Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2013)

Functional role of geminivirus encoded proteins in the host: Past and present

During plant-pathogen interaction, plant exhibits a strong defense system utilizing diverse groups of proteins to suppress the infection and subsequent establishment of the pathogen. However, in response, pathogens trigger an anti-silencing mechanism to overcome the host defense machinery. Among plant viruses, geminiviruses are the second largest virus family with a worldwide distribution and continue to be production constraints to food, feed, and fiber crops. These viruses are spread by a diverse group of insects, predominantly by whiteflies, and are characterized by a single-stranded DNA (ssDNA) genome coding for four to eight proteins that facilitate viral infection. The most effective means to managing these viruses is through an integrated disease management strategy that includes virus-resistant cultivars, vector management, and cultural practices. Dynamic changes in this virus family enable the species to manipulate their genome organization to respond to external changes in the environment. Therefore, the evolutionary nature of geminiviruses leads to new and novel approaches for developing virus-resistant cultivars and it is essential to study molecular ecology and evolution of geminiviruses. This review summarizes the multifunctionality of each geminivirus-encoded protein. These protein-based interactions trigger the abrupt changes in the host methyl cycle and signaling pathways that turn over protein normal production and impair the plant antiviral defense system. Studying these geminivirus interactions localized at cytoplasm-nucleus could reveal a more clear picture of host-pathogen relation. Data collected from this antagonistic relationship among geminivirus, vector, and its host, will provide extensive knowledge on their virulence mode and diversity with climate change.

Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes

Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10^- 4 (4.700 × 10^- 4-1.228 × 10^- 3) and 8.671 × 10^- 4 (6.143 × 10^- 4-1.130 × 10^- 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040-1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities.

Therapeutics for fulminant hepatitis caused by enteroviruses in neonates

Neonatal infection with nonpolio enteroviruses (EVs) causes nonspecific febrile illnesses and even life-threatening multiorgan failure. Hepatitis, which often results in hepatic necrosis followed by disseminated intravascular coagulopathy, is one of the most severe and frequent fatal neonatal EV infection complications. Coxsackievirus B (CVB) 1–5 and many echoviruses have been most commonly identified. Neonatal EV infection treatment has usually involved initial supportive care. Studies for CVB and echovirus infection treatments were developed for more than thirty years. Intravenous immunoglobulin and pleconaril therapy was performed in some clinical trials. Additionally, other studies demonstrated antiviral and/or anti-inflammatory pathogenesis mechanisms of neonatal EV hepatitis in in vitro or in vivo models. These treatments represented promising options for the clinical practice of neonatal EV hepatitis. However, further investigation is needed to elucidate the whole therapeutic potential and safety problems.

Global public health implications of human exposure to viral contaminated water

Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.

Human Pegivirus Type 1: A Common Human Virus That Is Beneficial in Immune-Mediated Disease?

Two groups identified a novel human flavivirus in the mid-1990s. One group named the virus hepatitis G virus (HGV) and the other named it GB Virus type C (GBV-C). Sequence analyses found these two isolates to be the same virus, and subsequent studies found that the virus does not cause hepatitis despite sharing genome organization with hepatitis C virus. Although HGV/GBV-C infection is common and may cause persistent infection in humans, the virus does not appear to directly cause any other known disease state. Thus, the virus was renamed “human pegivirus 1” (HPgV-1) for “persistent G” virus. HPgV-1 is found primarily in lymphocytes and not hepatocytes, and several studies found HPgV-1 infection associated with prolonged survival in people living with HIV. Co-infection of human lymphocytes with HPgV-1 and HIV inhibits HIV replication. Although three viral proteins directly inhibit HIV replication in vitro, the major effects of HPgV-1 leading to reduced HIV-related mortality appear to result from a global reduction in immune activation. HPgV-1 specifically interferes with T cell receptor signaling (TCR) by reducing proximal activation of the lymphocyte specific Src kinase LCK. Although TCR signaling is reduced, T cell activation is not abolished and with sufficient stimulus, T cell functions are enabled. Consequently, HPgV-1 is not associated with immune suppression. The HPgV-1 immunomodulatory effects are associated with beneficial outcomes in other diseases including Ebola virus infection and possibly graft-versus-host-disease following stem cell transplantation. Better understanding of HPgV-1 immune escape and mechanisms of inflammation may identify novel therapies for immune-based diseases.

Complete genome sequence of a novel bipartite begomovirus infecting the legume weed Macroptilium erythroloma

The natural occurrence of mixed infections and large populations of the polyphagous vector (Bemisia tabaci) are the main factors associated with the intensification of the genetic flow among begomoviruses in Neotropical areas, contributing to the emergence of novel recombinants. Here, high-throughput sequencing and metagenomic analyses were employed to discover and characterize a novel recombinant bipartite begomovirus, tentatively named "macroptilium bright yellow interveinal virus" (MaBYIV) in the weed Macroptilium erythroloma (Fabaceae). Recombination signals were detected in MaBYIV, involving bean golden mosaic virus (BGMV) and tomato mottle leaf curl virus (ToMoLCV) genome components. All of the original MaBYIV-infected M. erythroloma plants were found to have mixed infections with BGMV. MaBYIV was transmitted to bean and soybean cultivars via B. tabaci MEAM 1, indicating that M. erythroloma may play a role as a year-round reservoir of a potential new viral pathogen of economically important legume crops.

Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus

Background

Murine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents.

Results

A total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%.

Conclusion

The results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.

Occurrence and molecular characterization of human pegivirus-1 (HPgV-1) viraemia in healthy volunteer blood donors from northern Portugal

Human Pegivirus-1 (HPgV-1) is a member of the Flaviviridae family and the Pegivirus genus. Despite having been discovered 25 years ago, there is still much to know regarding HPgV-1 clinical impact, as this virus is currently not associated with any pathology. Yet, HPgV-1 prevalence and molecular characterization is still unknown in many countries, including Portugal. To fill in this knowledge gap, this study aimed to determine the occurrence and molecular characterization of HPgV-1 in a group of healthy blood donors from the north of Portugal. Blood samples from 465 Portuguese blood donors were collected from a major Hospital Center in the north of Portugal. RNA was extracted and an initial nested RT-PCR was performed targeting the conserved 5'-UTR region of HPgV-1 genome. A second nested RT-PCR targeting the E2 region was performed for genotyping. Only one sample tested positive for HPgV-1 RNA, resulting in a prevalence of approximately 0.22%. Phylogenetic analyses confirmed the characterization as genotype 2, the most prevalent in Europe. This article is protected by copyright. All rights reserved.

Immunodetection of Furcraea Necrotic Streak Virus-FNSV in fique plants (Furcraea macrophylla Baker) using a polyclonal antibody IgY produced in chicken egg yolk

The necrotic streak of the fique (Furcraea spp.) or "Macana" disease is considered the most limiting disease for this crop in Colombia, whose causal agent is the Furcraea Necrotic Streak Virus - FNSV (RNA+). Currently, there are no strategies to control the disease, being necessary to develop methods for detection of this pathogen in the planting material before being taken to the field. In this study, polyclonal antibodies produced in egg yolk (IgY) were produced and assesses for detection FNSV. Two immunoenzymatic methodologies were standardized: Dot Blot Immunobinding Assay (DBIA) and Enzyme Linked Immunosorbent Assay (ELISA), determining their specificity and sensitivity. The detection limit by DBIA corresponded to 8 μg/mL of purified virus suspension using 10 μg/mL of primary antibody. In the ELISA test, the primary antibody concentration of 3 μg/mL (1:800 dilution) detected the antigen at concentrations between 10 and 70 μg/mL. The polyclonal antibody anti-FNSV IgY allowed the detection of FNSV in samples of purified virus and extracts of roots and leaves of fique plants with symptoms of "Macana" disease and did not produce any signal with the control samples. Results showed the potential of using egg yolk IgY in immunological tests for the detection of FNSV in fique plants.

Human pegivirus infection after transplant: Is there an impact?

The microbiome's role in transplantation has received growing interest, but the role of virome remains understudied. Pegiviruses are single-stranded positive-sense RNA viruses, historically associated with liver disease, but their path-ogenicity is controversial. In the transplantation setting, pegivirus infection does not seem to have a negative impact on the outcomes of solid-organ and hematopoietic stem cell transplant recipients. However, the role of pegiviruses as proxies in immunosuppression monitoring brings novelty to the field of virome research in immunocompromised individuals. The possible immunomodulatory effect of pegivirus infections remains to be elucidated in further trials.

Infection of Glia by Human Pegivirus Suppresses Peroxisomal and Antiviral Signaling Pathways

Human pegivirus (HPgV) infects peripheral leukocytes but was recently shown to be a neurotropic virus associated with leukoencephalitis in humans. In the present study, we investigated the neural cell tropism of HPgV as well as its effects on host immune responses. HPgV wild type (WT) and a mutant virus with a deletion in the HPgV NS2 gene (ΔNS2) were able to productively infect human astrocytes and microglia but not neurons or an oligodendrocyte-derived cell line. Of note, the ΔNS2 virus replicated better than WT pegivirus in astrocytes, with both viruses being able to subsequently infect and spread in fresh human astrocyte cultures. Infection of human glia by HPgV WT and ΔNS2 viruses resulted in suppression of peroxisome-associated genes, including PEX11B, ABCD1, PEX7, ABCD3, PEX3, and PEX5L, during peak viral production, which was accompanied by reduced expression of IFNB, IRF3, IRF1, and MAVS, particularly in ΔNS2-infected cells. These data were consistent with analyses of brain tissue from patients infected with HPgV in which we observed suppression of peroxisome and type I interferon gene transcripts, including PEX11B, ABCD3, IRF1, and IRF3, with concurrent loss of PMP70 immunoreactivity in glia. Our data indicate that human astrocytes and microglia are permissive to HPgV infection, resulting in peroxisome injury and suppressed antiviral signaling that is influenced by viral diversity. IMPORTANCE Human pegiviruses are detected in 1 to 5% of the general population, principally infecting leukocytes, although their effects on human health remain uncertain. Here, we show that human pegivirus infects specific neural cell types in culture and human brain and, like other neurotropic flaviviruses, causes suppression of peroxisome and antiviral signaling pathways, which could favor ongoing viral infection and perhaps confer susceptibility to the development of neurological disease.

Phylogenetic analysis of human pegivirus from anti-hepatitis C virus IgG- positive patients

Human pegivirus type 1 (HPgV-1) is a non-pathogenic RNA virus in the Flaviviridae family that usually occurs as a co-infection with hepatitis B virus (HBV) or hepatitis C virus (HCV), though some evidence suggests it may play a role in certain cancers. The present study aimed to determine the prevalence of HPgV-1 infection in Iraqi anti-HCV IgG-positive patients, the risk factors associated with this infection, and the genotype of local isolates of this virus. A total of 88 anti-HCV IgG-positive patients participated in this cross-sectional study. Viral RAN was extracted from whole blood samples, and cDNA was produced using reverse transcriptase-polymerase chain reaction (RT-PCR). Two pairs of primers were used in nested PCR to amplify the virus genome's 5'-untranslated region (5'UTR). For direct sequencing, fourteen PCR products from the second round of PCR were chosen at random. A homology search was performed using the basic local alignment search tool (BLAST) program to identify the resultant sequencing. The phylogenetic tree of the local isolates and 31 reference isolates was constructed using MEGA X software to estimate the virus's genetic diversity and relatedness. Out of 88 patients included in this study, 27(30.68%) of patients were found to be positive for HPgV-1 RNA. The nucleotide homology between the 14 local isolates and the reference isolates. was found to be 87-97%. Phylogenetic analysis results in a tree with four main parts, which are distributed as follows: 10 local isolates are genotype 2; 2 are genotype 1; 1 is genotype 5, and 1 is genotype 6. We conclude that when compared to other countries, the infection rate of Iraqi anti-HCV IgG-positive patients with HPgV-1 is relatively high (30.68%). The most common HPgV-1 genotype in Iraq is genotype 2.

Synthesis and Antiviral Evaluation of Nucleoside Analogues Bearing One Pyrimidine Moiety and Two D-Ribofuranosyl Residues

A series of 1,2,3-triazolyl nucleoside analogues in which 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via polymethylene linkers to both nitrogen atoms of the heterocycle moiety (uracil, 6-methyluracil, thymine, quinazoline-2,4-dione, alloxazine) or to the C-5 and N-3 atoms of the 6-methyluracil moiety was synthesized. All compounds synthesized were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1) and coxsackievirus B3. Antiviral assays revealed three compounds, 2i, 5i, 11c, which showed moderate activity against influenza virus A H1N1 with IC₅₀ values of 57.5 µM, 24.3 µM, and 29.2 µM, respectively. In the first two nucleoside analogues, 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via butylene linkers to N-1 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine, respectively). In nucleoside analogue 11c, two 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached via propylene linkers to the C-5 and N-3 atoms of the 6-methyluracil moiety. Almost all synthesized 1,2,3-triazolyl nucleoside analogues showed no antiviral activity against the coxsackie B3 virus. Two exceptions are 1,2,3-triazolyl nucleoside analogs 2f and 5f, in which 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached to the C-5 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine respectively). These compounds exhibited high antiviral potency against the coxsackie B3 virus with IC₅₀ values of 12.4 and 11.3 µM, respectively, although both were inactive against influenza virus A H1N1. According to theoretical calculations, the antiviral activity of the 1,2,3-triazolyl nucleoside analogues 2i, 5i, and 11c against the H1N1 (A/PR/8/34) influenza virus can be explained by their influence on the functioning of the polymerase acidic protein (PA) of RNA-dependent RNA polymerase (RdRp). As to the antiviral activity of nucleoside analogs 2f and 5f against coxsackievirus B3, it can be explained by their interaction with the coat proteins VP1 and VP2.

Human Pegivirus Infection and Lymphoma Risk: A Systematic Review and Meta-analysis

BACKGROUND

Human pegivirus (HPgV) is a single-strand RNA virus belonging to the Flaviviridae. Although no definitive association between HPgV infection and disease has been identified, previous studies have suggested an association of HPgV viremia with risk of lymphomas.

METHODS

We conducted a systematic review and meta-analysis, including 1 cohort study and 14 case-control studies, assessing the association of HPgV viremia with adult lymphomas. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model, overall and by geographic region and lymphoma subtype.

RESULTS

The overall OR for lymphoma was 2.85 (95% CI, 1.98-4.11), with statistically significantly elevated ORs observed in 8 of 15 studies. There was a small amount of heterogeneity among studies (I2 = 28.9%; Q = 18.27, P = .16), and the funnel plot provided no evidence for publication bias. The strongest association with lymphoma risk was observed for studies from Southern Europe (OR, 5.68 [95% CI, 1.98-16.3]), whereas weaker ORs (with 95% CIs) were observed for studies from North America (2.24 [1.76-2.85]), Northern Europe (2.90 [.45-18.7), and the Middle East (2.51 [.87-7.27]), but all of similar magnitude. Participants with HPgV viremia had statistically significantly increased risks (OR [95% CI]) for developing diffuse large B-cell (3.29 [1.63-6.62]), follicular (3.01 [1.95-4.63]), marginal zone (1.90 [1.13-3.18]), and T-cell (2.11 [1.17-3.89]) lymphomas, while the risk for Hodgkin lymphoma (3.53 [.48-25.9]) and chronic lymphocytic leukemia (1.45 [.45-4.66]) were increased but did not achieve statistical significance.

CONCLUSIONS

This meta-analysis supports a positive association of HPgV viremia with lymphoma risk, overall and for the major lymphoma subtypes.

Type B coxsackieviruses and central nervous system disorders: critical review of reported associations

Type B coxsackieviruses (CV-B) frequently infect the central nervous system (CNS) causing neurological diseases notably meningitis and encephalitis. These infections occur principally among newborns and children. Epidemiological studies of patients with nervous system disorders demonstrate the presence of infectious virus, its components, or anti-CV-B antibodies. Some experimental studies conducted in vitro and in vivo support the potential association between CV-B and idiopathic neurodegenerative diseases such as amyotrophic lateral sclerosis and psychiatric illness such as schizophrenia. However, mechanisms explaining how CV-B infections may contribute to the genesis of CNS disorders remain unclear. The proposed mechanisms focus on the immune response following the viral infection as a contributor to pathogenesis. This review describes these epidemiological and experimental studies, the modes of transmission of CV-B with an emphasis on congenital transmission, the routes used by CV-B to reach the brain parenchyma, and plausible mechanisms by which CV-B may induce CNS diseases, with a focus on potential immunopathogenesis.

High abundance of human herpesvirus 8 in wastewater from a large urban area

AIMS

This study assesses the diversity and abundance of Human Herpesviruses (HHVs) in the influent of an urban wastewater treatment plant using shotgun sequencing, metagenomic analysis and qPCR.

METHODS AND RESULTS

Influent wastewater samples were collected from the three interceptors that serve the City of Detroit and Wayne, Macomb and Oakland counties between November 2017 to February 2018. The samples were subjected to a series of processes to concentrate viruses which were further sequenced and amplified using qPCR. All nine types of HHV were detected in wastewater. Human Herpesvirus 8 (HHV-8), known as Kaposi's sarcoma herpesvirus, which is only prevalent in 5-10% of USA population, was found to be the most abundant followed by HHV-3 or Varicella-zoster virus.

CONCLUSIONS

The high abundance of HHV-8 in the Detroit metropolitan area may be attributed to the HIV-AIDS outbreak that was ongoing in Detroit during the sampling period.

SIGNIFICANCE AND IMPACT OF THE STUDY

The approach described in this paper can be used to establish a baseline of viruses secreted by the community as a whole. Sudden changes in the baseline would identify changes in community health and immunity.

Identifying pathophysiological bases of disease in COVID-19

COVID-19 is an infectious disease caused by the SARS-CoV-2 virus that can affect lung physiology encompassing a wide spectrum of severities, ranging from asymptomatic and mild symptoms to severe and fatal cases; the latter including massive neutrophil infiltration, stroke and multiple organ failure. Despite many recents findings, a clear mechanistic description underlying symptomatology is lacking. In this article, we thoroughly review the available data involving risk factors, age, gender, comorbidities, symptoms of disease, cellular and molecular mechanisms and the details behind host/pathogen interaction that hints at the existence of different pathophysiological mechanisms of disease. There is clear evidence that, by targeting the angiotensin-converting enzyme II (ACE2) -its natural receptor-, SARS-CoV-2 would mainly affect the renin-angiotensin-aldosterone system (RAAS), whose imbalance triggers diverse symptomatology-associated pathological processes. Downstream actors of the RAAS cascade are identified, and their interaction with risk factors and comorbidities are presented, rationalizing why a specific subgroup of individuals that present already lower ACE2 levels is particularly more susceptible to severe forms of disease. Finally, the notion of endotype discovery in the context of COVID-19 is introduced. We hypothesize that COVID-19, and its associated spectrum of severities, is an umbrella term covering different pathophysiological mechanisms (endotypes). This approach should dramatically accelerate our understanding and treatment of disease(s), enabling further discovery of pathophysiological mechanisms and leading to the identification of specific groups of patients that may benefit from personalized treatments.

A recombinase polymerase amplification-based lateral flow strip assay for rapid detection of genogroup II noroviruses in the field

Human norovirus is the leading cause of viral gastroenteritis worldwide. Rapid detection facilitates management of disease outbreaks, but field diagnosis is difficult to achieve due to the lack of reliable and portable methods. Recombinase polymerase amplification (RPA) is a robust isothermal amplification method that is capable of rapidly amplifying and detecting nucleic acids using simple equipment. In this study, RPA combined with lateral flow (LF) strips specific for human genogroup II (GII) noroviruses was established and evaluated. The assay specifically detects purified GII noroviruses as well as RNA in boiled human stool samples, with a sensitivity of 50 norovirus genome copies per reaction. The whole detection procedure of the one-step RT-RPA-LF is completed within 20 min, which is eight times faster than that of the standard real-time RT-PCR. The RT-RPA-LF method described here is suitable for rapid field diagnosis of all GII noroviruses in human stool samples.

Structural and Functional Characterization of the Phosphoprotein Central Domain of Spring Viremia of Carp Virus

Spring viremia of carp virus (SVCV) is a highly pathogenic Vesiculovirus in the common carp. The phosphoprotein (P protein) of SVCV is a multifunctional protein that acts as a polymerase cofactor and an antagonist of cellular interferon (IFN) response. Here, we report the 1.5-Å-resolution crystal structure of the P protein central domain (P_CD) of SVCV (SVCV_PCD). The P_CD monomer consists of two β sheets, an α helix, and another two β sheets. Two P_CD monomers pack together through their hydrophobic surfaces to form a dimer. The mutations of residues on the hydrophobic surfaces of P_CD disrupt the dimer formation to different degrees and affect the expression of host IFN consistently. Therefore, the oligomeric state formation of the P protein of SVCV is an important mechanism to negatively regulate host IFN response.IMPORTANCE SVCV can cause spring viremia of carp with up to 90% lethality, and it is the homologous virus of the notorious vesicular stomatitis virus (VSV). There are currently no drugs that effectively cure this disease. P proteins of negative-strand RNA viruses (NSVs) play an essential role in many steps during the replication cycle and an additional role in immunosuppression as a cofactor. All P proteins of NSVs are oligomeric, but the studies on the role of this oligomerization mainly focus on the process of virus transcription or replication, and there are few studies on the role of P_CD in immunosuppression. Here, we present the crystal structure of SVCV_PCD A new mechanism of immune evasion is clarified by exploring the relationship between SVCV_PCD and host IFN response from a structural biology point of view. These findings may provide more accurate target sites for drug design against SVCV and provide new insights into the function of NSV_PCD.

Kobuviruses carried by Rattus norvegicus in Guangdong, China

Background

Murine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducted a survey of the prevalence and genomic characteristics of rat kobuvirus in Guangdong, China.

Results

Fecal samples from 223 rats (Rattus norvegicus) were collected from Guangdong and kobuviruses were detected in 12.6% (28) of samples. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions showed that rat kobuvirus obtained in this study were genetically closely related to those of rat/mouse kobuvirus reported in other geographical areas. Two near full-length rat kobuvirus genomes (MM33, GZ85) were acquired and phylogenetic analysis of these revealed that they shared very high nucleotide/amino acids identity with one another (95.4%/99.4%) and a sewage-derived sequence (86.9%/93.5% and 87.5%/93.7%, respectively). Comparison with original Aichivirus A strains, such human kobuvirus, revealed amino acid identity values of approximately 80%.

Conclusion

Our findings indicate that rat kobuvirus have distinctive genetic characteristics from other Aichivirus A viruses. Additionally, rat kobuvirus may spread via sewage.

Enterovirus detection and serotyping of fecal material collected from three children living on the outskirts of Belém city, Amazon region, Brazil, during the first 3 years of life (1983-1986)

In the current investigation, fecal material was obtained during a community-based longitudinal study conducted from 1983 to 1986. This study consisted of 71 children aged newborn to 3 years. A total of 216 samples from three of these children were screened by real-time quantitative polymerase chain reaction (RT-qPCR) for the presence of enteroviruses, and positive samples were serotyped by VP1 and VP3 sequencing of the viral genome. Of these, 12 (5.6%) came from symptomatic cases, and the remaining asymptomatic cases were collected fortnightly during the 3 years of study. A positivity of 63.4% (137/216) was obtained by RT-qPCR, with 58.3% (7/12) in relation to the symptomatic group and 63.7% (130/204) in relation to the asymptomatic group. The 137 positive samples were inoculated into the RD, HEp2C, and L20B cell lines, and the cytopathic effect was observed in 37.2% (51/137) samples. It was also possible to identify 40.9% (56/137), between isolated (n = 46) and nonisolated (n = 10). Enterovirus serotype diversity (n = 25) was identified in this study, with the predominant species being B (80.3%), followed by C (16.1%) and A (3.6%). Cases of reinfection by different serotypes were also observed in the three children studied. Analyses involving different age groups of these minors confirmed that the most affected age was between 12 to 24 months, with a prevalence of 77.6% (52/67). The enterovirus (EV) circulated in the 3 years of research, showed peaks in some months, without defined seasonality. This study demonstrated a high circulation and serotype diversity of EV in fecal samples, collected over 30 years ago. This endorsed the evaluation of important points of the epidemiology of these viruses, such as the presence of coinfection and reinfection of the same individual by different circulating serotypes. Understanding the frequency and duration of EV infections is important in determining their association with persistent diarrhea.

Immunopathology in the brain of mice following vertical transmission of Coxsackievirus B4

Coxsackie B viruses (CV-B) are associated with several central nervous system (CNS) disorders. These viruses are predominantly transmitted by fecal-oral route but vertical transmission can also occur. This work attempted to study the immune response ensuing vertical transmission of CV-B to the brain, and its eventual implementation in the brain pathogenesis. To this end, pregnant Swiss albino mice were inoculated with CV-B4 E2 or with sterile medium for control animals. At different ages after birth, brains were collected and analyzed for virus infection, histopathological changes and immune response. Infectious particles were detected in offspring's brain which demonstrates vertical transmission of the virus. This infection is persistent since the long lasting detection of viral RNA in offspring's brain. Some pathological signs including meningitis, edema and accumulation of inflammatory cells within and surrounding the inflammatory areas were observed. Immunoflorescence staining unveiled the presence of T lymphocytes and microgliosis in the sites of lesion for a long period after birth. Multiplex cytokines measurement upon supernatants of in vitro mixed brain cells and extracted mononuclear cells from offspring's brain has demonstrated an elevated secretion of the pro-inflammatory cytokines TNFα, IL-6 and IFNα and the chemokines RANTES and MCP-1. Hence, vertical transmission of CV-B4 and its persistence within offspring's brain can lead to pathological features linked to increased and sustained immune response.

Global prevalence of human pegivirus-1 in healthy volunteer blood donors: a systematic review and meta-analysis

BACKGROUND AND OBJECTIVES

The local prevalence of HPgV-1 has been reported from different countries worldwide, but the global prevalence of HPgV-1 remains unknown. The aim of this systematic review and meta-analysis was to gather data from the literature to estimate the prevalence of HPgV-1 in healthy volunteer blood donors in the world.

MATERIALS AND METHODS

We searched PubMed, EMBASE, Scopus and Google Scholar databases for records up to January 2019 and included studies reporting HPgV-1 virus prevalence amongst healthy volunteer blood donors based on the detection of HPgV-1 RNA.

RESULTS

In all, we included 79 studies for the systematic review and 63 for the meta-analysis. Based on the random effect meta-analysis of 35 468 volunteer blood donors, we found the global prevalence of HPgV-1 to be 3·1% (95% CI, 2·4-4·1). The pooled prevalences of HPgV-1 were 1·7% (95% CI, 1·1-2·6) in North America, 9·1% (95% CI, 6·4-12·7) in South America, 2·3% (95% CI, 2%, 2·8) in Europe and 2·4% (95% CI, 1·4-4) in Asia. Subgroup analyses based on age, gender or risk factors were not possible.

CONCLUSION

Approximately 3 in 100 blood donations worldwide are positive for HPgV-1 increasing the risk of infection from transfusion of their components to subsequent recipients. Further research on virus pathogenicity is required before recommending routine screening of HPgV-1 for healthy volunteer blood donors.

Diagnostic test accuracy when screening for Haliotid herpesvirus 1 (AbHV) in apparently healthy populations of Australian abalone Haliotis spp

The accuracy of 3 real-time PCR assays (ORF49, ORF66 and ORF77) and histopathology was evaluated for the purpose of demonstrating or certifying abalone free from Haliotid herpesvirus 1 (AbHV), the causative agent of abalone viral ganglioneuritis. Analytically, all 3 qPCRs showed equivalent limit of detection (20 copies per reaction); however, ORF49 could not detect 2 of the AbHV genotypes. A selection of 1452 archive specimens sourced from apparently healthy abalone populations was screened using all 4 tests. In the absence of a perfect reference standard, a Bayesian latent class analysis was built to estimate diagnostic sensitivity (DSe), diagnostic specificity (DSp) and likelihood ratios of a positive (LR+) and negative test result (LR-) for each individual test and for all possible combinations of test pairs interpreted either in series or in parallel. The pair ORF49/ORF66 interpreted in parallel performed the best both analytically and diagnostically to demonstrate freedom from AbHV in an established population of abalone and to certify individual abalone free from AbHV for trade or movement purposes (DSe = 96.0%, 95% posterior credibility interval [PCI]: 82.6 to 99.9; DSp = 97.7%, 95% PCI: 96.4 to 99.4; LR+ = 41.4, 95% PCI: 27.4 to 148.7; LR- = 0.041, 95% PCI: 0.001 to 0.176). Histopathology showed very poor DSe (DSe = 6.3%, 95% PCI: 2.4 to 13.1) as expected since most infected abalone in the study were likely sub-clinical with limited pathological change. Nevertheless, we recommend histopathology when clinically investigating outbreaks to find potential, new, emerging AbHV genotype(s) that may not be detectable by either ORF49 or ORF66.

Feline Virome-A Review of Novel Enteric Viruses Detected in Cats

Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.

Epidemiology of Aichi virus in fecal samples from outpatients with acute gastroenteritis in Northwestern Spain

BACKGROUND

In recent years, Aichi virus (AiV) has been involved in acute viral gastroenteritis outbreaks. However, the common pathogenesis of AiV releases more in subclinical infections underestimating the impact of AiV in human health.

OBJECTIVES

The present study describes the presence and genetic diversity of AiV in patients with gastroenteritis in Northwestern Spain.

STUDY DESIGN

A total of 2667 stool samples, obtained between July 2010 and June 2011, from diarrheic outpatients were studied for detection and molecular characterization of AiV using PCR techniques followed by sequencing and phylogenetic analyses.

RESULTS

The virus was detected in 124 (5.0%) of the samples among all age groups. Coinfections were also detected, from the 124 positive samples, 72 (58.1%) were positive only for AiV, whereas mixed contaminations with Norovirus genogroup I or genogroup II, Sapovirus, or other enteric pathogens were detected in 52 (41.9%) samples. A total of 70 positive samples could be genotyped, being characterized as genotype A (58.6%) or B (41.4%). AiV was detected from August to April, being the highest number of AiV positive samples detected during autumn and winter seasons.

CONCLUSIONS

This survey remarks the importance of emerging enteric viruses in patients who require medical assistance, and offers more information about the real importance of AiV as gastroenteritis agent.

Tracing the Lineage of Two Traits Associated with the Coat Protein of the Tombusviridae: Silencing Suppression and HR Elicitation in Nicotiana Species

In this paper we have characterized the lineage of two traits associated with the coat proteins (CPs) of the tombusvirids: Silencing suppression and HR elicitation in Nicotiana species. We considered that the tombusvirid CPs might collectively be considered an effector, with the CP of each CP-encoding species comprising a structural variant within the family. Thus, a phylogenetic analysis of the CP could provide insight into the evolution of a pathogen effector. The phylogeny of the CP of tombusvirids indicated that CP representatives of the family could be divided into four clades. In two separate clades the CP triggered a hypersensitive response (HR) in Nicotiana species of section Alatae but did not have silencing suppressor activity. In a third clade the CP had a silencing suppressor activity but did not have the capacity to trigger HR in Nicotiana species. In the fourth clade, the CP did not carry either function. Our analysis illustrates how structural changes that likely occurred in the CP effector of progenitors of the current genera led to either silencing suppressor activity, HR elicitation in select Nicotiana species, or neither trait.

Molecular and Clinical Profiles of Human Pegivirus Type 1 Infection in Individuals Living with HIV-1 in the Extreme South of Brazil

Human pegivirus type 1 (HPgV-1) infection has been associated with a beneficial effect on the prognosis of human immunodeficiency virus type 1 (HIV-1)-coinfected individuals. However, the mechanisms involved in this protection are not yet fully elucidated. To date, circulating HPgV-1 genotypes in HIV-1-infected individuals have not yet been identified in the extreme south of Brazil. The present study aimed to determine the genotypic circulation of HPgV-1 and the influence of HPgV-1 status and persistence time on the evolution of HIV-1 infection. A retrospective cohort of 110 coinfected individuals was analyzed. Samples were subjected to viral RNA extraction, cDNA synthesis, nested PCR, and genotyping. Genotypes 1 (2.8%), 2 (47.9% of subtype 2a and 42.3% of subtype 2b), and 3 (7%) were identified. In antiretroviral treatment-naïve subjects HPgV-1 subtype 2b was associated with lower HIV-1 viral load (VL) rates (p = 0.04) and higher CD4+ T-cell counts (p = 0.03) than was subtype 2a, and the positivity for HPgV-1 was associated with higher CD4+ T-cell counts (p = 0.02). However, there was no significant difference in HIV-1 VL between HPgV-1-positive and HPgV-1-negative subjects (p = 0.08). There was no significant association between the different groups in HPgV-1 persistence and median HIV-1 VL (p = 0.66) or CD4+ T-cell counts (p = 0.15). HPgV-1 subtype 2b is associated with better prognosis of HIV-1 infection. Although HPgV-1 infection is persistent, our data suggest that the time of infection does not influence HIV-1 VL or CD4+ T-cell counts in coinfected subjects.

Developing Picornaviruses for Cancer Therapy

Oncolytic viruses (OVs) form a group of novel anticancer therapeutic agents which selectively infect and lyse cancer cells. Members of several viral families, including Picornaviridae, have been shown to have anticancer activity. Picornaviruses are small icosahedral non-enveloped, positive-sense, single-stranded RNA viruses infecting a wide range of hosts. They possess several advantages for development for cancer therapy: Their genomes do not integrate into host chromosomes, do not encode oncogenes, and are easily manipulated as cDNA. This review focuses on the picornaviruses investigated for anticancer potential and the mechanisms that underpin this specificity.

Human Pegivirus in Patients with Encephalitis of Unclear Etiology, Poland

Sequence analysis of human pegivirus from 3 patients indicates that the central nervous system constitutes a separate viral compartment from serum.

Human pegivirus (HPgV), previously called hepatitis G virus or GB virus C, is a lymphotropic virus with undefined pathology. Because many viruses from the family Flaviviridae, to which HPgV belongs, are neurotropic, we studied whether HPgV could infect the central nervous system. We tested serum and cerebrospinal fluid samples from 96 patients with a diagnosis of encephalitis for a variety of pathogens by molecular methods and serology; we also tested for autoantibodies against neuronal antigens. We found HPgV in serum and cerebrospinal fluid from 3 patients who had encephalitis of unclear origin; that is, all the markers that had been tested were negative. Single-strand confirmation polymorphism and next-generation sequencing analysis revealed differences between the serum and cerebrospinal fluid–derived viral sequences, which is compatible with the presence of a separate HPgV compartment in the central nervous system. It is unclear whether HPgV was directly responsible for encephalitis in these patients.

Identification of a new recombinant strain of echovirus 33 from children with hand, foot, and mouth disease complicated by meningitis in Yunnan, China

Background

Hand, foot, and mouth disease (HFMD) is a common childhood disease, which is usually caused by enterovirus A (EV-A) serotypes. Enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) are the main etiologic agents. Multiple serotypes of enterovirus B serotypes (EV-B) have been detected in outbreaks or sporadic cases of HFMD.

Results

During HFMD surveillance in Yunnan, China in 2013, two echovirus 33 (E-33) isolates were recovered in cell culture and typed by molecular methods from the cerebrospinal fluid (CSF) and feces of two sporadic cases of HFMD complicated by meningitis. Sequence analysis indicated that the study isolates, YNK35 and YNA12, formed an independent branch, and belonged to E-33 genotype H. Recombination analysis indicated multiple recombination events in the genomic sequence of isolate YNK35. The recombination mainly occurred in the non-structural coding region of P2 and P3, and involved intra-species recombination of species B.

Conclusion

In this study, the complete sequences of two E-33 isolates were determined. This is the first report of severe HFMD associated with E-33 in Yunnan China, and it enriches the number of full-length genome sequences of E-33 in the GenBank database.

Electronic supplementary material

The online version of this article (10.1186/s12985-019-1164-2) contains supplementary material, which is available to authorized users.

Alpha-Herpesvirus Thymidine Kinase Genes Mediate Viral Virulence and Are Potential Therapeutic Targets

Alpha-herpesvirus thymidine kinase (TK) genes are virulence-related genes and are nonessential for viral replication; they are often preferred target genes for the construction of gene-deleted attenuated vaccines and genetically engineered vectors for inserting and expressing foreign genes. The enzymes encoded by TK genes are key kinases in the nucleoside salvage pathway and have significant substrate diversity, especially the herpes simplex virus 1 (HSV-1) TK enzyme, which phosphorylates four nucleosides and various nucleoside analogues. Hence, the HSV-1 TK gene is exploited for the treatment of viral infections, as a suicide gene in antitumor therapy, and even for the regulation of stem cell transplantation and treatment of parasitic infection. This review introduces the effects of α-herpesvirus TK genes on viral virulence and infection in the host and classifies and summarizes the current main application domains and potential uses of these genes. In particular, mechanisms of action, clinical limitations, and antiviral and antitumor therapy development strategies are discussed.

Structure and oligomerization state of the C-terminal region of the Middle East respiratory syndrome coronavirus nucleoprotein

Middle East respiratory syndrome coronavirus (MERS-CoV) is a human pathogen responsible for a severe respiratory illness that emerged in 2012. Structural information about the proteins that constitute the viral particle is scarce. In order to contribute to a better understanding of the nucleoprotein (N) in charge of RNA genome encapsidation, the structure of the C-terminal domain of N from MERS-CoV obtained using single-crystal X-ray diffraction is reported here at 1.97 Å resolution. The molecule is present as a dimer in the crystal structure and this oligomerization state is confirmed in solution, as measured by additional methods including small-angle X-ray scattering measurements. Comparisons with the structures of the C-terminal domains of N from other coronaviruses reveals a high degree of structural conservation despite low sequence conservation, and differences in electrostatic potential at the surface of the protein.

Molecular basis for the acid-initiated uncoating of human enterovirus D68

Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.

Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China

Feline kobuvirus (FeKoV), a novel picornavirus of the genus kobuvirus, was initially identified in the feces of cats with diarrhea in South Korea in 2013. To date, there is only one report of the circulation of kobuvirus in cats in southern China. To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. Kobuvirus was identified in 28 fecal samples with an overall prevalence of 14.2% (28/197) of which 20 samples were co-infected with feline parvovirus (FPV) and/or feline bocavirus (FBoV). Diarrhoeic cats had a higher kobuvirus prevalence (19.1%, 20/105) than asymptomatic cats (8.7%, 8/92). By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%-97.8% and 96.6%-100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. Furthermore, two complete FeKoV polyprotein genomes were successfully obtained from two positive samples and designated 16JZ0605 and 17CC0811, respectively. The two strains shared 92.9%-94.9% nucleotide identities and 96.8%-98.4% amino acid identities to FeKoV prototype strains. Phylogenetic analysis indicated that FeKoVs were clustered according to their geographical regions, albeit with limited sequences support. This study provides the first molecular evidence that FeKoV circulates in cats in northeast China, and these FeKoVs exhibit genetic diversity and unique evolutionary trend.

High prevalence and autochtonous transmission of human pegivirus (HPgV-1) in blood donors in the extreme southern of Brazil

Recent studies have suggested that human pegivirus 1 (HPgV-1) may have some pathogenic potential. In the southernmost region of Brazil, studies on HPgV-1 are scarce, and circulating genotypes have not yet been identified. The current study aimed to evaluate the prevalence of HPgV-1 among blood donors from the southernmost region of Brazil and identify the genotypes involved with associated factors. A cross-sectional study was conducted with 281 blood donors, who had their plasma subjected to RNA extraction, complementary DNA synthesis, HPgV-1 detection by nested polymerase chain reaction, and subsequent genotyping. The observed prevalence of HPgV-1-RNA was 21.7%. The only variable that was significantly associated with virus infection was the relationship status of the donor. Single or no fixed partner blood donors were twice as likely to have HPgV-1 (95% CI, 1.12 to 4.56; P = 0.02). Genotype 2-subtypes 2b (69%) and 2a (29%)-was the most prevalent. In the absence of risk factors for parenteral transmission, it is likely that sexual transmission was the route of infection in the individuals studied. Further work will be needed to determine whether this virus is inert in the population, or if there are potential deleterious effects in infected individuals.

Inhibition of HIV-1 infection by human pegivirus type 1-derived peptides is affected by human pegivirus type 1 genotype and HIV-1 coreceptor tropism

OBJECTIVE(S)

Up to 40% of HIV-1 infected individuals are coinfected with human pegivirus type 1 (HPgV-1). The majority of studies, but not all, have reported a beneficial effect of HPgV-1 coinfection on HIV-1 disease progression. So far, the impact of different HPgV-1 genotypes on different HIV-1 subtypes remains unclear.

METHODS

Peptides derived from HPgV-1 envelope protein E2, and representing different viral genotypes, were synthesized using Fmoc/t-Bu-based solid phase peptide synthesis. The inhibitory effect of these peptides on the infection of reporter cell lines was tested using an HIV-1 subtype panel representing clades A (n = 2), AG (n = 2), B (n = 6), C (n = 2), D (n = 2), F (n = 2), G (n = 1), G/H (n = 1), and group O (n = 2).

RESULTS

HIV-1 infection was blocked more efficiently by peptides derived from HPgV-1 GT2 than GT1 (P = 0.05). The HIV-1 subtype did not affect the degree of inhibition by a peptide derived from HPgV-1 GT2. All CXCR4-/dual-tropic isolates (n = 12), but only half (four out of eight) CCR5-tropic viruses were inhibited by this peptide (P = 0.014).

CONCLUSION

Our data indicate that the inhibitory effect of peptides derived from HPgV-1 E2 protein is dependent on the genotype, suggesting that coinfection with HPgV-1 GT1 is less likely to confer a beneficial effect on HIV-1 disease progression than GT2. The preferential suppression of more pathogenic CXCR4-tropic HIV-1 by peptides derived from HPgV-1 GT2 may explain the favorable effect in patients harboring these HIV-1 isolates. Consequently, HPgV-1 genotype and HIV-1 coreceptor tropism are likely determinants for the beneficial effect of HPgV-1 co-infection in HIV-1-infected individuals.

Design and evaluation of nested PCR primers for specific detection of genogroup I noroviruses in oysters

A pair of nested PCR universal primers (NGIOF and NGIOR) specific for genogroup I (GI) noroviruses was designed based on all GI sequences available in public databases. The primers were evaluated for their specificity, sensitivity and coverage, which demonstrate their reliable performance upon detection of GI noroviruses in oysters.

Multifunctional roles of geminivirus encoded replication initiator protein

Geminivirus infection has been a threat to cultivation worldwide by causing huge losses to the crop. The single-stranded DNA genome of a geminivirus possesses a limited coding potential and many of the open reading frames (ORFs) are overlapping. Out of 5-7 ORFs that a geminivirus genome codes for, the AC1 ORF encodes for the replication initiator protein (Rep) which is involved in the replication of virus within the infected plant cell. Rep is the only viral protein absolutely required for the in planta viral replication. Across different genera of the Geminiviridae family, the AC1 ORF exhibits a high degree of sequence conservation thus it has been used as an effective target for developing broad spectrum resistance against the invading geminiviruses. This multifunctional protein is required for initiation, elongation as well as termination of the viral replication process. Rep is also involved in stimulation of viral transcription. In addition, it also functions as suppressor of gene silencing and is involved in the process of transcription by regulating the expression of certain viral genes. Rep protein also interacts with few viral proteins such as coat protein, replication enhancer protein and with several host factors involved in different pathways and processes for its replication and efficient infection. This review will summarise our current understanding about the role of this early viral protein in viral propagation as well as in establishment of pathogenesis in a permissive host.

First report and genetic characterization of feline kobuvirus in diarrhoeic cats in China

Feline kobuvirus (FeKoV) is a newly discovered organism, classified under the species Aichivirus A of the genus Kobuvirus. Since it was first reported in 2013, molecular evidence for FeKoV in the feline population has been restricted to two countries: Korea and Italy. In this study, we collected faecal samples from cats in southern China and detected the FeKoV RNA in these samples. A prevalence rate of 9.9% (8/81) was identified by RT‐PCR, and all positive samples were obtained from diarrhoeic animals. In addition, FeKoV was shown positive associated with diarrhoea in cats, with a correlation coefficient of 0.25. Next, we designed three primer pairs with degenerate bases, which targeted the conservative overlapping region of the entire published FeKoV genome, and sequenced the near‐complete genome of the first Chinese field FeKoV strain, WHJ‐1, using long‐fragment PCR. Finally, we analysed WHJ‐1's homology and phylogeny using the polyprotein gene. The results indicated that FeKoV has rapidly mutated since it was first discovered. This study will help to better understand FeKoV's epidemiology, evolutionary pattern and genetic diversity.

Human Pegivirus infection and lymphoma risk and prognosis: a North American study

We evaluated the association of Human Pegivirus (HPgV) viraemia with risk of developing lymphoma, overall and by major subtypes. Because this virus has also been associated with better prognosis in the setting of co-infection with human immunodeficiency virus, we further assessed the association of HPgV with prognosis. We used risk factor data and banked plasma samples from 2094 lymphoma cases newly diagnosed between 2002 and 2009 and 1572 frequency-matched controls. Plasma samples were tested for HPgV RNA by reverse transcription polymerase chain reaction (RT-PCR), and those with RNA concentrations <5000 genome equivalents/ml were confirmed using nested RT-PCR methods. To assess the role of HPgV in lymphoma prognosis, we used 2948 cases from a cohort study of newly diagnosed lymphoma patients (included all cases from the case-control study). There was a positive association of HPgV viraemia with risk of lymphoma overall (Odds ratio = 2·14; 95% confidence interval [CI] 1·63-2·80; P < 0·0001), and for all major subtypes except Hodgkin lymphoma and chronic lymphocytic leukaemia/small lymphocytic lymphoma, and this was not confounded by other lymphoma risk factors. In contrast, there was no association of HPgV viraemia with event-free survival (Hazard ratio [HR] = 1·00; 95% CI 0·85-1·18) or overall survival (HR = 0·97; 95% CI 0·79-1·20) for lymphoma overall, or any of the subtypes. These data support the hypothesis for a role of HPgV in the aetiology of multiple lymphoma subtypes.

Enteroviruses: Classification, Diseases They Cause, and Approaches to Development of Antiviral Drugs

The genus Enterovirus combines a portion of small (+)ssRNA-containing viruses and is divided into 10 species of true enteroviruses and three species of rhinoviruses. These viruses are causative agents of the widest spectrum of severe and deadly epidemic diseases of higher vertebrates, including humans. Their ubiquitous distribution and high pathogenici- ty motivate active search to counteract enterovirus infections. There are no sufficiently effective drugs targeted against enteroviral diseases, thus treatment is reduced to supportive and symptomatic measures. This makes it extremely urgent to develop drugs that directly affect enteroviruses and hinder their development and spread in infected organisms. In this review, we cover the classification of enteroviruses, mention the most common enterovirus infections and their clinical man- ifestations, and consider the current state of development of anti-enteroviral drugs. One of the most promising targets for such antiviral drugs is the viral Internal Ribosome Entry Site (IRES). The classification of these elements of the viral mRNA translation system is also examined.

Characterization of a novel thogotovirus isolated from Amblyomma testudinarium ticks in Ehime, Japan: A significant phylogenetic relationship to Bourbon virus

The genus Thogotovirus, as represented by Thogoto virus and Dhori virus, comprises a group of arthropod-borne viruses, most members of which are transmitted by ticks. Here we report the genetic and biological characterization of a new thogotovirus, designated Oz virus (OZV), isolated from the hard tick Amblyomma testudinarium in Ehime, Japan. OZV efficiently replicated and induced a cytopathic effect in Vero cells, from which enveloped pleomorphic virus particles were formed by budding. OZV could also replicate in BHK-21 and DH82 cells and caused high mortality in suckling mice after intracerebral inoculation. Phylogenetic analyses of six viral proteins indicated that OZV is clustered with Dhori and related viruses, and is most closely related in glycoprotein (GP) and matrix protein (M) sequences to Bourbon virus, a human-pathogenic thogotovirus discovered recently in the United States. Our findings emphasize the need for understanding the geographic distribution and ecology of OZV and related viruses and for reevaluation of the medical and public health importance of thogotoviruses.

Human Rhinovirus 3C protease cleaves RIPK1, concurrent with caspase 8 activation

Human Rhinovirus (HRV) is a pathogen of significant medical importance, being a major cause of upper respiratory tract infections (common colds) as well as causing the majority of virus-induced asthma exacerbations. We investigated whether HRV could modulate apoptosis, an innate antiviral response. Apoptotic signals are generated either extrinsically or intrinsically and are propagated via caspase cascades that lead to cell death, reducing viral replication, which relies on cellular machinery. Using HRV16 infected cells, in combination with chemical inducers and inhibitors of extrinsic apoptosis we show that HRV16 3C protease cleaves a key intermediate in extrinsic apoptosis. Receptor-interacting protein kinase-1 (RIPK1), an extrinsic apoptosis adaptor protein, was cleaved by caspase 8, as expected, during chemical induction of apoptosis. RIPK1 was cleaved in HRV infection albeit at a different site. Caspase 8 activation, which is associated with extrinsic apoptosis, was concurrent with HRV 3C protease mediated cleavage of RIPK1, and potentially increased the accessibility of the HRV 3C cleavage site within RIPK1 in-vitro. The caspase 8 mediated RIPK1 cleavage product has a pro-apoptotic function, and further cleavage of this pro-apoptotic cleavage product by HRV 3C may provide a mechanism by which HRV limits apoptosis.

Maintenance of Cotton Leaf Curl Multan Betasatellite by Tomato Leaf Curl New Delhi Virus-Analysis by Mutation

Viruses of the genus Begomovirus (family Geminiviridae) are economically important phytopathogens that are transmitted plant-to-plant by the whitefly Bemisia tabaci. Most Old World (OW) begomoviruses are monopartite and many of these interact with symptoms and host range determining betasatellites. Tomato leaf curl New Delhi virus (ToLCNDV) is one of only a few OW begomoviruses with a bipartite genome (components known as DNA A and DNA B). Four genes [AV2, coat protein (CP), transcriptional-activator protein (TrAP), and AC4] of ToLCNDV were mutated and the effects of the mutations on infectivity, symptoms and the ability to maintain Cotton leaf curl Multan betasatellite (CLCuMuB) were investigated. Infectivity and virus/betasatellite DNA titer were assessed by Southern blot hybridization, PCR, and quantitative PCR. The results showed TrAP of ToLCNDV to be essential for maintenance of CLCuMuB and AV2 to be important only in the presence of the DNA B. AC4 was found to be important for the maintenance of CLCuMuB in the presence of, but indispensable in the absence of, the DNA B. Rather than being required for maintenance, the CP was shown to possibly interfere with maintenance of the betasatellite. The findings show that the interaction between a bipartite begomovirus and a betasatellite is more complex than just trans-replication. Clearly, multiple levels of interactions are present and such associations can cause additional significant losses to crops although the interaction may not be stable.

First molecular identification of kobuviruses in wolves (Canis lupus) in Italy

Canine kobuviruses (CaKoVs) were first identified in diarrhoeic and asymptomatic dogs in 2011 in the USA. Subsequent studies have demonstrated a worldwide distribution of these viruses, but it is not clear if CaKoVs play a role as enteric pathogens of dogs. More recently, CaKoV RNA has been detected in wild carnivores, including red fox, golden jackal, side-striped jackal and spotted hyena. In this study, we addressed the hypothesis that wolves are susceptible to CaKoV infections. A total of 185 wolf stool samples were collected from necropsied animals and from transects in the Liguria, Piemonte and Valle D'Aosta regions of Italy, and CaKoV RNA was identified in two of these specimens. Both samples were obtained from necropsied wolves, with a prevalence rate of 4.9% (2/41). Sequence analysis of the full-length VP1 region showed that these strains displayed the highest nucleotide (nt) sequence identity (86.3-98.5%) to canine strains identified in the UK and Africa, and to kobuviruses that were previously detected in other African wild carnivores. This suggests that genetically related CaKoV strains circulate in domestic and wild carnivores, with interspecies transmission being not uncommon among carnivores of different ecosystems.