bluuebunny/crossref_metadata_2025 huggingface dataset:
Precursors of Viral Proteases as Distinct Drug Targets
Authors: Majerová Taťána , Novotný Pavel
Published: October 2021

Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
Measles in Vaccinated People: Epidemiology and Challenges in Surveillance and Diagnosis in the Post-Elimination Phase. Spain, 2014–2020
Authors: López-Perea Noemí , Fernández-García Aurora , Echevarría Juan Emilio , de Ory Fernando , Pérez-Olmeda Mayte , Masa-Calles Josefa
Published: October 2021

The MMR vaccination program was introduced in Spain in 1981. Consistently high vaccination coverage has led to Spain being declared free of endemic measles transmission since 2014. A few imported and import-related cases were reported during the post-elimination phase (2014 to 2020), with very low incidence: three cases per million of inhabitants a year, 70% in adults. In the post-elimination phase an increasing proportion of measles appeared in two-dose vaccinated individuals (up to 14%), posing a challenge to surveillance and laboratory investigations. Severity and clinical presentation were milder among the vaccinated. The IgM response varied and the viral load decreased, making the virus more difficult to detect. A valid set of samples (serum, urine and throat swab) is strongly recommended for accurate case classification. One third of measles in fully vaccinated people was contracted in healthcare settings, mainly in doctors and nurses, consistent with the important role of high intensity exposure in measles breakthrough cases. Surveillance protocols and laboratory algorithms should be adapted in advanced elimination settings. Reinforcing the immunity of people working in high exposure environments, such as healthcare settings, and implementing additional infection control measures, such as masking and social distancing, are becoming crucial for the global aim of measles eradication.
Identification of Novel Rodent-Borne Orthohantaviruses in an Endemic Area of Chronic Kidney Disease of Unknown Etiology (CKDu) in Sri Lanka
Authors: Muthusinghe Devinda S. , Shimizu Kenta , Lokupathirage Sithumini M. W. , Wei Zhouoxing , Sarathkumara Yomani D. , Fonseka G. R. Amanda , Senarathne Pavani , Koizumi Nobuo , Kawakami Tomonori , Koizumi Akio , Wickramasinghe Chaminda , Ebihara Hideki , Matsuno Keita , Tsuda Yoshimi , Arikawa Jiro , Gamage Chandika D. , Yoshimatsu Kumiko
Published: October 2021

We reported the genetic evidence of circulating hantaviruses from small mammals captured in a chronic kidney disease of unknown etiology (CKDu) hotspot area of Sri Lanka. The high seroprevalence of anti-hantavirus antibodies against Thailand orthohantavirus (THAIV) has been reported among CKDu patients and rodents in Sri Lankan CKDu hotspots. We captured 116 small mammals from CKDu endemic regions in the Polonnaruwa District of Sri Lanka. Seven animals (five out of 11 Mus booduga and two out of 99 Rattus rattus) were PCR-positive for the hantavirus. A rat-borne sequence was grouped with a THAIV-like Anjozorobe virus. In contrast, Mus-borne sequences belonged to the THAIV lineage, suggesting a novel orthohantavirus species according to the phylogenetic analyses and whole-genome comparisons. Our genetic evidence indicates the presence of two THAIV-related viruses circulating in this CKDu endemic area, suggesting a basis for further investigations to identify the infectious virus in patients with CKDu and the CKDu induction mechanism of these viruses.
Construction, Characterization and Application of Recombinant Porcine Deltacoronavirus Expressing Nanoluciferase
Authors: Fang Puxian , Zhang Huichang , Sun He , Wang Gang , Xia Sijin , Ren Jie , Zhang Jiansong , Tian Liyuan , Fang Liurong , Xiao Shaobo
Published: October 2021

Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, causes diarrhoea in suckling piglets and has the potential for cross-species transmission. No effective PDCoV vaccines or antiviral drugs are currently available. Here, we successfully generated an infectious clone of PDCoV strain CHN-HN-2014 using a combination of bacterial artificial chromosome (BAC)-based reverse genetics system with a one-step homologous recombination. The recued virus (rCHN-HN-2014) possesses similar growth characteristics to the parental virus in vitro. Based on the established infectious clone and CRISPR/Cas9 technology, a PDCoV reporter virus expressing nanoluciferase (Nluc) was constructed by replacing the NS6 gene. Using two drugs, lycorine and resveratrol, we found that the Nluc reporter virus exhibited high sensibility and easy quantification to rapid antiviral screening. We further used the Nluc reporter virus to test the susceptibility of different cell lines to PDCoV and found that cell lines derived from various host species, including human, swine, cattle and monkey enables PDCoV replication, broadening our understanding of the PDCoV cell tropism range. Taken together, our reporter viruses are available to high throughput screening for antiviral drugs and uncover the infectivity of PDCoV in various cells, which will accelerate our understanding of PDCoV.
Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals
Authors: Meekins David A. , Gaudreault Natasha N. , Richt Juergen A.
Published: October 2021

SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human–animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.
SDAV, the Rat Coronavirus—How Much Do We Know about It in the Light of Potential Zoonoses
Authors: Bartak Michalina , Słońska Anna , Bańbura Marcin W , Cymerys Joanna
Published: October 2021

Sialodacryoadenitis virus (SDAV) is known to be an etiological agent, causing infections in laboratory rats. Until now, its role has only been considered in studies on respiratory and salivary gland infections. The scant literature data, consisting mainly of papers from the last century, do not sufficiently address the topic of SDAV infections. The ongoing pandemic has demonstrated, once again, the role of the Coronaviridae family as extremely dangerous etiological agents of human zoonoses. The ability of coronaviruses to cross the species barrier and change to hosts commonly found in close proximity to humans highlights the need to characterize SDAV infections. The main host of the infection is the rat, as mentioned above. Rats inhabit large urban agglomerations, carrying a vast epidemic threat. Of the 2277 existing rodent species, 217 are reservoirs for 66 zoonotic diseases caused by viruses, bacteria, fungi, and protozoa. This review provides insight into the current state of knowledge of SDAV characteristics and its likely zoonotic potential.
Phylogenetic Analysis of European Brown Hare Syndrome Virus Strains from Poland (1992–2004)
Authors: Fitzner Andrzej , Kwit Ewa , Niedbalski Wiesław , Bigoraj Ewelina , Kęsy Andrzej , Rzeżutka Artur
Published: October 2021

European brown hare syndrome (EBHS) is lethal to several species of free-living hares worldwide. The genetic characterization of its virus (EBHSV) strains in European circulation and epidemiological knowledge of EBHSV infections is not yet complete. The study determined the nucleotide sequences of the genomes of EBHSV strains from Poland and analyzed their genetic and phylogenetic relationships to a group of hare lagoviruses. The genome of five virus strains detected in Poland between 1992 and 2004 was obtained by RT-PCR and sequencing of the obtained amplicons. The genetic relationships of the EBHSV strains were analyzed using the full genome and VP60 gene sequences. Additionally, the amino acid sequence of the VP60 gene was analyzed to identify mutations specific to recognized EBHSV subgroups. Partial amplification of the virus open reading frame (ORF)1 and ORF2 regions obtained nearly complete nucleotide genome sequences of the EBHSV strains. Phylogenetic analysis placed them in a GII.1 cluster with other European strains related to nonpathogenic hare caliciviruses. VP60 gene analysis allocated these EBHSV strains to the G1.2, G2.2–2.3 or G3 virus genetic groups. The amino acid sequence differences in the entire genome ranged from 1.1 to 2.6%. Compared to a reference French EBHSV-GD strain, 22 variable amino acid sites were identified in the VP60 region of the Polish strains, but only six were in VP10. Single amino acid changes appeared in different sequence positions among Polish and other European virus strains from different genetic groups, as well as in VP10 sequences of nonpathogenic hare caliciviruses. The results of the study showed a high genetic homogeneity of EBHSV strains from Poland despite their different location occurrence and initial detection times. These strains are also phylogenetically closely related to other EBHSV strains circulating in Europe, likely confirming the slow evolutionary dynamics of this lagovirus species.
The Current Evidence Regarding COVID-19 and Pregnancy: Where Are We Now and Where Should We Head to Next?
Authors: Kalampokas Theodoros , Rapani Anna , Papageorgiou Maria , Grigoriadis Sokratis , Maziotis Evangelos , Anifandis George , Triantafyllidou Olga , Tzanakaki Despoina , Neofytou Spyridoula , Bakas Panagiotis , Simopoulou Mara , Vlahos Nikolaos
Published: October 2021

Despite the volume of publications dedicated to unraveling the biological characteristics and clinical manifestations of SARS-CoV-2, available data on pregnant patients are limited. In the current review of literature, we present an overview on the developmental course, complications, and adverse effects of COVID-19 on pregnancy. A comprehensive review of the literature was performed in PubMed/Medline, Embase, and Cochrane Central databases up to June 2021. This article collectively presents what has been so far reported on the identified critical aspects, namely complications during pregnancy, delivery challenges, neonatal health care, potential routes of viral transmission, including vertical transmission or breastfeeding, along with the risks involved in the vaccination strategy during pregnancy. Despite the fact that we are still largely navigating uncharted territory, the observed publication explosion in the field is unprecedented. The overwhelming need for data is undoubtable, and this serves as the driver for the plethora of publications witnessed. Nonetheless, the quality of data sourced is variable. In the midst of the frenzy for reporting on SARS-CoV-2 data, monitoring this informational overload is where we should head to next, considering that poor quality research may in fact hamper our attempts to prevail against this unparalleled pandemic outbreak.
Neutralization of SARS-CoV-2 Variants by Serum from BNT162b2 Vaccine Recipients
Authors: Valleriani Fabrizia , Mancuso Elisa , Vincifori Giacomo , Teodori Liana , Di Marcantonio Lisa , Spedicato Massimo , Leone Alessandra , Savini Giovanni , Morelli Daniela , Bonfini Barbara , Lorusso Alessio
Published: October 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly, leading to viral lineages characterized by multiple mutations in the spike protein, which could potentially confer to the virus the ability to avoid the vaccine-induced immune response, making the vaccines less effective or ineffective. Here, we initially evaluated the neutralization capabilities in vitro by serum neutralization (SN) of six serum samples collected from recipients of the BNT162b2 vaccine against 11 SARS-CoV-2 isolates belonging to the major SARS-CoV-2 lineages that had been circulating in Italy. Then, we considered 30 additional serum samples by SN assay against the dominant B.1.617.2 (Delta) variant. A B.1 lineage isolate was used as a reference. In the first analysis, significant differences when compared with the reference strain (p > 0.05) were not evidenced; instead, when the panel of 30 sera was tested against the B.1.617.2 (Delta) variant, a significant (p = 0.0015) 2.38-fold reduction in neutralizing titres compared with the reference after the first vaccine dose was demonstrated. After the second vaccine dose, the reduction was not significant (p = 0.1835). This study highlights that the BNT162b2 vaccine stimulates a humoral response able to neutralize all tested SARS-CoV-2 variants, thus suggesting a prominent role in mitigating the impact of the SARS-CoV-2 pandemic in real-world conditions. Long-term follow-up is currently ongoing.
Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program
Authors: Thannesberger Jakob , Edermayr Anna , Karimi Alireza , Mueller Mathias , Karnthaler Ursula , Gauss Richard , Penz Daniela , Ferlitsch Arnulf , Steininger Christoph
Published: October 2021

Currently countries across the globe are preparing for the fourth wave of SARS-CoV-2 infections, which is mainly driven by the rapid spread of novel SARS-CoV-2 variants. Austria and, in particular, the capital city of Vienna, witnessed a disproportionally steep rise in SARS-CoV-2 infection rates during the last wave of infections. By the end of January 2021, the government of Vienna launched an innovative, state-wide SARS-CoV-2 screening program based on PCR analysis of self-collected mouthwash samples. More than 400,000 mouthwash samples were collected in Vienna during the third wave of infection from January to March 2021. All preanalytical and analytical steps were carried out in a highly standardized manner at a single certified testing center. SARS-CoV-2 specific PCR analysis revealed in these samples a positivity rate of 0.43%. The relative proportion of N501Y positive virus samples increased continually to 68% of weekly samples. Mutation K417N was detected only in three samples. With this study, we were able to map the temporal occurrence of SARS-CoV-2 variants in a highly unbiased manner. Positivity rates and variant prevalence rates in this study were lower than in other nationwide programs. The results presented in this study indicate that actual virus prevalence tends to be overestimated by surveillance programs such as results of cluster analysis or contact tracing programs.
Viral Enteritis in Solid-Organ Transplantation
Authors: Abbas Anum , Zimmer Andrea J. , Florescu Diana
Published: October 2021

Solid organ transplant recipients are at increased risk for infections due to chronic immunosuppression. Diarrhea is a commonly encountered problem post transplantation, with infectious causes of diarrhea being a frequent complication. Viral infections/enteritides in solid organ transplant recipients often result from frequently encountered pathogens in this population such as cytomegalovirus, adenovirus, and norovirus. However, several emerging viral pathogens are increasingly being recognized as more sensitive diagnostic techniques become available. Treatment is often limited to supportive care and reduction in immunosuppression, though antiviral therapies mayplay a role in the treatment in certain diseases. Viral enteritis is an important entity that contributes to morbidity and mortality in transplant recipients.
Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea
Authors: Lee Seung-Ho , Kim Kijin , Kim Jongwoo , No Jin Sun , Park Kyungmin , Budhathoki Shailesh , Lee Seung Ho , Lee Jingyeong , Cho Seung Hye , Cho Seungchan , Lee Geum-Young , Hwang Jusun , Kim Heung-Chul , Klein Terry A. , Uhm Chang-Sub , Kim Won-Keun , Song Jin-Won
Published: October 2021

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3′-N-P-M-F-G-L-5′) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews.
Molecular Identification of Prune Dwarf Virus (PDV) Infecting Sweet Cherry in Canada and Development of a PDV Full-Length Infectious cDNA Clone
Authors: Simkovich Aaron J. , Li Yinzi , Kohalmi Susanne E. , Griffiths Jonathan S. , Wang Aiming
Published: October 2021

Prune dwarf virus (PDV) is a member of ilarviruses that infects stone fruit species such as cherry, plum and peach, and ornamentally grown trees worldwide. The virus lacks an RNA silencing suppressor. Infection by PDV either alone, or its mixed infection with other viruses causes deteriorated fruit marketability and reduced fruit yields. Here, we report the molecular identification of PDV from sweet cherry in the prominent fruit growing region of Ontario, Canada known as the Niagara fruit belt using next generation sequencing of small interfering RNAs (siRNAs). We assessed its incidence in an experimental farm and determined the full genome sequence of this PDV isolate. We further constructed an infectious cDNA clone. Inoculation of the natural host cherry with this clone induced a dwarfing phenotype. We also examined its infectivity on several common experimental hosts. We found that it was infectious on cucurbits (cucumber and squash) with clear symptoms and Nicotiana benthamiana without causing noticeable symptoms, and it was unable to infect Arabidopsis thaliana. As generating infectious clones for woody plants is very challenging with limited success, the PDV infectious clone developed from this study will be a useful tool to facilitate molecular studies on PDV and related Prunus-infecting viruses.
Molecular Characterization of the First Alternavirus Identified in Fusarium oxysporum
Authors: Wen Caiyi , Wan Xinru , Zhang Yuanyuan , Du Hongyan , Wei Chenxing , Zhong Rongrong , Zhang Han , Shi Yan , Xie Jiatao , Fu Yanping , Zhao Ying
Published: October 2021

A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting Fusarium oxysporum strain BH19, which was isolated from a fusarium wilt diseased stem of Lilium brownii. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family “Alternaviridae”. Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family “Alternaviridae” members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1—and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family “Alternaviridae”. Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family “Alternaviridae”, and provide a potential agent for the biocontrol of diseases caused by F. oxysporum.
Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
Authors: Hale Richard , Crowley Peter , Dervisevic Samir , Coupland Lindsay , Cliff Penelope R. , Ebie Saidat , Snell Luke B. , Paul Joel , Williams Cheryl , Randell Paul , Pond Marcus , Stanley Keith
Published: October 2021

The emergence of variants of SARS-CoV-2 has created challenges for the testing infrastructure. Although large-scale genome sequencing of SARS-CoV-2 has facilitated hospital and public health responses, access to sequencing facilities globally is variable and turnaround times can be significant, so there is a requirement for rapid and cost-effective alternatives. Applying a polymerase chain reaction (PCR)-based single nucleotide polymorphism (SNP) approach enables rapid (<4 h) identification of SARS-CoV-2 lineages from nucleic acid extracts, through the presence or absence of a panel of defined of genomic polymorphisms. For example, the B.1.1.7 lineage (“UK”, “Alpha”, or “Kent” variant) is characterised by 23 mutations compared to the reference strain, and the most biologically significant of these are found in the S gene. We have developed a SARS-CoV-2 typing assay focused on five positions in the S gene (HV69/70, N501, K417, E484 and P681). This configuration can identify a range of variants, including all the “Variants of Concern” currently designated by national and international public health bodies. The panel has been evaluated using a range of clinical isolates and standardised control materials at four UK hospitals and shows excellent concordance with the known lineage information derived from full sequence analysis. The assay has a turnaround time of about three hours for a set of up to 24 samples and has been utilised to identify emerging variants in a clinical setting.
USP38 Inhibits Zika Virus Infection by Removing Envelope Protein Ubiquitination
Authors: Wang Yingchong , Li Qin , Hu Dingwen , Gao Daolong , Wang Wenbiao , Wu Kailang , Wu Jianguo
Published: October 2021

Zika virus (ZIKV) is a mosquito-borne flavivirus, and its infection may cause severe neurodegenerative diseases. The outbreak of ZIKV in 2015 in South America has caused severe human congenital and neurologic disorders. Thus, it is vitally important to determine the inner mechanism of ZIKV infection. Here, our data suggested that the ubiquitin-specific peptidase 38 (USP38) played an important role in host resistance to ZIKV infection, during which ZIKV infection did not affect USP38 expression. Mechanistically, USP38 bound to the ZIKV envelope (E) protein through its C-terminal domain and attenuated its K48-linked and K63-linked polyubiquitination, thereby repressed the infection of ZIKV. In addition, we found that the deubiquitinase activity of USP38 was essential to inhibit ZIKV infection, and the mutant that lacked the deubiquitinase activity of USP38 lost the ability to inhibit infection. In conclusion, we found a novel host protein USP38 against ZIKV infection, and this may represent a potential therapeutic target for the treatment and prevention of ZIKV infection.
RNA-Seq Analysis of Influenza A Virus-Induced Transcriptional Changes in Mice Lung and Its Possible Implications for the Virus Pathogenicity in Mice
Authors: Ma Tianxin , Nagy Abdou , Xu Guanlong , Xin Lingxiang , Bao Danqi , Lu Chenyang , Niu Shiqi , Wu Zihua , Ren Chaochao , Zhang Ting , Yang Jianmei , Teng Qiaoyang , Li Xuesong , Li Zejun , Liu Qinfang
Published: October 2021

The influenza A virus (IAV) is an important cause of respiratory disease worldwide. It is well known that alveolar epithelial cells are the target cells for the IAV, but there is relatively limited knowledge regarding the role of macrophages during IAV infection. Here, we aimed to analyze transcriptome differences in mouse lungs and macrophage (RAW264.7) cell lines infected with either A/California/04/2009 H1N1 (CA09) or A/chicken/SD/56/2015 H9N2 (SD56) using deep sequencing. The uniquely differentially expressed genes (UDEGs) were analyzed with the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases; the results showed that the lungs infected with the two different viruses had different enrichments of pathways and terms. Interestingly, CA09 virus infection in mice was mostly involved with genes related to the extracellular matrix (ECM), while the most significant differences after SD56 infection in mice were in immune-related genes. Gene set enrichment analysis (GSEA) of RAW264.7 cells revealed that regulation of the cell cycle was of great significance after CA09 infection, whereas the regulation of the immune response was most enriched after SD56 infection, which was consistent with analysis results in the lung. Similar results were obtained from weighted gene co-expression network analysis (WGCNA), where cell cycle regulation was extensively activated in RAW264.7 macrophages infected with the CA09 virus. Disorder of the cell cycle is likely to affect their normal immune regulation, which may be an important factor leading to their different prognoses. These results provide insight into the mechanism of the CA09 virus that caused a pandemic and explain the different reactivities of monocytes/macrophages infected by H9N2 and H1N1 IAV subtypes.
A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae
Authors: Materatski Patrick , Jones Susan , Patanita Mariana , Campos Maria Doroteia , Dias António Bento , Félix Maria do Rosário , Varanda Carla M. R.
Published: October 2021

Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA-A and DNA-B) of the OEGV-PT is similar to Old World begomoviruses in length, but it lacks a pre-coat protein (AV2), which is a typical feature of New World begomoviruses (NW). DNA-A genome organization is closer to NW, containing four ORFs; three in complementary-sense AC1/Rep, AC2/TrAP, AC3/REn and one in virion-sense AV1/CP, but no AC4, typical of begomoviruses. DNA-B comprises two ORFs; MP in virion sense with higher similarity to the tyrosine phosphorylation site of NW, but in opposite sense to begomoviruses; BC1, with no known conserved domains in the complementary sense and no NSP typical of bipartite begomoviruses. Our results show that OEGV presents the longest common region among the begomoviruses, and the TATA box and four replication-associated iterons in a completely new arrangement. We propose two new putative conserved regions for the geminiviruses CP. Lastly, we highlight unique features that may represent a new evolutionary direction for geminiviruses and suggest that OEGV-PT evolution may have occurred from an ancient OW monopartite Begomovirus that lost V2 and C4, gaining functions on cell-to-cell movement by acquiring a DNA-B component.
Immune Responses to Orally Administered Recombinant Lactococcus lactis Expressing Multi-Epitope Proteins Targeting M Cells of Foot-and-Mouth Disease Virus
Authors: Zhang Fudong , Zhang Zhongwang , Li Xian , Li Jiahao , Lv Jianliang , Ma Zhongyuan , Pan Li
Published: October 2021

Foot and mouth disease virus (FMDV), whose transmission occurs through mucosal surfaces, can also be transmitted through aerosols, direct contact, and pollutants. Therefore, mucosal immunity can efficiently inhibit viral colonization. Since vaccine material delivery into immune sites is important for efficient oral mucosal vaccination, the M cell-targeting approach is important for effective vaccination given M cells are vital for luminal antigen influx into the mucosal lymph tissues. In this study, we coupled M cell-targeting ligand Co1 to multi-epitope TB1 of FMDV to obtain TB1-Co1 in order to improve delivery efficiency of the multi-epitope protein antigen TB1. Lactococcus lactis (L. lactis) was engineered to express heterologous antigens for applications as vaccine vehicles with the ability to elicit mucosal as well as systemic immune responses. We successfully constructed L. lactis (recombinant) with the ability to express multi-epitope antigen proteins (TB1 and TB1-Co1) of the FMDV serotype A (named L. lactis-TB1 and L. lactis-TB1-Co1). Then, we investigated the immunogenic potential of the constructed recombinant L. lactis in mice and guinea pigs. Orally administered L. lactis-TB1 as well as L. lactis-TB1-Co1 in mice effectively induced mucosal secretory IgA (SIgA) and IgG secretion, development of a strong cell-mediated immune reactions, substantial T lymphocyte proliferation in the spleen, and upregulated IL-2, IFN-γ, IL-10, and IL-5 levels. Orally administered ligand-conjugated TB1 promoted specific IgG as well as SIgA responses in systemic and mucosal surfaces, respectively, when compared to orally administered TB1 alone. Then, guinea pigs were orally vaccinated with L. lactis-TB1-Co1 plus adjuvant CpG-ODN at three different doses, L. lactis-TB1-Co1, and PBS. Animals that had been immunized with L. lactis-TB1-Co1 plus adjuvant CpG-ODN and L. lactis-TB1-Co1 developed elevated antigen-specific serum IgG, IgA, neutralizing antibody, and mucosal SIgA levels, when compared to control groups. Particularly, in mice, L. lactis-TB1-Co1 exhibited excellent immune effects than L. lactis-TB1. Therefore, L. lactis-TB1-Co1 can induce elevations in mucosal as well as systemic immune reactions, and to a certain extent, provide protection against FMDV. In conclusion, M cell-targeting approaches can be employed in the development of effective oral mucosa vaccines for FMDV.
The Novel PKC Activator 10-Methyl-Aplog-1 Combined with JQ1 Induced Strong and Synergistic HIV Reactivation with Tolerable Global T Cell Activation
Authors: Washizaki Ayaka , Murata Megumi , Seki Yohei , Kikumori Masayuki , Tang Yinpui , Tan Weikeat , Wardani Nadita P. , Irie Kazuhiro , Akari Hirofumi
Published: October 2021

The presence of latent human immunodeficiency virus (HIV) reservoirs is a major obstacle to a cure. The “shock and kill” therapy is based on the concept that latent reservoirs in HIV carriers with antiretroviral therapy are reactivated by latency-reversing agents (LRAs), followed by elimination due to HIV-associated cell death or killing by virus-specific cytotoxic T lymphocytes. Protein kinase C (PKC) activators are considered robust LRAs as they efficiently reactivate latently infected HIV. However, various adverse events hamper the intervention trial of PKC activators as LRAs. We found in this study that a novel PKC activator, 10-Methyl-aplog-1 (10MA-1), combined with an inhibitor of bromodomain and extra-terminal domain motifs, JQ1, strongly and synergistically reactivated latently infected HIV. Notably, higher concentrations of 10MA-1 alone induced the predominant side effect, i.e., global T cell activation as defined by CD25 expression and pro-inflammatory cytokine production in primary CD4+ T lymphocytes; however, JQ1 efficiently suppressed the 10MA-1-induced side effect in a dose-dependent manner. Considering the reasonable accessibility and availability of 10MA-1 since the chemical synthesis of 10MA-1 requires fewer processes than that of bryostatin 1 or prostratin, our results suggest that the combination of 10MA-1 with JQ1 may be a promising pair of LRAs for the clinical application of the “shock and kill” therapy.
Swinepox Virus Strains Isolated from Domestic Pigs and Wild Boar in Germany Display Altered Coding Capacity in the Terminal Genome Region Encoding for Species-Specific Genes
Authors: Kaiser Franziska K. , Wiedemann Anastasia , Kühl Bianca , Menke Laura , Beineke Andreas , Baumgärtner Wolfgang , Wohlsein Peter , Rigbers Kerstin , Becher Paul , Peters Martin , Osterhaus Albert D. M. E. , Ludlow Martin
Published: October 2021

Swinepox virus (SWPV) is a globally distributed swine pathogen that causes sporadic cases of an acute poxvirus infection in domesticated pigs, characterized by the development of a pathognomonic proliferative dermatitis and secondary ulcerations. More severe disease with higher levels of morbidity and mortality is observed in congenitally SWPV-infected neonatal piglets. In this study, we investigated the evolutionary origins of SWPV strains isolated from domestic pigs and wild boar. Analysis of whole genome sequences of SWPV showed that at least two different virus strains are currently circulating in Germany. These were more closely related to a previously characterized North American SWPV strain than to a more recent Indian SWPV strain and showed a variation in the SWPV-specific genome region. A single nucleotide deletion in the wild boar (wb) SWPV strain leads to the fusion of the SPV019 and SPV020 open reading frames (ORFs) and encodes a new hypothetical 113 aa protein (SPVwb020-019). In addition, the domestic pig (dp) SWPV genome contained a novel ORF downstream of SPVdp020, which encodes a new hypothetical 71aa protein (SPVdp020a). In summary, we show that SWPV strains with altered coding capacity in the SWPV specific genome region are circulating in domestic pig and wild boar populations in Germany.
Escherichia coli Reduction in Water by Zero-Valent Iron–Sand Filtration Is Based on Water Quality Parameters
Authors: Kim Seongyun , Eckart Katherine , Sabet Sarah , Chiu Pei C. , Sapkota Amy Rebecca , Handy Eric T. , East Cheryl L. , Kniel Kalmia E. , Sharma Manan
Published: October 2021

Improving the microbial quality of agricultural water through filtration can benefit small farms globally. The incorporation of zero-valent iron (ZVI) into sand filters (ZVI–sand) has been effective in reducing E. coli, Listeria spp., and viruses from agricultural water. This study evaluated ZVI–sand filtration in reducing E. coli levels based on influent water type and the percentage of ZVI in sand filters. A ZVI–sand filter (50% ZVI/50% sand) significantly (p < 0.001) reduced E. coli levels in deionized water by more than 1.5 log CFU/mL compared to pond water over six separate trials, indicating that water type impacts E. coli removal. Overall reductions in E. coli in deionized water and pond water were 98.8 ± 1.7% and 63 ± 24.0% (mean ± standard deviation), respectively. Filters constructed from 50% ZVI/50% sand showed slightly more reduction in E. coli in pond water than filters made from a composition of 35% ZVI/65% sand; however, the difference was not statistically significant (p = 0.48). Principal component analysis identified that the turbidity and conductivity of influent water affected E. coli reductions in filtered water in this study. ZVI–sand filtration reduces Escherichia coli levels more effectively in waters that contain low turbidity values.
Biochar and Zeolite as Alternative Biofilter Media for Denitrification of Aquaculture Effluents
Authors: Paul Diplina , Hall Steven G.
Published: October 2021

Denitrification processes are crucial in aquaculture as they convert the undesirable nitrate to safer forms of nitrogen. Conventionally, plastic media are used for the biofiltration of wastewater. However, alternative media may be as effective/better than plastic and enhance the sustainability of the system. This study evaluated biochar and zeolite as alternatives for the denitrification of aquaculture effluents. Triplicates of laboratory-scale bioreactors were fabricated to compare the denitrification efficiencies of biochar and zeolite to that of plastic. The bioreactors were fed synthetic aquaculture wastewater having nitrate loading rates of 50, 125, and 150 mg/L. Zeolite exhibited highest values of surface roughness in terms of arithmetic mean height (0.89 µm), maximum height (6.52 µm), and root-mean-square height (1.17 µm), as corroborated by surface profilometry and scanning electron microscopy. The results revealed that under pseudo-steady-state conditions, zeolite displayed the highest nitrate removal efficiency (maximum 95.02 ± 0.01%), which was followed by biochar and plastic (maximum 92.91 ± 0.01% and 92.57 ± 0.02%, respectively) due to its extraordinary surface roughness that provided better adhesion to the bacteria. However, by the end of the study, all the media exhibited comparable rates. Thus, both zeolite and biochar are sustainable alternatives of biomedia for nitrate removal. However, time and labor constraints must be accounted for to scale-up such bioreactors.
Photocatalytic Treatment of Stained Wastewater Coming from Handicraft Factories. A Case Study at the Pilot Plant Level
Authors: Murcia Mesa Julie Joseane , Hernández Niño Jhon Sebastián , González Wilson , Rojas Hugo , Hidalgo María Carmen , Navío José Antonio
Published: October 2021

UV/H2O2 process and TiO2-based photocatalysis were studied in the present work. The effectiveness of these methods was tested in the treatment of effluents taken from handicraft factories. Microorganisms, dyes, and different organic pollutants were detected in the industrial effluents. The experimental procedure for the wastewater treatment was carried out in a patented sunlight reactor on a pilot plant scale. From this study, UV/H2O2 was found to be the best treatment for dye elimination. The optimal peroxide dosage for the degradation of dyes and the elimination of bacteria was 0.07 M. In this case, 70.80% of discoloration was achieved after 7 h of sunlight exposure, under an average sunlight intensity of 3.42 W/m2. The photocatalytic treatment based on TiO2 achieved the highest elimination of coliform bacteria and the lowest TOC value; however, the presence of this material in the reactor had a detrimental effect on the overall elimination of dyes. A combination of both UV/H2O2 and TiO2 treatments significantly improves the dyes discoloration, the elimination of bacteria, and the organic compounds degradation. Some of the results of this study were presented at the 4th Congreso Colombiano de Procesos Avanzados de Oxidación, 4CCPAOx.
Numerical Investigation of Hydraulics in a Vertical Slot Fishway with Upgraded Configurations
Authors: Ahmadi Mohammad , Ghaderi Amir , MohammadNezhad Hossein , Kuriqi Alban , Di Francesco Silvia
Published: October 2021

The implementation of vertical slot fishway (VSF) has been demonstrated to be an effective mitigation measure to alleviate extensive river fragmentation by artificial hydraulic structures such as weirs and dams. However, non-suitable flow velocity and turbulent kinetic energy significantly affect fish swimming behavior and, as a result, hinder such facilities’ performance. Therefore, this study’s main objective is to propose a new configuration of VSF that can allow the passage of different fish species under frequent variations of flow discharge. To achieve that objective several novel configurations of VSF were numerically investigated using the FLOW-3D® model. Namely, five variants of angles between baffles, four different pool widths, and another upgraded version of VSF by introducing cylindrical elements positioned after the opening behind the baffles were tested. Results show that smaller angles between baffles increase the Vmax and decrease the maximum turbulent kinetic energy (TKEmax); the opposite result was obtained when increasing angles between baffles. Namely, the Vmax was increased up to 17.9% for α = 0° and decreased up to 20.37% for α = 37°; in contrast, TKEmax decreased up to −20% for α = 0° and increased up to 26.5% for α = 37°. Narrowing the pool width increased the Vmax linearly; nevertheless, it did not significantly affect the TKEmax as the maximum difference was only +3.5%. Using cylinders with a large diameter decreased the Vmax and increased TKEmax; in contrast, using cylinders with smaller diameters further reduced the Vmax velocity inside the pool while increasing the TKEmax. However, in the case of cylinders, the dimension of the recirculation depended on the configuration and arrangement of the cylinder within the pool. Overall, the maximum velocity was reached at near 77% of the water depth in all cases. Finally, solution-oriented findings resulted from this study would help water engineers to design cost-effective VSF fishways to support the sustainable development of hydraulic structures while preserving aquatic biodiversity.
Crop Field Level Estimation of Nitrogen Input from Fertilizer Use in Jeju Island, South Korea: Management Methods to Prevent Groundwater NO3-N Contamination
Authors: Koh Eun-Hee , Hyun Beom-Seok , Lee Eunhee , Kim Min-Chul , Kang Bong-Rae , Park Won-Bae , Jun Seong-Chun
Published: October 2021

The application of synthetic nitrogen (N) fertilizers has boosted crop yields globally. However, it has also imposed on environmental pollution problems. An estimation of actual fertilizer N inputs at the crop field level is needed to establish effective N management plans to control groundwater NO3-N contamination. Here, a survey to collect the types of cultivated crop and fertilizer application rate was conducted during 2016–2018, covering 44,253 small crop fields (7730 ha) in the western part (Hanrim and Hankyung regions) of Jeju Island, South Korea. Foreign vegetables, citrus fruits, and bulb vegetables are the major crop types grown in the total cultivated areas of 2165.6 ha, 1718.7 ha, and 944.9 ha, respectively. For several crops (green garlic, potato, and chives), the over-use of N fertilizers is observed, the amount of which is 1.73–4.95 times greater than the standard fertilizer application rate. The highest level of fertilizer N input is observed for bulb vegetables in both the regions (Hanrim: 500.5 kg/ha, Hankyung: 487.1 kg/ha), with nearly 80% of the N fertilizer input turned into surplus N loading. A comparison between a spatial interpolation map of the fertilizer N input and that of the groundwater NO3-N concentration implies that the excessive use of synthetic fertilizer results in the degradation of groundwater quality by NO3-N. N management plans for the study area are suggested based on the N fertilizer input at the crop field level. This study highlights that sustainable N management plans should be arranged at the crop field level, considering the spatial heterogeneity of N fertilizer use.
Analysis of the Effect of Daily Water Intake on Oral Health: Result from Seven Waves of a Population-Based Panel Study
Authors: Kim Yu-Rin
Published: October 2021

Proper moisture is an essential condition for maintaining the homeostasis of the body, enhancing immunity, and preventing constipation, and it is an indispensable substance for maintaining human life and health. As the bacteria that cause oral disease are affected by water intake, there is a strong relationship between water intake and oral disease. Therefore, the purpose of this study is to determine the effect of daily water intake on oral disease. The data analyzed were from a seven-year period (2010–2017) from the National Health and Nutrition Survey, conducted annually by the Korea Centers for Disease Control and Prevention. Out of a total of 48,422 people, 134 people in the ‘<1 cup’ group, 27,223 people in the ‘1–4 cups’ group, 14,693 people in the ‘5–7 cups’ group and 6372 people in the ‘>7 cups’ group were selected as subjects. Each time a person drank one less cup of water per day, the prevalence of periodontal disease increased by 1.018 times, the prevalence of dental caries increased by 1.032 times, and the experience of dental caries increased by 1.075 times. Even in Model 2, for which age and gender were adjusted, there was a significant effect. In addition, there was a significant impact in Model 3, which adjusted for oral health behavior, except for permanent caries prevalence. Based on the above results, oral health behavior and state were positive in those who consumed more water per day. Therefore, it is suggested that the government’s active promotion of water intake recommendations and policies should be prepared to include water intake as a component of improving oral health.
Assessing the Impact of Soil Moisture on Canopy Transpiration Using a Modified Jarvis-Stewart Model
Authors: Yu Songping , Guo Jianbin , Liu Zebin , Wang Yanhui , Ma Jing , Li Jiamei , Liu Fan
Published: October 2021

In dryland regions, soil moisture is an important limiting factor for canopy transpiration (T). Thus, clarifying the impact of soil moisture on T is critical for comprehensive forest—water management and sustainable development. In this study, T, meteorological factors (reference evapotranspiration, ETref), soil moisture (relative soil water content, RSWC), and leaf area index (LAI) in a Larix principis-rupprechtii plantation of Liupan Mountains in the dryland region of Northwest China were simultaneously monitored during the growing seasons in 2017–2019. A modified Jarvis—Stewart model was established by introducing the impact of RSWC in different soil layers (0–20, 20–40, and 40–60 cm, respectively) to quantify the independent contribution of RSWC of different soil layers to T. Results showed that with rising ETref, T firstly increased and then decreased, and with rising RSWC and LAI, T firstly increased and then gradually stabilised, respectively. The modified Jarvis—Stewart model was able to give comparable estimates of T to those derived from sap flow measurements. The contribution of RSWC to T in different soil layers has obvious specificity, and the contribution rate of 20–40 cm (13.4%) and 0–20 cm soil layers (6.6%) where roots are mainly distributed is significantly higher than that of 40–60 cm soil layer (1.9%). As the soil moisture status changes from moist (RSWC0–60cm ≥ 0.4) to drought (RSWC0–60cm < 0.4), the role of the soil moisture in the 0–20 cm soil layer increased compared with other layers. The impacts of soil moisture that were coupled into the Jarvis—Stewart model can genuinely reflect the environmental influence and can be used to quantify the contributions of soil moisture to T. Thus, it has the potential to become a new tool to guide the protection and management of forest water resources.