xia
Published: October 2022

Pig diarrhea is a universal problem in the process of pig breeding, which seriously affects the development of the pig industry. Porcine enteric coronaviruses (PECoVs) are common pathogens causing diarrhea in pigs, currently including transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV) and swine acute diarrhea syndrome coronavirus (SADS-CoV). With the prosperity of world transportation and trade, the spread of viruses is becoming wider and faster, making it even more necessary to prevent PECoVs. In this paper, the host factors required for the efficient replication of these CoVs and the compounds that exhibit inhibitory effects on them were summarized to promote the development of drugs against PECoVs. This study will be also helpful in discovering general host factors that affect the replication of CoVs and provide references for the prevention and treatment of other CoVs.
Identification of a Novel Solinvivirus with Nuclear Localization Associated with Mass Mortalities in Cultured Whiteleg Shrimp (Penaeus vannamei)
Authors: Cruz-Flores Roberto , Andrade Thales P.D. , Mai Hung N. , Alenton Rod Russel R. , Dhar Arun K.
Published: October 2022

The emergence and spread of disease-causing viruses in shrimp aquaculture is not uncommon. Since 2016, unusual mortalities have been affecting the Brazilian shrimp industry and we have associated these unusual mortalities with a novel variant of infectious myonecrosis virus (IMNV). The transcriptome analysis of these diseased shrimp showed an additional divergent viral sequence that we have assigned to the family Solinviviridae. The novel virus has been tentatively termed Penaeus vannamei solinvivirus (PvSV) (GenBank accession: OP265432). The full-length genome of the PvSV is 10.44 kb (excluding the poly A tail) and codes for a polyprotein of 3326 aa. Five conserved domains coding for a helicase, RdRp, calicivirus coat protein, G-patch and tegument protein were identified. The genome organization of the PvSV is similar to other (Nylan deria fulva virus 1) solinvivirus. A unique feature of this virus that differs from other members of the Solinviviridae is the presence of putative nuclear localization signals. The tissue tropism of this virus is wide, infecting cells of the hepatopancreas, gastrointestinal tract, lymphoid organ and muscle tissue. Another unique feature is that it is the only RNA virus of penaeid shrimp that shows a nuclear localization by in situ hybridization. The PvSV has a wide distribution in Brazil and has been found in the states of Maranhão State (Perizes de Baixo), Piaui State (Mexeriqueira), Ceará State (Camocim, Jaguaruana, Aracati and Alto Santo) and Pará State where it has been detected in coinfections with IMNV. The diagnostic methods developed here (real-time RT-PCR and in situ hybridization) are effective for the detection of the pathogen and should be employed to limit its spread. Furthermore, the identification of the PvSV shows the increasing host range of the relatively new family Solinviviridae.
Crystal Structures of Epstein–Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides
Authors: Suraweera Chathura D. , Hinds Mark G. , Kvansakul Marc
Published: October 2022

Apoptosis is a powerful defense mechanism used by multicellular organisms to counteract viral infection. In response to premature host cell suicide, viruses have evolved numerous countermeasures to ensure cell viability to optimize their replication by encoding proteins homologous in structure and function to cellular pro-survival Bcl-2 proteins. Epstein–Barr virus (EBV), a member of the Gammaherpesviridae, encodes the Bcl-2 homolog BHRF1, a potent inhibitor of Bcl-2-mediated apoptosis. BHRF1 acts by directly targeting Bid and Puma, two proapoptotic proteins of the Bcl-2 family. Here, we determined the crystal structures of BHRF1 bound to peptides spanning the Bcl-2 binding motifs (Bcl-2 homology 3 motif, BH3) of Bid and Puma. BHRF1 engages BH3 peptides using the canonical ligand-binding groove of its Bcl-2 fold and maintains a salt bridge between an Arg residue with a conserved Asp residue in the BH3 motif mimicking the canonical ionic interaction seen in host Bcl-2:BH3 motif complexes. Furthermore, both Bid and Puma utilize a fifth binding pocket in the canonical ligand binding groove of BHRF1 to provide an additional hydrophobic interaction distinct from the interactions previously seen with Bak and Bim. These findings provide a structural basis for EBV-mediated suppression of host cell apoptosis and reveal the flexibility of virus encoded Bcl-2 proteins in mimicking key interactions from the endogenous host signaling pathways.
Phylogeography of Rotavirus G8P[8] Detected in Argentina: Evidence of Transpacific Dissemination
Authors: Degiuseppe Juan Ignacio , Torres Carolina , Mbayed Viviana Andrea , Stupka Juan Andrés
Published: October 2022

Rotavirus is one of the leading causes of diarrhea in children. In 2018, G8P[8], an unusual association of genotypes, was detected with moderate frequency in symptomatic children in Argen-tina, unlike a previous sporadic identification in 2016. The aim of this study was to analyze the dissemination pattern of the G8P[8]-lineage IV strains detected in Argentina. Nucleotide sequences of the VP7 gene of Argentine G8P[8] strains (2016, 2018 and 2019) were studied by discrete phylodynamic analyses, together with other worldwide relevant G8-lineage IV strains. Bayes Factor (BF) was used to assess the strength of the epidemiological association between countries. Phylodynamic analyses determined an evolutionary rate of 3.7 × 10−3 (HDP95%: 1.4 × 10−3–8.2 × 10−3) substitutions/site/year. Likewise, the most recent common ancestor was 32.2 years old, dating back to 1986 (HDP95% = 1984–1988). The spatiotemporal dynamics analysis revealed South Korea as being the country of origin of the Argentine strains (posterior probability of the ancestral state: 0.8471), which was also evidenced by a significant rate of diffusion from South Korea to Argentina (BF: 55.1). The detection of G8 in South America in 2016–2017 was not related to the cases detected in 2018–2019, revealing a new G8 introduction to the region and supporting a transpacific dissemination.
Detection of HPV RNA in Extracellular Vesicles from Neuroendocrine Cervical Cancer Cells
Authors: Alkhilaiwi Faris , Yuan Hang
Published: October 2022

Background: Neuroendocrine carcinoma of the cervix (NECC) is an aggressive and rare type of cervical cancer. The five-year overall survival is low at 30% and there is no standardized therapy based on controlled trials for this type of tumour. Most are locally advanced or metastasized at the time of the diagnosis. Extracellular vesicles (EVs) could be a carrier of viral DNA/RNA, given their vital role in cellular communication. The content of EV derived from NECC cells has not been investigated due to the lack of cell line, and it is not known whether they contain human papillomaviruses (HPV) DNA/RNA or not. Methods: The presence of viral E7 DNA/RNA in EVs purified from a culture of a recently established NECC cell line, GUMC-395, was evaluated by using droplet digital polymerase chain reaction (ddPCR). These EVs were characterized using nanoparticle tracking analysis (NTA) for size distribution, transmission electron microscopy (TEM) for morphology, Western blot for CD63, and bioanalyser for RNA quantity and quality. Results: HPV16 viral-RNA, but not DNA, was detected in EVs from GUMC-395 using ddPCR. NTA identified EVs with a mean diameter of 105.0 nm, TEM confirmed normal morphological shape and size, and Western blot analysis confirmed the presence of EV-associated proteins CD63. The EVs were found to be enriched with small RNAs using a bioanalyser. Conclusions: HPV16 RNA is found in EVs from a neuroendocrine cervical cancer and could be involved in the pathogenesis of the disease and used as a diagnostic biomarker.
Antiviral Activities of Asarones and Rhizomes of Acorus gramineus on Murine Norovirus
Authors: Kim Hyojin , Maeng Jin Young , Lee Dan Bi , Kim Kyung Hyun , Chung Mi Sook
Published: October 2022

Noroviruses (NVs) are a major cause of foodborne diseases worldwide. The rhizomes of Acorus gramineus (AGR) have been used as a traditional medicinal plant and a food additive. In this study, AGR and its bioactive components—α-asarone and β-asarone—showed significant antiviral activities against murine NV (MNV) with pre-treatment, with more than two log reductions in viral plaques. They also demonstrated strong inhibition on binding to A- and O-type saliva by the recombinant P domain derived from human NV (HuNV) GII.4. Both α- and β-asarones also inhibited the binding of the P domain to the receptor at 0.125–1 mM in a concentration-dependent manner and induced a marked reduction in Tm, suggesting that they may reduce structural stability and block receptor binding by the P domain. In simulated digestive conditions, the AGR extract, α-asarone, or β-asarone further showed a significant reduction of MNV plaques by 1.5–2.8 logs. The asarones show a potential for development as a scaffold for anti-NV agents.
Assessment of Adherence to Clinical Guidelines in Patients with Chronic Hepatitis B
Authors: Katwaroe Warshan K. , Brakenhoff Sylvia M. , van der Spek Daniël P. C. , de Knegt Robert J. , van Kleef Laurens A. , de Man Robert A. , van der Meer Adriaan J. P. , Sonneveld Milan J. ,   the ICARUS Study Group
Published: October 2022

Background and aims: Adherence to guidelines is associated with improved long-term outcomes in patients with chronic hepatitis B (CHB). We aimed to study the degree of adherence and determinants of non-adherence to management guidelines in a low endemic country. Methods: We reviewed the medical records of all CHB patients who visited our outpatient clinic in 2020. Adherence to guidelines was assessed based on predefined criteria based on the EASL guidance, and included the initiation of antiviral therapy when indicated, the optimal choice of antiviral therapy based on comorbidities, an assessment of HAV/HCV/HDV/HIV serostatus, renal function monitoring and enrolment in a HCC surveillance program if indicated. The adherence rates were compared across types of outpatient clinic (dedicated viral hepatitis clinic versus general hepatology clinic). Results: We enrolled 482 patients. Among the 276 patients with an indication for antiviral therapy, 268 (97.1%) received treatment. Among the patients with renal and/or bone disease, 26/29 (89.7%) received the optimal choice of antiviral agent. The assessment of HAV/HCV/HDV/HIV serostatus was performed in 86.1/91.7/94.4/78.4%. Among the 91 patients treated with tenofovir disoproxil, 57 (62.6%) underwent monitoring of renal function. Of the 241 patients with an indication for HCC surveillance, 212 (88.3%) were enrolled in a surveillance program. Clinics dedicated to viral hepatitis had superior adherence rates compared to general hepatology clinics (complete adherence rates 63.6% versus 37.2%, p < 0.001). Conclusions: Follow-up at a dedicated viral hepatitis clinic was associated with superior adherence to management guidelines.
Construction of a Vero Cell Line Expressing Human ICAM1 for the Development of Rhinovirus Vaccines
Authors: van den Braak Wouter Johannes Petrus , Monica Bella , Limpens Diana , Rockx-Brouwer Dedeke , de Boer Matthijn , Oosterhoff Dinja
Published: October 2022

Human rhinoviruses (HRVs) are small non-enveloped RNA viruses that belong to the Enterovirus genus within the Picornaviridae family and are known for causing the common cold. Though symptoms are generally mild in healthy individuals, the economic burden associated with HRV infection is significant. A vaccine could prevent disease. The Vero-cell-based viral vaccine platform technology was considered for such vaccine development. Unfortunately, most HRV strains are unable to propagate on Vero cells due to a lack of the major receptor of HRV group A and B, intercellular adhesion molecule (ICAM1, also known as CD54). Therefore, stable human ICAM1 expressing Vero cell clones were generated by transfecting the ICAM1 gene in Vero cells and selecting clones that overexpressed ICAM1 on the cell surface. Cell banks were made and expression of ICAM1 was stable for at least 30 passages. The Vero_ICAM1 cells and parental Vero cells were infected with four HRV prototypes, B14, A16, B37 and A57. Replication of all four viruses was detected in Vero_ICAM1, but not in the parental Vero cells. Altogether, Vero cells expressing ICAM1 could efficiently propagate the tested HRV strains. Therefore, ICAM1-expressing cells could be a useful tool for the development and future production of polyvalent HRV vaccines or other viruses that use ICAM1 as a receptor.
The Epidemiological Features of the SARS-CoV-2 Omicron Subvariant BA.5 and Its Evasion of the Neutralizing Activity of Vaccination and Prior Infection
Authors: Tian Dandan , Nie Wenjian , Sun Yanhong , Ye Qing
Published: October 2022

From December 2021 to May 2022, the Omicron BA.1 and BA.2 subvariants successively became the most dominant strains in many countries around the world. Subsequently, Omicron subvariants have emerged, and Omicron has been classified into five main lineages, including BA.1, BA.2, BA.3, BA.4, BA.5, and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6, BA.5.1, and BA.5.2). The recent emergence of several Omicron subvariants has generated new concerns about further escape from immunity induced by prior infection and vaccination and the creation of new COVID-19 waves globally. In particular, BA.5 (first found in southern Africa, February 2022) displays a higher transmissibility than other Omicron subvariants and is replacing the previously circulating BA.1 and BA.2 in several countries.
210-Day Kinetics of Total, IgG, and Neutralizing Spike Antibodies across a Course of 3 Doses of BNT162b2 mRNA Vaccine
Authors: Lau Chin Shern , Oh May Lin Helen , Phua Soon Kieng , Liang Ya-Li , Aw Tar Choon
Published: October 2022

Introduction: We tested the total spike antibody (S-Ab), IgG/IgM S-Ab, and neutralizing antibody (N-Ab) responses of COVID-19-naïve subjects from before their first BNT162b2 vaccination up to 210 days after boosting. Methods: We studied 136 COVID-19-naïve subjects who received three doses of the Pfizer mRNA vaccine (39 males, 97 females, mean age 43.8 ± 13.5 years) from January 2021 to May 2022. Serum was assessed for total S-Ab (Roche), IgG/M (Abbott), and N-Ab (Snibe). Results: Peak antibody levels were measured 20-30 days after each dose, with booster dosing eliciting significantly higher peak antibodies than the second dose: total S-Ab 2219 vs. 19,551 BAU/mL (difference 16,667 BAU/mL, p < 0.0001); IgG 2270 vs. 2932 BAU/mL (difference 660 BAU/mL, p = 0.04); and N-Ab 3.52 vs. 26.4 µg/mL (difference 21.4 µg/mL, p < 0.0001). Only IgM showed a lower peak post-booster antibody titer (COI 2.11 vs. 0.23, difference 1.63, 95% CI 1.05 to 2.38, p < 0.0001). By 180–210 days after the second or third vaccination, total S-Ab/IgG/N-Ab had decreased by 68.7/93.8/73.6% vs. 82.8/86.3/79.5%. The half-lives of IgG and N-Ab antibodies were longer after the third vaccination (IgG: 65 vs. 34 days, N-Ab: 99 vs. 78 days). Conclusion: Total S-Ab/IgG/N-Ab showed a greater increase post-booster, with IgG/N-Ab having a longer half-life.
Autonomous Vehicle Control Comparison
Authors: Banginwar Pruthvi , Sands Timothy
Published: October 2022

Self-driving features rely upon autonomous control of vehicle kinetics, and this manuscript compares several disparate approaches to control predominant kinetics. Classical control using feedback of state position and velocities, open-loop optimal control, real-time optimal control, double-integrator patching filters with and without gain-tuning, and control law inversion patching filters accompanying velocity control are assessed in Simulink, and their performances are compared. Optimal controls are found via Pontryagin’s method of optimization utilizing three necessary conditions: Hamiltonian minimization, adjoint equations, and terminal transversality of the endpoint Lagrangian. It is found that real-time optimal control and control-law patching filter with velocity control incorporating optimization are the two best methods overall as judged in Monte Carlo analysis by means and standard deviations of position and rate errors and cost.
Exfoliation Syndrome and Exfoliation Glaucoma in the Navajo Nation
Authors: Patil Ayesha , Swiston Cole , Wallace Ryan T. , Paulson Chase , Conley Matthew E. , McCoy Lori , Chaya Craig , Wirostko Barbara
Published: October 2022

(1) Background: Exfoliation syndrome (XFS) is a common cause of secondary open angle glaucoma. In 1971, Faulkner et al. estimated the prevalence of XFS among 50 Navajo Nation residents as 38%. Given that XFS can cause irreversible blindness secondary to glaucoma (XFG), this study aims to identify the current prevalence of XFS among Navajo Nation residents within the Four Corners region of the U.S. (2) Methods: A retrospective chart review was conducted from 2016 to 2021 for patients aged 18 and older. All patients with XFS or XFG diagnosed by slit lamp exam were identified through chart review. (3) Results: Of the 1152 patient charts available for review, eight patients (11 eyes) were diagnosed with XFS with three patients (4 eyes) demonstrating concomitant XFG. Within this XFS population, 50% of the patients identified as male, with a mean age of 73 years. The overall prevalence of XFS was 0.7% and the overall prevalence of XFG was found to be 0.26%. The rate of XFG among patients with XFS was 37.5%. (4) Conclusion: Compared to Faulkner’s study of Navajo Nation residents in 1971, our findings show a considerably lower prevalence of XFS at 0.7%. We present the largest study to date of XFS among this population.
The Role of Carbon to Nitrogen Ratio on the Performance of Denitrifying Biocathodes for Decentralized Wastewater Treatment
Authors: Castro Cynthia J. , Taha Kamal , Kenney Itzé , Yeh Daniel H.
Published: October 2022

Bioelectrochemical systems with denitrifying biocathodes have been of interest for the removal of nitrate in decentralized wastewater treatment applications. Only a few studies have directly focused on this application, but the removal rates have been very low. This study evaluated the operational parameters that affect the nitrate removal of two-chambered microbial fuel cells (MFCs) with a biocathode, particularly, the carbon to nitrogen ratio (C:N) and proton diffusivity across electrode chambers. The results show that proton diffusion across a proton exchange membrane is not a limiting step in nitrogen removal performance. At C:N ratios of 4 and 8, biocathodes with a continuously supplied carbon source at the anode were able to achieve complete nitrogen removal at a rate of 0.97 ± 0.21 and 1.15 ± 0.13 mg N L−1 d−1, respectively. However, as the C:N ratio increased from 4, 8, 16, and 32, the electrode potentials decreased accordingly. Ratio 4 C:N had a cathodic reduction potential of +66.1 ± 5.3 mV vs. SHE and dropped to −78.6 ± 9.8 mV vs. SHE at 32 C:N. The cathode electrode potential can be controlled by way of the carbon concentrations at the anode, which can have major indirect implications on the evolution of cathodic microbial communities that have preference to particular ranges of reduction potentials. The cathodic biofilms in this study were dominated by the phyla Proteobacteria, Acidobacteria, Bacteroidetes and Nitrospirae, which are known to have key denitrifying microorganisms. The genus Stenotrophomonas was found in abundance within the attached cathode biofilm and to a lesser extent in the suspended biomass. Vibrio, Acidobacteria_Gp4, Nitrosomonas, and Candidatus Competibacter were also cultivated in both the suspended and attached biomass. Nitrospira was only found in the attached biofilm. Regardless of operational scheme, nitrogen removal was improved at low C:N ratios, with 8 C:N having the best performance overall. This indicates that higher C:N ratios than were previously explored (>4 C:N) provide sufficient coulombs to facilitate denitrification at the cathode even while the anodic CEs remain low. Reactor design modifications should be considered to fully support robust denitrifying communities, enhancing the overall nitrogen removal for decentralized wastewater treatment applications.
Climate Change Impacts on the Water Resources and Vegetation Dynamics of a Forested Sardinian Basin through a Distributed Ecohydrological Model
Authors: Sirigu Serena , Montaldo Nicola
Published: October 2022

Climate change is impacting Mediterranean basins, bringing warmer climate conditions. The Marganai forest is a natural forest protected under the European Site of Community Importance (Natura 2000), located in Sardinia, an island in the western Mediterranean basin, which is part of the Fluminimaggiore basin. Recent droughts have strained the forest′s resilience. A long-term hydrological database collected from 1922 to 2021 shows that the Sardinian forested basin has been affected by climate change since the middle of the last century, associated with a decrease in winter precipitation and annual runoff, reduced by half in the last century, and an increase of ~1 °C in the mean annual air temperature. A simplified model that couples a hydrological model and a vegetation dynamics model for long-term ecohydrological predictions in water-limited basins is proposed. The model well predicted almost one century of runoff observations. Trees have suffered from the recent warmer climate conditions, with a tree leaf area index (LAI) decreasing systematically due to the air temperature and a vapor pressure deficit (VPD) rise at a rate of 0.1 hPa per decade. Future climate scenarios of the HadGEM2-AO climate model are predicting even warmer conditions in the Sardinian forested basin, with less annual precipitation and higher air temperatures and VPD. Using these climate scenarios, we predicted a further decrease in runoff and tree transpiration and LAI in the basin, with a reduction of tree LAI by half in the next century. Although the annual runoff decreases drastically in the worst scenarios (up to 26%), runoff extremes will increase in severity, outlining future scenarios that are drier and warmer but, at the same time, with an increased flood frequency. The future climate conditions undermine the forest’s sustainability and need to be properly considered in water resources and forest management plans.
Mathematical Modeling-Based Management of a Sand Trap throughout Operational and Maintenance Periods (Case Study: Pengasih Irrigation Network, Indonesia)
Authors: Pradipta Ansita Gupitakingkin , Loc Ho Huu , Nurhady Sigit , Murtiningrum  , Mohanasundaram S. , Park Edward , Shrestha Sangam , Arif Sigit Supadmo
Published: October 2022

Surface irrigation networks in Indonesia are damaged by several factors, and sedimentation is among the most severe challenges. Sand traps play a substantial role in improving irrigation system efficiency by reducing sedimentation. There are two periods in sand trap operation: the operational and maintenance periods. Pengasih is one of the irrigation schemes implemented in the Progo Opak Serang (POS) River Basin, which has a high level of erosion. This study aimed to propose an appropriate management strategy for the Pengasih sand trap as the first barrier in irrigation network sedimentation based on mathematical modeling. The HEC-RAS simulation software was used to simulate the sand trap hydraulic behaviour. The results show that the validated Manning’s coefficient was 0.025. The optimal transport parameters were Laursen for the potential function, Exner 5 for the sorting method, and Rubey for the fall velocity method. The recommended flushing timeframe is 315 min, with a discharge of 2 m3/s. We suggest that the sand trap flushing frequency be performed twice a year, and it can be performed at the end of March and October. This coincides with the end of the first and third planting seasons of the irrigation scheme.