Showing papers in "Archives of Virology in 2019"
Washington University in St. Louis1, Technical University of Madrid2, Beijing Institute of Genomics3, Georgia State University4, United States Army Medical Research Institute of Infectious Diseases5, Commonwealth Scientific and Industrial Research Organisation6, Columbia University7, University of Texas Medical Branch8, Friedrich Loeffler Institute9, National Institutes of Health10, Instituto Biológico11, Albert Einstein College of Medicine12, Erasmus University Rotterdam13, University of Queensland14, University of Marburg15, Humboldt University of Berlin16, Robert Koch Institute17, International Atomic Energy Agency18, University of Pittsburgh19, University of Warwick20, World Health Organization21, Empresa Brasileira de Pesquisa Agropecuária22, Boston University23, Public Health England24, Kyoto University25, Murdoch University26, Huazhong Agricultural University27, University of São Paulo28, Laval University29, Okayama University30, United States Geological Survey31, United States Department of Agriculture32, Northwestern University33, Icahn School of Medicine at Mount Sinai34, Institut de recherche pour le développement35, Ohio State University36, Katholieke Universiteit Leuven37, South Dakota State University38, Novosibirsk State University39, University of Medicine and Health Sciences40, University of Veterinary Medicine Vienna41, University of Bergen42, Texas A&M University43, Queen's University Belfast44, Centers for Disease Control and Prevention45, University of Sydney46, University of Oxford47, Defence Science and Technology Laboratory48, Queensland University of Technology49, Colorado State University50, Hokkaido University51, Pasteur Institute52, National University of Singapore53, North Carolina State University54, Universidade Federal de Viçosa55, Chinese Center for Disease Control and Prevention56, Fudan University57
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
238 citations
Centers for Disease Control and Prevention1, United States Department of Agriculture2, University of Naples Federico II3, University of Ljubljana4, Mississippi State University5, University of Texas Medical Branch6, Friedrich Loeffler Institute7, Colorado State University8, Columbia University9, University of California, Irvine10, University of the Free State11, Xinjiang University12, Aix-Marseille University13, International Rice Research Institute14, Scripps Research Institute15, Public Health Agency of Canada16, Mayo Clinic17, Hacettepe University18, United States Army Medical Research Institute of Infectious Diseases19, Chinese Center for Disease Control and Prevention20, Kansas State University21, Bernhard Nocht Institute for Tropical Medicine22, Paris Diderot University23, University of Queensland24, University of Helsinki25, University of Zurich26, Public Health England27, Seoul National University28, Charité29, Slovak Academy of Sciences30, Karolinska Institutet31, Katholieke Universiteit Leuven32, University of Washington33, Wuhan University of Science and Technology34, University of Louisville35, University of São Paulo36, University of Bari37, Hokkaido University38, University of Hamburg39, Public Health Agency of Sweden40, Washington State University41, Aristotle University of Thessaloniki42, Oswaldo Cruz Foundation43, University of Brasília44, National University of La Plata45, Pasteur Institute46, University of Maryland, Baltimore47, National Agriculture and Food Research Organization48, University of Glasgow49, University of Tokyo50, University of Oxford51, Korea University52, National Research Council53, Fujian Agriculture and Forestry University54, North Carolina State University55, Universidade Federal de Viçosa56, Fudan University57, National Institutes of Health58
TL;DR: The updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV) is presented.
Abstract: In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).
237 citations
Katholieke Universiteit Leuven1, United States Department of Agriculture2, University of Ljubljana3, Mississippi State University4, University of Texas Medical Branch5, Friedrich Loeffler Institute6, Centers for Disease Control and Prevention7, Colorado State University8, Columbia University9, University of California, Irvine10, University of the Free State11, National Health Laboratory Service12, Aix-Marseille University13, International Rice Research Institute14, Scripps Research Institute15, University of California, San Francisco16, Public Health Agency of Canada17, Mayo Clinic18, Hacettepe University19, United States Army Medical Research Institute of Infectious Diseases20, Chinese Center for Disease Control and Prevention21, Kansas State University22, Fudan University23, Bernhard Nocht Institute for Tropical Medicine24, Paris Diderot University25, University of Queensland26, Public Health England27, Indian Agricultural Research Institute28, Seoul National University29, Slovak Academy of Sciences30, Karolinska Institutet31, Wageningen University and Research Centre32, University of Washington33, University of Louisville34, University of Bari35, University of Hamburg36, Washington State University37, Aristotle University of Thessaloniki38, University of Helsinki39, University of Brasília40, National University of La Plata41, Pasteur Institute42, University of Maryland, Baltimore43, National Agriculture and Food Research Organization44, University of Glasgow45, University of Tokyo46, University of Oxford47, Korea University48, Fujian Agriculture and Forestry University49, North Carolina State University50, National Chung Hsing University51, Universidade Federal de Viçosa52, National Institutes of Health53
TL;DR: The updated taxonomy of the order Bunyavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
105 citations
University of Bristol1, University of Queensland2, University of Alabama at Birmingham3, National Science Foundation4, Radboud University Nijmegen5, Utrecht University6, Moscow State University7, Leiden University Medical Center8, Hungarian Academy of Sciences9, Agricultural Research Service10, Humboldt University of Berlin11, Institute for Animal Health12, University of Guelph13, Pasteur Institute14, National Institutes of Health15, Harvard University16, Mississippi State University17, Agriculture and Agri-Food Canada18, University of Oxford19, Arizona State University20, Universidade Federal de Viçosa21, University of Glasgow22
TL;DR: The ICTV has approved, by an absolute majority, the creation of additional taxonomical ranks above those recognized previously, to encompass the entire spectrum of virus diversity.
Abstract: This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in October 2018. Of note, the ICTV has approved, by an absolute majority, the creation of additional taxonomical ranks above those recognized previously. A total of 15 ranks (realm, subrealm, kingdom, subkingdom, phylum, subphylum, class, subclass, order, suborder, family, subfamily, genus, subgenus, and species) are now available to encompass the entire spectrum of virus diversity. Classification at ranks above genus is not obligatory but can be used by the authors of new taxonomic proposals when scientific justification is provided.
98 citations
Katholieke Universiteit Leuven1, Washington University in St. Louis2, Technical University of Madrid3, Georgia State University4, United States Army Medical Research Institute of Infectious Diseases5, Commonwealth Scientific and Industrial Research Organisation6, Columbia University7, University of Texas Medical Branch8, Friedrich Loeffler Institute9, National Institutes of Health10, Yeshiva University11, Leidos12, Erasmus University Rotterdam13, University of Queensland14, University of Marburg15, University of Illinois at Urbana–Champaign16, Humboldt University of Berlin17, Robert Koch Institute18, International Atomic Energy Agency19, University of Pittsburgh20, University of Warwick21, World Health Organization22, Empresa Brasileira de Pesquisa Agropecuária23, New York University24, Boston University25, Public Health England26, Kyoto University27, Murdoch University28, Huazhong Agricultural University29, Laval University30, Okayama University31, United States Geological Survey32, Northwestern University33, Icahn School of Medicine at Mount Sinai34, Ohio State University35, South Dakota State University36, Novosibirsk State University37, University of Veterinary Medicine Vienna38, University of Medicine and Health Sciences39, Texas A&M University40, Queen's University Belfast41, Centers for Disease Control and Prevention42, University of Oxford43, Defence Science and Technology Laboratory44, University of Missouri45, Colorado State University46, Hokkaido University47, Pasteur Institute48, National University of Singapore49, North Carolina State University50, Zhejiang University51, Universidade Federal de Viçosa52, Chinese Center for Disease Control and Prevention53, Fudan University54
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
68 citations
TL;DR: Baicalein and baicalin were found to be capable of downregulating ZIKV replication up to 10 hours postinfection, while prophylactic effects were evident in pre-treated cells.
Abstract: At present, there is no effective antiviral agent for Zika virus (ZIKV), an arbovirus that is known for its teratogenic effects on newborns. Baicalein and baicalin were found to be capable of downregulating ZIKV replication up to 10 hours postinfection, while prophylactic effects were evident in pre-treated cells. Baicalein exhibited its highest potency during intracellular ZIKV replication, whereas baicalin was most effective against virus entry. Our in silico interaction assays predicted that both compounds exhibited the strongest binding affinities towards ZIKV NS5, while the virus envelope glycoprotein was the least likely target protein. These findings serve as a crucial platform for further in-depth studies to decipher the underlying anti-ZIKV mechanism(s) of each compound.
64 citations
TL;DR: The enteric virome of red-crowned cranes is increased and provides a baseline for comparison to those of other birds or following disease outbreaks, and numerous viruses believed to infect insects, plants, and crustaceans were identified.
Abstract: The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus "Chapparvovirus", and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
50 citations
TL;DR: Comparing clinical symptoms, viremia, and seroconversion of cattle inoculated either with a virulent field strain from North Macedonia isolated from diseased cattle in 2016 or with the attenuated LSDV vaccine strain “Neethling” shows a high analytical sensitivity of both tested duplex real-time qPCR systems for the reliable distinction of LSDV field and vaccine strains.
Abstract: Lumpy skin disease virus (LSDV) infections can cause massive clinical signs in cattle and have great economic impact due to severe trade restrictions. For LSDV control, only live attenuated vaccines are commercially available, but they currently are not authorized in the European Union. Moreover, these vaccine virus strains can induce substantial side effects with clinical signs similar to infections with virulent LSDV. In our study, we compared clinical symptoms, viremia, and seroconversion of cattle inoculated either with a virulent field strain from North Macedonia isolated from diseased cattle in 2016 or with the attenuated LSDV vaccine strain “Neethling”. Using specimens from the field and from experimental inoculation, different diagnostic tools, including a pan-capripox real-time qPCR, newly developed duplex real-time qPCR assays for differentiation between virulent and attenuated LSDV strains, and several serological methods (ELISA, indirect immunofluorescence test and serum neutralization test [SNT]) were evaluated. Our data show a high analytical sensitivity of both tested duplex real-time qPCR systems for the reliable distinction of LSDV field and vaccine strains. Moreover, the commercially available capripox double-antigen ELISA seems to be as specific as the SNT and therefore provides an excellent tool for rapid and simple serological examination of LSDV-vaccinated or infected cattle.
47 citations
TL;DR: The findings suggest that PLE can potentially be used as an antiviral agent, as it helps in platelet augmentation and exhibits antiviral activity against DENV.
Abstract: Dengue disease is characterized by a marked decrease in platelet count, which is life threatening. In the present study, we investigated the antiviral activity of an aqueous extract of Carica papaya leaves (PLE) against dengue virus (DENV) and its effect on platelet augmentation. The anti-dengue activity of PLE in DENV-infected THP-1 cells was examined by immunoblotting and flow cytometry. The effect of PLE on erythrocyte damage was investigated using hemolytic and anti-hemolytic assays. Virus-infected THP-1 cells were assayed for IFN-α secretion. The effect of PLE on platelet augmentation in rats with cyclophosphamide-induced thrombocytopenia was also investigated. The platelet count of blood from the retro-orbital plexus of rats was determined on the 1st, 4th, 7th, 11th and 14th day of study. On the 14th day, the rats were sacrificed for histopathological examination of the liver, kidney and spleen. Plasma of thrombocytopenic rats was tested for thrombopoietin (TPO) and IL-6 secretion. The data suggest that PLE significantly decreases the expression of the envelope and NS1 proteins in DENV-infected THP-1 cells. A marked decrease in intracellular viral load upon PLE treatment confirmed its antiviral activity. This also resulted in a significant decrease in erythrocyte damage and hydrogen-peroxide-induced lipid peroxidation. A significant increase in the number of platelets was found in thrombocytopenic rats treated with PLE, along with an increase in IL-6 and TPO levels. These findings suggest that PLE can potentially be used as an antiviral agent, as it helps in platelet augmentation and exhibits antiviral activity against DENV.
43 citations
TL;DR: The results suggest that a strategy incorporating priming with a vector-expressed antigen followed by boosting with an attenuated live virus may broaden the recognition of ASFV epitopes.
Abstract: In this study, an alphavirus vector platform was used to deliver replicon particles (RPs) expressing African swine fever virus (ASFV) antigens to swine. Alphavirus RPs expressing ASFV p30 (RP-30), p54 (RP-54) or pHA-72 (RP-sHA-p72) antigens were constructed and tested for expression in Vero cells and for immunogenicity in pigs. RP-30 showed the highest expression in Vero cells and was the most immunogenic in pigs, followed by RP-54 and RP-sHA-p72. Pigs primed with two doses of the RP-30 construct were then boosted with a naturally attenuated ASFV isolate, OURT88/3. Mapping of p30 identified an immunodominant region within the amino acid residues 111–130. However, the principal effect of the prime-boost was enhanced recognition of an epitope covered by the peptide sequence 61–110. The results suggest that a strategy incorporating priming with a vector-expressed antigen followed by boosting with an attenuated live virus may broaden the recognition of ASFV epitopes.
39 citations
TL;DR: The ICTV Business Secretary from 2011 until 2017, at that point standing down to enjoy proper retirement, Mike’s great efficiency, broad grasp of taxonomic issues, good humour and, most of all, constant wisdom were greatly appreciated by his colleagues on the Executive Committee.
Abstract: We are pleased to announce that Dr Michael J Adams has been elected as a Life Member, following nomination by the President, recommendation by the Executive Committee, and ratification by the ICTV membership. Mike obtained his degrees at the University of Oxford and Imperial College London, and was a plant pathologist at Rothamsted Research (Harpenden, UK) from 1973 until his retirement from that post in 2006. The later phase of his research was on the epidemiology and control of soil-borne cereal viruses and their vector Polymyxa graminis, with particular reference to barley yellow mosaic virus and barley mild mosaic virus. Mike became involved in the work of the ICTV in 2001 as a member of the Potyviridae Study Group, a position that he held for 16 years. He joined the Executive Committee as chair of the Plant Virus Subcommittee in 2005. He then took on the important role of ICTV Business Secretary from 2011 until 2017, at that point standing down to enjoy proper retirement. He served for a total of 14 years as chair of the Flexiviridae Study Group (2003-2011) and the Virgaviridae Study Group (2011-2017), and co-edited the Ninth Report of the ICTV published in 2011. Mike’s great efficiency, broad grasp of taxonomic issues, good humour and, most of all, constant wisdom, were greatly appreciated by his colleagues on the Executive Committee. Life membership is an honorary appointment bestowed in recognition of outstanding service to virus taxonomy. Life members have voting rights in ratifying taxonomic proposals, when changes to the ICTV Statutes or Rules are proposed, and in elections to the Executive Committee. Information on Life Members is available at the ICTV web site (https ://www.ictvo nline .org).
TL;DR: In the same year, a few regions of the Privolzhsky Federal District of Russia along the northern border of Kazakhstan, which then necessitated vaccination cattle with a live attenuated LSDV vaccine as discussed by the authors.
Abstract: Lumpy skin disease (LSD) has affected many regions of Russia since its first occurrence in 2015. The most devastating year for Russia was 2016, when the virus resurged following a modified stamping-out campaign, causing 313 outbreaks in 16 regions. To avoid unwanted adverse reactions following the use of live attenuated vaccines against LSD virus (LSDV), sheeppox-based vaccines were administered during vaccination campaigns. As a result, LSD was successfully contained in all Russian regions in 2017. In the same year, however, LSD emerged anew in a few regions of the Privolzhsky Federal District of Russia along the northern border of Kazakhstan, which then necessitated vaccinating cattle with a live attenuated LSDV vaccine. Although live attenuated LSDV vaccines are prohibited in Russia, several vaccine-like LSDV strains were identified in the 2017 outbreaks, including commercial farms and backyard animals exhibiting clinical signs consistent with those of field LSDV strains. Sequence alignments of three vaccine-like LSDV strains showed clear similarity to the corresponding RPO30 and GPCR gene sequences of commercial attenuated viruses. How vaccine-like strains spread into Russian cattle remains to be clarified.
TL;DR: The use of Pepper mild mottle virus (PMMoV) as a fecal indicator of wastewater contamination and a process indicator for the performance of the treatment process is supported.
Abstract: There is increasing evidence that the fecal indicator bacteria that are routinely used for testing water quality are inadequate for ensuring protection of the public health. Pepper mild mottle virus (PMMoV) has recently been suggested as an alternative indicator of human fecal contamination in water; however, in Egypt there are no data available about its occurrence and concentration in aquatic environment. The concentration of PMMoV in the influent and effluent of three wastewater treatment plants was measured using qRT-PCR over a period of one year and compared to that of human adenovirus (HAdV), which is considered an indicator for human fecal contamination. PMMoV was detected in ~ 94% of the influent samples and 78% of the effluent samples, with concentrations ranging from 3.9 × 104 to 3.3 × 108 genome copies/l (GC/l) in the influent and 3.9 × 104 to 1.2 × 107 GC/l in the effluent. Similarly, HAdV was identified in 88% and 78% of the influent and effluent samples, respectively. The HAdV concentration ranged between 1.5 × 104 and 1.5 × 107 GC/l for the influent and 2.6 × 104 and 4.4 × 106 GC/l for the effluent. No significant difference was found between the removal ratio of PMMoV and HAdV. Viral reduction of 0.2-1.9 log10 and 0.2- 2.3 log10 by the treatment process was observed for PMMoV and HAdV, respectively. Both viruses showed no clear seasonality. Our data support the use of PMMoV as a fecal indicator of wastewater contamination and a process indicator for the performance of the treatment process.
TL;DR: The results of this study show that this mPCR assay can simultaneously detect and differentiate FPV, FBoV and FeAstV and can be used as an easy, specific and efficient detection tool for clinical diagnosis and epidemiological investigation of these three viruses.
Abstract: A multiplex polymerase chain reaction (mPCR) assay was developed to detect and distinguish feline panleukopenia virus (FPV), feline bocavirus (FBoV) and feline astrovirus (FeAstV). Three pairs of primers were designed based on conserved regions in the genomic sequences of the three viruses and were used to specifically amplify targeted fragments of 237 bp from the VP2 gene of FPV, 465 bp from the NP1 gene of FBoV and 645 bp from the RdRp gene of FeAstV. The results showed that this mPCR assay was effective, because it could detect at least 2.25-4.04 × 104 copies of genomic DNA of the three viruses per μl, was highly specific, and had a good broad-spectrum ability to detect different genotypes of the targeted viruses. A total of 197 faecal samples that had been screened previously for FeAstV and FBoV were collected from domestic cats in northeast China and were tested for the three viruses using the newly developed mPCR assay. The total positive rate for these three viruses was 59.89% (118/197). From these samples, DNA from FPV, FBoV and FeAstV was detected in 73, 51 and 46 faecal samples, respectively. The mPCR testing results agreed with the routine PCR results with a coincidence rate of 100%. The results of this study show that this mPCR assay can simultaneously detect and differentiate FPV, FBoV and FeAstV and can be used as an easy, specific and efficient detection tool for clinical diagnosis and epidemiological investigation of these three viruses.
TL;DR: The development of a simple protocol for point-of-use detection of GRBV is reported, which is 10,000 times more sensitive than conventional PCR, costs under a dollar per sample, and can be completed from sampling to readout in just over half an hour.
Abstract: Grapevine red blotch virus (GRBV) is an emerging virus of significant viticultural importance throughout North America. Here, we report the development of a simple protocol for point-of-use detection of GRBV. Extraction of nucleic acids is not required; instead, the whole intact plant can simply be pricked with a sterile pipette tip, which is then incubated in sterile distilled water to provide the sample template in a loop-mediated isothermal amplification (LAMP) reaction. This method is 10,000 times more sensitive than conventional PCR, costs under a dollar per sample, and can be completed from sampling to readout in just over half an hour.
TL;DR: Phylogenetic analysis indicated thatBFTV-1 is closely related to datura yellow vein nucleorhabdovirus and that BFTV-2 clusters into a monophyletic lineage of legume-associated enamoviruses, which provides insights into the evolutionary history of the enamviruses.
Abstract: Here, we report the identification and characterization of two novel viruses associated with bird's-foot trefoil. Virus sequences related to those of enamoviruses (ssRNA (+); Luteoviridae; Enamovirus) and nucleorhabdoviruses (ssRNA (-); Rhabdoviridae; Nucleorhabdovirus) were detected in Lotus corniculatus transcriptome data. The genome of the tentatively named "bird's-foot trefoil-associated virus 1" (BFTV-1) is a 13,626-nt-long negative-sense ssRNA. BFTV-1 encodes six predicted gene products in the antigenome orientation in the canonical order 3'-N-P-P3-M-G-L-5'. The genome of the proposed "bird's-foot trefoil-associated virus 2" (BFTV-2) is 5,736 nt long with a typical 5΄-PO-P1-2-IGS-P3-P5-3' enamovirus genome structure. Phylogenetic analysis indicated that BFTV-1 is closely related to datura yellow vein nucleorhabdovirus and that BFTV-2 clusters into a monophyletic lineage of legume-associated enamoviruses. This subclade of highly related and co-divergent legume-associated viruses provides insights into the evolutionary history of the enamoviruses.
TL;DR: The results showed absolute consistency with RSV RT-qPCR analysis, demonstrating 100% diagnostic sensitivity and specificity, and indicate that the duplex-rtRAA has great potential for the rapid detection of RSV with a high sensitivity.
Abstract: Human respiratory syncytial virus (RSV) is a common viral pathogen that causes lower respiratory tract infections in infants and children globally. In this study, we developed a duplex reverse transcription recombinase-aided amplification (duplex-rtRAA) assay containing an internal control in a single closed tube for the detection of human RSV. The internal control in the amplification effectively eliminated false-negative results and ensured the accuracy of the duplex-rtRAA system. We first developed and evaluated a universal singleplex-rtRAA assay for RSV. The sensitivity of this assay for RSV was determined as 4.4 copies per reaction, and the specificity was 100%. Next, a duplex-rtRAA assay with an internal control was established. The sensitivity of the duplex-rtRAA assay approached 5.0 copies per reaction, and no cross-reaction with other common respiratory viruses was observed. The two detection methods (singleplex-rtRAA and duplex-rtRAA) developed in this study were used to test 278 clinical specimens, and the results showed absolute consistency with RSV RT-qPCR analysis, demonstrating 100% diagnostic sensitivity and specificity. These data indicate that the duplex-rtRAA has great potential for the rapid detection of RSV with a high sensitivity.
TL;DR: Analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PD coV and facilitate further investigation of this newly emerged pathogen.
Abstract: Porcine deltacoronavirus (PDCoV) was first detected in Hong Kong and has recently spread to many countries around the world. PDCoV causes acute diarrhea and vomiting in pigs, resulting in significant economic losses in the global pork industry. In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Subsequently, the virus was identified by an indirect immunofluorescence assay and electron microscopy. A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Analysis of potential recombination sites showed that CHN-HG-2017 is a possible recombinant originating from the strains CH/SXD1/2015 and Vietnam/HaNoi6/2015. Furthermore, the pathogenicity of this recombinant PDCoV strain was investigated in 5-day-old piglets by oral inoculation. The challenged piglets developed typical symptoms, such as vomiting, anorexia, diarrhea and lethargy, from 1 to 7 days post-inoculation (DPI). Viral shedding was detected in rectal swabs until 14 DPI in the challenged piglets. Interestingly, high titers of virus-neutralizing antibodies in sera were detected at 21 DPI. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. Our analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PDCoV and facilitate further investigation of this newly emerged pathogen.
TL;DR: Phylogenetic analysis showed that 13 newly emerged NADC30-like PRRSV strains, together with some reference strains, formed a new subgroup (subgroup 5), characterized by a predicted 131-amino-acid deletion in the nonstructural protein (NSP) 2, and low levels of whole-genome similarity and a wide variety of recombination patterns complicated the classification.
Abstract: Different strains of porcine reproductive and respiratory syndrome virus (PRRSV) have emerged and circulated in different regions of mainland China since 1996, particularly after 2006. In 2012, NADC30-like PRRSV was first isolated in Henan Province. By 2016, it had spread to most provinces in China. In the present study, the whole genomes (excluding the poly(A) tails) of 13 newly emerged NADC30-like PRRSV strains were sequenced and analyzed. Furthermore, the pathogenicity of SD53-1603, one of the 13 PRRSV strains, was assessed. Phylogenetic analysis showed that these 13 newly emerged NADC30-like PRRSV strains, together with some reference strains, formed a new subgroup (subgroup 5), characterized by a predicted 131-amino-acid deletion in the nonstructural protein (NSP) 2. However, low levels of whole-genome similarity and a wide variety of recombination patterns complicated the classification of the NADC30-like PRRSV isolates. Interestingly, almost all of the recombination breakpoints found in these 13 PRRSV isolates and other NADC30-like PRRSV isolates occurred in genes encoding NSPs and/or minor structural proteins. In addition, piglets infected with the newly emerged NADC30-like strain SD53-1603 displayed clear clinical respiratory symptoms and underwent typical pathological changes. The findings may be useful for elucidating the characteristics and epidemic status of NADC30-like PRRSV in China.
TL;DR: It is suggested that HAdV and HAstV are common in children with diarrhea in Ethiopia, and children under 6 months of age, were less often infected with both viruses.
Abstract: Human adenovirus (HAdV) and human astrovirus (HAstV) are common causes of gastroenteritis. Data on the prevalence and diversity of enteric viruses are important for control and preventive measures. However, epidemiological information regarding HAdV and HAstV infections in Ethiopia are limited. Fecal specimens were collected from 450 outpatient diarrheic infants and young children in Gondar and Bahir Dar from November 2015 to April 2016. Socio-demographic information was recorded. All fecal specimens were screened for the presence of HAdV and classical HAstV using PCR. Genotyping was performed by sequencing and phylogenetic analysis. Human HAdV and HAstV were detected in 144 (32%) and 16 (3.6%) of the children, respectively. Overall, 182 different adenovirus genotypes were detected, including mixed infections. Species F adenoviruses (HAdV-40, HAdV-41) were less common than other adenoviruses (HAdV-1, -2, -3, -5,-12, -16, -31, species D types) with a frequency of 32 versus 150, respectively. The HAstV genotypes were classified as HAstV-8 (n = 10), HAstV-1 (n = 3), HAstV-2 (n = 3), and HAstV-3 (n = 1). HAstV was detected only in Gondar. Thirty-eight coinfections HAdV and one HAstV coinfections were detected. There was no significant difference in the detection rate of HAdV and HAstV between boys and girls. The detection rates also did not differ between children from rural and urban areas. Children under 6 months of age, were less often infected with both viruses. These findings suggest that HAdV and HAstV are common in children with diarrhea in Ethiopia.
TL;DR: A novel genotyping method using 34 short tandem repeat regions of the viral genome concurrently, which is highly sensitive to strain differences when compared to previous methods is described, and will provide a valuable epidemiological tool for white spot disease.
Abstract: White spot disease, caused by infection with white spot syndrome virus (WSSV), is a serious panzootic affecting prawn aquaculture. The disease has spread rapidly around the prawn-culturing regions of the world through a number of previously identified mechanisms. The ability to distinguish and trace strains of WSSV is of great benefit to identify, and then limit, the translocation routes of the disease. Here, we describe a novel genotyping method using 34 short tandem repeat regions of the viral genome concurrently. This technique is highly sensitive to strain differences when compared to previous methods. The efficacy of the described method is demonstrated by testing WSSV isolates from around the globe, showing regional genotypic differences. The differences in the genotypes were used to create a global minimum spanning network, and in most cases the observed relationships were substantiated with verification of transboundary movement. This novel panel of STR markers will provide a valuable epidemiological tool for white spot disease. We have applied this to an outbreak of the disease in Queensland, Australia, that occurred in 2016. While the results indicate that the source of this outbreak currently remains cryptic, the analyses have provided valuable insights with which to further study the origins of the strains involved.
TL;DR: The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently.
Abstract: Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still largely incomplete. Next-generation and Sanger sequencing was performed to provide complete (n = 73) and partial genomic sequence data (n = 38) for NDV isolates collected from domestic and wild birds in Nigeria during 2002-2015, including the first complete genome sequences of genotype IV and subgenotype VIh from the African continent. Phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating high genetic diversity of NDV for a single country. In addition, a high degree of similarity between NDV isolates from domestic and wild birds was observed, suggesting that spillovers had occurred, including to three species that had not previously been shown to be susceptible to NDV infection. Furthermore, the first spillover of a mesogenic Komarov vaccine virus is documented, suggesting a previous spillover and evolution of this virus. The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently. This is especially significant when considering that some viruses were isolated from species of conservation concern. The high diversity of NDV observed in both domestic and wild birds in Nigeria emphasizes the need for active surveillance and epidemiology of NDV in all bird species.
TL;DR: The aim of this study was to determine the frequency of BCoV infections and their genetic diversity in Uruguayan calves and to describe the evolutionary history of the virus in South America.
Abstract: Bovine coronavirus (BCoV) is a recognized cause of severe neonatal calf diarrhea, with a negative impact on animal welfare, leading to economic losses to the livestock industry. Cattle production is one of the most important economic sectors in Uruguay. The aim of this study was to determine the frequency of BCoV infections and their genetic diversity in Uruguayan calves and to describe the evolutionary history of the virus in South America. The overall detection rate of BCoV in Uruguay was 7.8% (64/824): 7.7% (60/782) in dairy cattle and 9.5% (4/42) in beef cattle. The detection rate of BCoV in samples from deceased and live calves was 10.0% (6/60) and 7.6% (58/763), respectively. Interestingly, there was a lower frequency of BCoV detection in calves born to vaccinated dams (3.3%, 8/240) than in calves born to unvaccinated dams (12.2%, 32/263) (OR: 4.02, 95%CI: 1.81–8.90; p = 0.00026). The frequency of BCoV detection was higher in colder months (11.8%, 44/373) than in warmer months (1.5%, 3/206) (OR: 9.05, 95%CI: 2.77–29.53, p = 0.000013). Uruguayan strains grouped together in two different lineages: one with Argentinean strains and the other with Brazilian strains. Both BCoV lineages were estimated to have entered Uruguay in 2013: one of them from Brazil (95%HPD interval: 2011–2014) and the other from Argentina (95%HPD interval: 2010–2014). The lineages differed by four amino acid changes, and both were divergent from the Mebus reference strain. Surveillance should be maintained to detect possible emerging strains that can clearly diverge at the antigenic level from vaccine strains.
TL;DR: This review focuses on updating the research progress of these novel vaccines for foot-and-mouth disease eradication, summarizing their merits and including ideas for improvement.
Abstract: Foot-and-mouth disease (FMD) is a major worldwide viral disease in animals, affecting the national and international trade of livestock and animal products and leading to high economic losses and social consequences. Effective control measures of FMD involve prevention through vaccination with inactivated vaccines. These inactivated vaccines, unfortunately, require short-term protection and cold-chain and high-containment facilities. Major advances and pursuit of hot topics in vaccinology and vectorology are ongoing, involving peptide vaccines, DNA vaccines, live vector vaccines, and novel attenuated vaccines. DIVA capability and marker vaccines are very important in differentiating infected animals from vaccinated animals. This review focuses on updating the research progress of these novel vaccines, summarizing their merits and including ideas for improvement.
TL;DR: Results indicate that all three PCV2 genotypes are present on pig farms and thatPCV2d has become the predominant genotype, and the epidemic trend of PCV3 should be closely monitored.
Abstract: A total of 472 samples from domestic pigs collected in China from 2015 to 2018 were tested for the presence of porcine circovirus types 2 and 3 (PCV2 and PCV3, respectively) by conventional polymerase chain reaction analysis. The prevalence of PCV2, PCV3, and PCV2/3 co-infection was 50.0%, 13.3%, and 6.78%, respectively. The complete genomic sequences of 66 PCV2 isolates and four PCV3 isolates were determined. Based phylogenetic analysis, the PCV2 isolates were assigned to three genotypes, PCV2a, PCV2b, and PCV2d, representing 13.6% (9/66), 25.8% (17/66), and 60.6% (40/66) of the total, respectively. All four PCV3 isolates shared a high degree of similarity in their complete nucleotide sequences (98.8-99.8% identity) and ORF2 amino acid sequences (98.6-99.5% identity). These results indicate that all three PCV2 genotypes (PCV2a, PCV2b, and PCV2d) are present on pig farms and that PCV2d has become the predominant genotype. The predicted amino acid sequences of the four PCV3 isolates indicated that PCV3-CN-JL53/PCV3-CN-LN56, PCV3-CN-HLJ3, and PCV3-CN-0710, belonged to the genotypes PCV3a, PCV3b, and PCV3a-IM, respectively. In view of the great harm that PCV2 causes to the pig industry, the epidemic trend of PCV3 should continue to be closely monitored. This study provides information about the prevalence, genetic diversity, and molecular epidemiology of PCV2 and PCV3 in China from 2015 to 2018.
TL;DR: According to the current classification criteria, PE–088 represents a new species in the genus Begomovirus, tentatively named as cowpea bright yellow mosaic virus (CoBYMV), which presented the typical genomic organization of New World begomoviruses.
Abstract: A new bipartite begomovirus (family Geminiviridae) was detected on cowpea (Vigna unguiculata) plants exhibiting bright golden mosaic symptoms on leaves under field conditions in Brazil. Complete consensus sequences of DNA-A and DNA-B components of an isolate of the virus (PE-088) were obtained by nanopore sequencing and confirmed by Sanger sequencing. The genome components presented the typical genomic organization of New World (NW) begomoviruses. Pairwise sequence comparisons revealed low levels of identity with other begomovirus species previously reported infecting cowpea around the world. Phylogenetic analysis using complete sequences of DNA-A components revealed that the closest relatives of PE-088 (85-87% nucleotide sequence identities) were three legume-infecting begomoviruses from Brazil: bean golden mosaic virus, macroptilium common mosaic virus and macroptilium yellow vein virus. According to the current classification criteria, PE-088 represents a new species in the genus Begomovirus, tentatively named as cowpea bright yellow mosaic virus (CoBYMV).
TL;DR: The first sequences of RHDV in Africa are reported, isolated from Moroccan rabbits, and these resemble GI.1b/GI.2 recombinants found in the Iberian Peninsula.
Abstract: Rabbit hemorrhagic disease virus (RHDV) is highly lethal to the European rabbit (Oryctolagus cuniculus). It was first reported in 1984 in China, but in 2010, a new variant of the virus was detected (GI.2) in France. Several recombination events with pathogenic and non-pathogenic strains have been described. Here, we report the first sequences of RHDV in Africa, isolated from Moroccan rabbits, and these resemble GI.1b/GI.1b/GI.2 recombinants found in the Iberian Peninsula. Monitoring and characterization of strains from future outbreaks are advised to guarantee the success of current programs on small-rabbit production for poverty alleviation in African countries.
TL;DR: The newly developed RT-RPA assay offers a reliable, sensitive and efficient method for rapid detection of MCMV in maize in equipment-limited diagnostic laboratories and on-site facilities.
Abstract: Maize chlorotic mottle virus (MCMV), an important quarantine virus, causes lethal necrosis in maize when coinfected with a potyvirid, which is seriously threatening the production of maize worldwide. In this study, recombinase polymerase amplification (RPA), a novel isothermal DNA amplification and detection technique, was developed to detect MCMV in maize crops. A pair of specific primers was designed based on the conserved sequences of the MCMV coat protein region. The RT-RPA assay was carried out as an isothermal reaction at 38 °C that was complete within 30 min, and no cross-reactivity was detected with other viruses infecting maize in China. The limit of detection of the RT-RPA assay was tenfold lower than that of ordinary RT-PCR. Moreover, this method was successfully applied to test field-collected samples. The newly developed RT-RPA assay offers a reliable, sensitive and efficient method for rapid detection of MCMV in maize in equipment-limited diagnostic laboratories and on-site facilities.
TL;DR: The results of these studies indicated that Glycyrrhiza glabra saponins show great promise as safe and effective adjuvants.
Abstract: Numerous studies have shown that immunostimulatory complexes containing Quil-A saponin and various antigens are effective in stimulating the immune response and can be used as vaccine preparations for animals and humans. However, Quil-A saponin possesses toxicity and haemolytic activity. In the present work, a saponin-containing preparation named "Glabilox" was isolated from the roots of a Glycyrrhiza glabra L. plant by high-performance liquid chromatography (HPLC). The results showed that Glabilox has no toxicity or haemolytic activity and can form stable immunostimulatory complexes. Subcutaneous immunization of mice with an immunostimulating complex containing Glabilox and H7N1 influenza virus antigens stimulated high levels of humoral and cellular immunity. Vaccination of chickens with the same immunostimulating complex protected 100% of the animals after experimental infection with a homologous virus. Comparative studies showed that the immunogenic and protective activity of immunostimulatory complexes containing Quil-A and immunostimulatory complexes containing Glabilox are comparable to each other. The results of these studies indicated that Glycyrrhiza glabra saponins show great promise as safe and effective adjuvants.
TL;DR: The presence or absence of anti-HBs antibodies in the context of HBV immunity has been the subject of extensive discussion and clinical, laboratory and epidemiological interest.
Abstract: Anti-HBs antibodies develop after natural infection with hepatitis B virus (HBV) or vaccination against this virus, as a result of activation of the human immune system by the HBV surface antigen (HBsAg). Anti-HBs-positive individuals are immunologically competent against HBV infection. This immunity is determined by the antibody levels in the bloodstream after resolution of natural infection or after vaccination. Anti-HBs antibody levels have been observed to decrease to below the protective level years after natural infection or vaccination, and there is reason to doubt that protective immunity to HBV is maintained after that. Factors that affect the maintenance of the anti-HBs antibody level in the bloodstream have been reported. Maintenance of immunity to HBV has been reported in anti-HBs negative individuals and those with detectable but low levels after natural infection or after vaccination. On the other hand, detection of anti-HBs antibodies without protective activity has also been observed. The presence or absence of anti-HBs antibodies in the context of HBV immunity has been the subject of extensive discussion and clinical, laboratory and epidemiological interest. These three scenarios of the anti-HBs response are discussed in this review article.