Multiple mycoviruses identified in Pestalotiopsis spp. from Chinese bayberry

Abstract Background Chinese bayberry (Myrica rubra) is a subtropical fruit crop widely grown in southern China. Twig dieback is a disease of Chinese bayberry caused by Pestalotiopsis spp. and results in great economic losses to Chinese bayberry production. A virus survey was conducted in the population of Pestalotiopsis spp. infecting M. rubra in China. We explored the viral diversity in Pestalotiopsis spp., which may provide resources for further development as biocontrol agents of twig dieback. Methods Strains of Pestalotiopsis spp. were isolated from diseased twigs of M. rubra, and cultured on potato dextrose agar for RNA extraction. The total RNA of each strain was extracted, mixed, and used for RNA sequencing. The resulting sequences were deduplicated, annotated, and then used for phylogenetic analysis. Results Seven novel viruses were characterized from 59 isolates of M. rubra collected from 14 localities in China. Based on the phylogenetic analysis, these viruses were classified into five viral families/orders, Botourmiaviridae, Mitoviridae, Partitiviridae, Tymovirales and Bunyavirales, and one virus, Pestalotiopsis negative-stranded RNA virus 1, which likely belongs to a new viral family. Conclusions Metatranscriptomics analysis showed the presence of various mycoviruses in Pestalotiopsis spp. isolated from M. rubra in China. The genomes of eight putative viruses were identified, seven of which were nearly full-length. Some of these viruses of Pestalotiopsis spp. may have the potential for the biological control of twig dieback of M. rubra.

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Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽

10.1371/journal.pone.0258318 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0258318

Author(s):

Marta Antas ◽

Monika Olech ◽

Anna Szczotka-Bochniarz

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

Rna Virus ◽

Economic Losses ◽

High Morbidity ◽

Antigenic Analysis ◽

S Gene ◽

Porcine Epidemic Diarrhoea Virus ◽

Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

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Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea

Pathogens ◽

10.3390/pathogens10020241 ◽

2021 ◽

Vol 10 (2) ◽

pp. 241

Author(s):

Joon Moh Park ◽

Jachoon Koo ◽

Se Won Kang ◽

Sung Hee Jo ◽

Jeong Mee Park

Keyword(s):

Phylogenetic Analysis ◽

South Korea ◽

Nicotiana Benthamiana ◽

Economic Value ◽

Virulence Gene ◽

Economic Losses ◽

Herbaceous Perennials ◽

Rhodococcus Fascians ◽

Different Strains

Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.

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Ever-increasing viral diversity associated with the red imported fire ant Solenopsis invicta (Formicidae: Hymenoptera)

Virology Journal ◽

10.1186/s12985-020-01469-w ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

César Augusto Diniz Xavier ◽

Margaret Louise Allen ◽

Anna Elizabeth Whitfield

Keyword(s):

Solenopsis Invicta ◽

De Novo ◽

Rna Virus ◽

Housekeeping Genes ◽

Virus Genome ◽

Single Strand ◽

Viral Diversity ◽

Red Imported Fire Ant ◽

Sequence Comparisons ◽

Data Set

Abstract Background Advances in sequencing and analysis tools have facilitated discovery of many new viruses from invertebrates, including ants. Solenopsis invicta is an invasive ant that has quickly spread worldwide causing significant ecological and economic impacts. Its virome has begun to be characterized pertaining to potential use of viruses as natural enemies. Although the S. invicta virome is the best characterized among ants, most studies have been performed in its native range, with less information from invaded areas. Methods Using a metatranscriptome approach, we further identified and molecularly characterized virus sequences associated with S. invicta, in two introduced areas, U.S and Taiwan. The data set used here was obtained from different stages (larvae, pupa, and adults) of S. invicta life cycle. Publicly available RNA sequences from GenBank’s Sequence Read Archive were downloaded and de novo assembled using CLC Genomics Workbench 20.0.1. Contigs were compared against the non-redundant protein sequences and those showing similarity to viral sequences were further analyzed. Results We characterized five putative new viruses associated with S. invicta transcriptomes. Sequence comparisons revealed extensive divergence across ORFs and genomic regions with most of them sharing less than 40% amino acid identity with those closest homologous sequences previously characterized. The first negative-sense single-stranded RNA virus genomic sequences included in the orders Bunyavirales and Mononegavirales are reported. In addition, two positive single-strand virus genome sequences and one single strand DNA virus genome sequence were also identified. While the presence of a putative tenuivirus associated with S. invicta was previously suggested to be a contamination, here we characterized and present strong evidence that Solenopsis invicta virus 14 (SINV-14) is a tenui-like virus that has a long-term association with the ant. Furthermore, based on virus sequence abundance compared to housekeeping genes, phylogenetic relationships, and completeness of viral coding sequences, our results suggest that four of five virus sequences reported, those being SINV-14, SINV-15, SINV-16 and SINV-17, may be associated to viruses actively replicating in the ant S. invicta. Conclusions The present study expands our knowledge about viral diversity associated with S. invicta in introduced areas with potential to be used as biological control agents, which will require further biological characterization.

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Molecular Detection of Novel Borrelia Species, Candidatus Borrelia javanense, in Amblyomma javanense Ticks from Pangolins

Pathogens ◽

10.3390/pathogens10060728 ◽

2021 ◽

Vol 10 (6) ◽

pp. 728

Author(s):

Bao-Gui Jiang ◽

Ai-Qiong Wu ◽

Jia-Fu Jiang ◽

Ting-Ting Yuan ◽

Qiang Xu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Molecular Detection ◽

Southern China ◽

Natural Circulation ◽

Rrna Gene ◽

The Novel ◽

Flagellin Gene ◽

Manis Javanica ◽

The 16S Rrna Gene ◽

Novel Agent

A novel Borrelia species, Candidatus Borrelia javanense, was found in ectoparasite ticks, Amblyomma javanense, from Manis javanica pangolins seized in anti-smuggling operations in southern China. Overall, 12 tick samples in 227 (overall prevalence 5.3%) were positive for Candidatus B. javanense, 9 (5.1%) in 176 males, and 3 (5.9%) in 51 females. The phylogenetic analysis, based on the 16S rRNA gene and the flagellin gene sequences of the Borrelia sp., exhibited strong evidence that Candidatus B. javanense did not belong to the Lyme disease Borrelia group and the relapsing fever Borrelia group but another lineage of Borrelia. The discovery of the novel Borrelia species suggests that A. javanense may be the transmit vector, and the M. javanica pangolins should be considered a possible origin reservoir in the natural circulation of these new pathogens. To our knowledge, this is the first identification of a novel Borrelia species agent in A. javanense from pangolins. Whether the novel agent is pathogenic to humans is unknown and needs further research.

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Porcine Reproductive and Respiratory Syndrome Virus: Immune Escape and Application of Reverse Genetics in Attenuated Live Vaccine Development

Vaccines ◽

10.3390/vaccines9050480 ◽

2021 ◽

Vol 9 (5) ◽

pp. 480

Author(s):

Honglei Wang ◽

Yangyang Xu ◽

Wenhai Feng

Keyword(s):

Immune Responses ◽

Reverse Genetics ◽

Vaccine Development ◽

Immune Escape ◽

Rna Virus ◽

Economic Losses ◽

Respiratory Syndrome Virus ◽

Live Vaccines ◽

Host Immune Responses ◽

Inactivated Vaccines

Porcine reproductive and respiratory syndrome virus (PRRSV), an RNA virus widely prevalent in pigs, results in significant economic losses worldwide. PRRSV can escape from the host immune response in several processes. Vaccines, including modified live vaccines and inactivated vaccines, are the best available countermeasures against PRRSV infection. However, challenges still exist as the vaccines are not able to induce broad protection. The reason lies in several facts, mainly the variability of PRRSV and the complexity of the interaction between PRRSV and host immune responses, and overcoming these obstacles will require more exploration. Many novel strategies have been proposed to construct more effective vaccines against this evolving and smart virus. In this review, we will describe the mechanisms of how PRRSV induces weak and delayed immune responses, the current vaccines of PRRSV, and the strategies to develop modified live vaccines using reverse genetics systems.

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The Function of the PRRSV–Host Interactions and Their Effects on Viral Replication and Propagation in Antiviral Strategies

Vaccines ◽

10.3390/vaccines9040364 ◽

2021 ◽

Vol 9 (4) ◽

pp. 364

Author(s):

Jun Ma ◽

Lulu Ma ◽

Meiting Yang ◽

Wei Wu ◽

Wenhai Feng ◽

...

Keyword(s):

Immune Response ◽

Molecular Mechanisms ◽

Immune Escape ◽

Rna Virus ◽

Economic Losses ◽

Respiratory Syndrome Virus ◽

Swine Industry ◽

Live Virus ◽

Virus Challenge ◽

Host Interactions

Porcine reproductive and respiratory syndrome virus (PRRSV) affects the global swine industry and causes disastrous economic losses each year. The genome of PRRSV is an enveloped single-stranded positive-sense RNA of approximately 15 kb. The PRRSV replicates primarily in alveolar macrophages of pig lungs and lymphatic organs and causes reproductive problems in sows and respiratory symptoms in piglets. To date, studies on how PRRSV survives in the host, the host immune response against viral infections, and pathogenesis, have been reported. PRRSV vaccines have been developed, including inactive virus, modified live virus, attenuated live vaccine, DNA vaccine, and immune adjuvant vaccines. However, there are certain problems with the durability and effectiveness of the licensed vaccines. Moreover, the high variability and fast-evolving populations of this RNA virus challenge the design of PRRSV vaccines, and thus effective vaccines against PRRSV have not been developed successfully. As is well known, viruses interact with the host to escape the host’s immune response and then replicate and propagate in the host, which is the key to virus survival. Here, we review the complex network and the mechanism of PRRSV–host interactions in the processes of virus infection. It is critical to develop novel antiviral strategies against PRRSV by studying these host–virus interactions and structures to better understand the molecular mechanisms of PRRSV immune escape.

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TaffiX® nasal powder spray forms an effective barrier against infectious new variants of SARS-CoV-2 (COVID-19)

10.21203/rs.3.rs-420365/v1 ◽

2021 ◽

Author(s):

Michal Mandelboim ◽

Ella Mendelson ◽

Yaron Drori ◽

Nofar Atari ◽

Tair Lapidot ◽

...

Keyword(s):

South African ◽

Rna Virus ◽

Rna Extraction ◽

Real Life ◽

Preclinical Study ◽

Viral Rna ◽

Pcr Analysis ◽

Effective Barrier ◽

Gel Layer

Abstract Introduction: While vaccination efforts against SARS-CoV-2 around the world are ongoing -, new high-infectious variants of the virus are being detected. The protection of the available vaccines against some of the new variants is weaker, and experts are concerned that newer as yet undescribed variants of this mutated RNA virus will eventually prove stable against the current vaccines. Additional preventive measures will therefore be needed to protect the population until effective vaccinations are widely available.TaffiX® is a personal, anti-viral nasal powder spray comprised of low pH Hypromellose that upon insufflation into the nose creates a thin gel layer covering the nasal mucosa and forming a protective mechanical barrier that prevents viruses from engaging with nasal cells- the main portal of entry for viruses. Taffix is commercially available in many countries across Europe, Asia America and Africa. In a prior preclinical study, TaffiX® was found to be effective against SARS-CoV-2 Hong Kong/VM20001061/2020 in experimental in vitro conditions. A real-life clinical survey demonstrated that TaffiX® nasal spray significantly reduced the SARS-CoV-2 infection rate post mass-gathering event in a highly endemic community.Objective: The current study aimed to test the protective effect of Taffix against new pathogenic, highly infectious SARS-CoV-2 variants in vitro: the “British” B.1.1.7 (hCoV-19/Israel/CVL-46879-ngs/2020) and the “South African” B.1.351 (hCoV-19/Israel/CVL-2557-ngs/2020) variants.Study design: A TaffiX® gel was formed on a nylon filter, using an amount equivalent to a clinical dose of Taffix . Filters were then seeded with SARS-CoV-2 B.1.1.7 (“British”) and B.1.351 (“South African”) variants. After a 10 -minute incubation at room temperature, the bottom of each filter was washed, and the resulting flow-through was collected and seeded into 24 -well plates containing Vero-E6 cells. After 5 days of incubation, a 200 µl sample from each well was taken for viral RNA extraction followed by SARS-CoV 2 RT-PCR analysis.Results: The TaffiX® gel completely blocked SARS-CoV-2 highly infectious variants B.1.1.7 and B.1.351 in vitro, reducing the titer of recoverable infectious virus as well as viral RNA by 100%.Conclusions: Under in vitro conditions, TaffiX® formed an effective protective barrier against SARS-COV-2 variants (British variant and South African Variant). These results are consistent with prior findings demonstrating the in vitro high efficacy of Taffix gel in preventing viruses from reaching cells and infecting them. These results, added to clinical real-life studies performed with Taffix , support its use as an effective barrier against new variants of SARS-CoV-2 in conjunction with other protective measures.

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Three new Russula species in sect. Ingratae (Russulales, Basidiomycota) from southern China

MycoKeys ◽

10.3897/mycokeys.84.68750 ◽

2021 ◽

Vol 84 ◽

pp. 103-139

Author(s):

Guo-Jie Li ◽

Shou-Mian Li ◽

Bart Buyck ◽

Shi-Yi Zhao ◽

Xue-Jiao Xie ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Internal Transcribed Spacer ◽

Southern China ◽

Its Region ◽

Line Drawings ◽

Phylogenetic Data ◽

Three New Species ◽

First Time

Three new species of Russulasection Ingratae, found in Guizhou and Jiangsu Provinces, southern China, are proposed: R. straminella, R. subpectinatoides and R. succinea. Photographs, line drawings and detailed morphological descriptions for these species are provided with comparisons against closely-related taxa. Phylogenetic analysis of the internal transcribed spacer (ITS) region supported the recognition of these specimens as new species. Additionally, R. indocatillus is reported for the first time from China and morphological and phylogenetic data are provided for the Chinese specimens.

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Morphometry and Phylogeny of the Different Populations of Selaginella tamariscina (P. Beauv.) Spring and S. pulvinata (Hook. & Grev.) Maxim. in Northern Thailand

Chiang Mai University Journal of Natural Sciences ◽

10.12982/cmujns.2021.077 ◽

2021 ◽

Vol 20 (4) ◽

Author(s):

Udon Pongkawong ◽

◽

Jatupol Kampuansai ◽

Rossarin Pollawatn ◽

Arunothai Jampeetong ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Southern China ◽

Phylogenetic Analyses ◽

Dna Barcode ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Morphological Characters ◽

The Philippines ◽

Northern Thailand ◽

Selaginella Tamariscina

Abstract “Dok Hin” is the Thai local name for Selaginella species that form rosettes. They commonly distributes in Siberia, Manchuria, southern China, Japan, the Philippines and Thailand. Morphology of Dok Hin is very resemble leading to misidentification. So, exactly number of species of Dok Hin in Thailand and their differences in morphological characteristics is not well understood. Thus, revision of morphological characters and phylogenetic confirmation of the taxonomic identification are needed. This study aims to examine morphological charateristics and phylogenetic patterns in eight populations of the Dok Hin in Northern Thailand. Morphology of Dok Hin from each populations was quantitatively examined using 15 vegetative and 6 reproductive characters meanwhile phylogenetic analyses was explored by DNA barcode ITS2. The results of the phylogenetic analysis revealed the existence of two species of Dok Hin, S. tamariscina and S. pulvinata. Selaginella tamariscina can be distinguished from S. pulvinata by its presence of a pseudotrunk above ground and ridges of dorsal leaves. On the other hand, the results of phylogenetic analysis indicated the differences among populations of S. pulvinata as well. Chiang Mai populations of S. pulvinata was characterized by peculiar set of characters long leaves and leaf apices look like caudate, while the rest of their populations have shorter leaves and leaf apices look like aristate. It indicates that S. pulvinata has genetic and phenotypic divergence among populations. However, additional studies of Dok Hin populations in other parts of Thailand and studies on different genetic markers are necessary to confirm the taxonomic status of S. pulvinata. Keywords: Dok Hin, Morphometric, Phylogeny, Pseudotrunk, Resurrection plant

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Current status of porcine epidemic diarrhoea (PED) in European pigs

Journal of Veterinary Research ◽

10.2478/jvetres-2019-0064 ◽

2019 ◽

Vol 63 (4) ◽

pp. 465-470

Author(s):

Marta Antas ◽

Grzegorz Woźniakowski

Keyword(s):

Rna Virus ◽

Acute Diarrhoea ◽

Current Status ◽

Economic Losses ◽

Porcine Epidemic Diarrhoea Virus ◽

Diarrhoea Virus ◽

The Us ◽

The Usa ◽

Suckling Piglets ◽

Farming Industry

Abstract Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. The disease is clinically similar to other forms of porcine gastroenteritis. Pigs are the only known host of the disease, and the occurrence of PED in wild boars is unknown. The virus causes acute diarrhoea, vomiting, dehydration, and high mortality in suckling piglets reaching 100%. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The loss in the US pig industry has been estimated at almost seven million pigs. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA.

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