Virus classification for viral genomic fragments using PhaGCN2.

Viruses are the most ubiquitous and diverse entities in the biome. Due to the rapid growth of newly identified viruses, there is an urgent need for accurate and comprehensive virus classification, particularly for novel viruses. Here, we present PhaGCN2, which can rapidly classify the taxonomy of viral sequences at the family level and supports the visualization of the associations of all families. We evaluate the performance of PhaGCN2 and compare it with the state-of-the-art virus classification tools, such as vConTACT2, CAT and VPF-Class, using the widely accepted metrics. The results show that PhaGCN2 largely improves the precision and recall of virus classification, increases the number of classifiable virus sequences in the Global Ocean Virome dataset (v2.0) by four times and classifies more than 90% of the Gut Phage Database. PhaGCN2 makes it possible to conduct high-throughput and automatic expansion of the database of the International Committee on Taxonomy of Viruses. The source code is freely available at https://github.com/KennthShang/PhaGCN2.0.

A discussion of RNA virus taxonomy based on the 2020 International Committee on Taxonomy of Viruses report.

RNA viruses have a higher mutation rate than DNA viruses; however, RNA viruses are insufficiently studied outside disease settings. The International Committee on Taxonomy of Viruses (ICTV) is an organization set up by virologists to standardize virus classification. To better understand ICTV taxonomy and the characteristics and rules of different RNA virus families, we analyzed the 3,529 RNA viruses included in the 2020 ICTV report using five widely used metrics: length, host, GC content, number of predicted ORFs, and sequence similarity. The results show that host type has a significant influence on viral genome length and GC content. The genome lengths of virus members within the same genus are quite similar: 98.28% of the genome length differences within any particular genus are less than 20%. The species within those genera containing segmented viruses also have a similar length and number of segments. The number of predicted ORFs in the RNA viral genomes also shows a strong, statistically significant correlation with genome length. We suggest that due to the high mutation rate of RNA virus genomes, current RNA virus classification should mainly rely on protein similarities rather than nucleic acid similarities.

Risk assessment and genomic characterization of Zika virus in China and its surrounding areas.

BACKGROUND: Zika virus (ZIKV) has emerged as a global pathogen causing significant public health concerns. China has reported several imported cases where ZIKV were carried by travelers who frequently travel between China and ZIKV-endemic regions. To fully characterize the ZIKV strains isolated from the cases reported in China and assess the risk of ZIKV transmission in China, comprehensive phylogenetic and genetic analyses were performed both on all ZIKV sequences of China and on a group of scientifically selected ZIKV sequences reported in some of the top interested destinations for Chinese travelers. METHODS: ZIKV genomic sequences were retrieved from the National Center for Biotechnology Information database through stratified sampling. Recombination event detection, maximum likelihood (ML) phylogenetic analysis, molecular clock analysis, selection pressure analysis, and amino acid substitution analysis were used to reconstruct the epidemiology and molecular transmission of ZIKV. RESULTS: The present study investigated 18 ZIKV sequences from China and 70 sequences from 16 selected countries. Recombination events rarely happens in all ZIKV Asian lineage. ZIKV genomes were generally undergone episodic positive selection (17 sites), and only one site was under pervasive positive selection. All ZIKV imported into China were Asian lineage and were assigned into two clusters: Venezuela-origin (cluster A) and Samoa-origin cluster (cluster B) with common ancestor from French Polynesia. The time of most recent common ancestors of Cluster A dated to approximately 2013/11 (95% highest posterior density [HPD] 2013/06, 2014/03) and cluster B dated to 2014/08 (95% HPD 2014/02, 2015/01). Cluster B is more variable than Cluster A in comparison with other clusters, but no varied site of biological significance was revealed. ZIKV strains in Southeast Asia countries are independent from strains in America epidemics. CONCLUSIONS: The genetic evolution of ZIKV is conservative. There are two independent introductions of ZIKV into China and China is in danger of autochthonous transmission of ZIKV because of high-risk surrounding areas. Southeast Asia areas have high risk of originating the next large-scale epidemic ZIKV strains.

Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica).

The Malayan pangolin (Manis javanica) is an unusual, scale-covered, toothless mammal that specializes in myrmecophagy. Due to their threatened status and continuing decline in the wild, concerted efforts have been made to conserve and rescue this species in captivity in China. Maintaining this species in captivity is a significant challenge, partly because little is known of the molecular mechanisms of its digestive system. Here, the first large-scale sequencing analyses of the salivary gland, liver and small intestine transcriptomes of an adult M. javanica genome were performed, and the results were compared with published liver transcriptome profiles for a pregnant M. javanica female. A total of 24,452 transcripts were obtained, among which 22,538 were annotated on the basis of seven databases. In addition, 3,373 new genes were predicted, of which 1,459 were annotated. Several pathways were found to be involved in myrmecophagy, including olfactory transduction, amino sugar and nucleotide sugar metabolism, lipid metabolism, and terpenoid and polyketide metabolism pathways. Many of the annotated transcripts were involved in digestive functions: 997 transcripts were related to sensory perception, 129 were related to digestive enzyme gene families, and 199 were related to molecular transporters. One transcript for an acidic mammalian chitinase was found in the annotated data, and this might be closely related to the unique digestive function of pangolins. These pathways and transcripts are involved in specialization processes related to myrmecophagy (a form of insectivory) and carbohydrate, protein and lipid digestive pathways, probably reflecting adaptations to myrmecophagy. Our study is the first to investigate the molecular mechanisms underlying myrmecophagy in M. javanica, and we hope that our results may play a role in the conservation of this species.

[Study on steroidal compounds from Dioscorea zingiberensis].

OBJECTIVE: To study the chemical constituents of Dioscorea zingiberensis. METHOD: Manifold chromatography methods were used to separate the chemical constituents, and the chemical stuctures were determined by spectral analyses. RESULT: 6 compounds were isolated from Dioscorea zingiberensis and identified as deltonin, protodeltonin, zingiberensis newsaponin, dioscin, 3-O-[beta-D-glucopyranosyl(1 --> 4)]-beta-D-glucopyranosyl-diosgenin, diosgenin. CONCLUSION: Deltonin and protodeltonin were isolated from this plant for the first time.

[Expression and antigenicity analysis of p46000 antigen from newborn larvae of Trichinella spiralis].

OBJECTIVE: To express and analyze p46000 antigen from newborn larvae of Trichinella spiralis. METHODS: p46000 antigen gene was subcloned to the pET28a expression system by PCR. The recombinant transformant was induced by IPTG and the antigenicity was analyzed with ELISA and Western blotting. RESULTS: The molecular weight of the expressed protein was about Mr 48000. ELISA and Western blotting showed that this recombinant protein could be recognized by T. spiralis infected swine serum and rabbit anti-recombinant protein serum, and the rabbit anti-recombinant protein serum could recognize a Mr 46000 protein from newborn larvae of T. spiralis. CONCLUSION: p46000 recombinant antigen from newborn larvae of T. spiralis was expressed which shows a specific antigenicity.

[Immunoscreening of newborn larvae cDNA library of Trichinella spiralis].

OBJECTIVE: To obtain antigenic genes encoding newborn larvae antigens of Trichinella spiralis. METHODS: Newborn larvae (NBL) cDNA library of Trichinella spiralis was screened using the infected swine serum and positive clones were sequenced and analysed. RESULTS: 158 positive clones were obtained from 4.5 x 10(5) recombinant clones by immunoscreening. The sequence analysis of positive clones showed that there are 36 novel cDNAs, 5 reported cDNAs and 12 cDNAs without the ORF showing high similarity to the mitochondrial DNA of Trichinella spiralis. CONCLUSION: Some cDNAs encoding antigenic protein of newborn larvae of Trichinella spiralis were obtained.

[Study on the flavonoids of Eupatorium lindleyanum].

OBJECTIVE: Study on the flavonoids from the air part of Eupatorium lindleyanum. METHOD: Alcohol percolation, silica gel column chromatography and re-crystallization et al. RESULT: Jaceosidin, kaempferol, quceritin, astragalin, trifolin and hypersoide were isolated from E. lindleyanum. Their structures were elucidated on the basis of spectral evidence. CONCLUSION: Jaceosidin, kaempferol, quceritin, astragalin and trifolin were isolated from E. lindleyanum for the first time.

[Study on the anticancer activities (in vivo) of the extract from Citrus reticulata Blanco and its influence on sarcoma-180 cells cycle].

OBJECTIVE: To study the anticancer activity of the extract from Citrus reticulata in vivo. METHOD: Anticancer activities were tested with tumor model in vivo (Sarcoma-180 cells, Heps cells, EAC cells implanted in mice). RESULT: The extract from Citrus reticulata showed marked anticancer activities on Sarcoma-180 cells and Heps cells implanted in mice, had no marked anticancer activities on EAC cells implanted in mice and induced apoptosis of Sarcoma-180 cell. CONCLUSION: The extract from Citrus reticulata will have promising prospects as an anticancer Chinese medicine, but further studies will be needed.