Characterizationof complete genome sequence of a rat coronavirus / 中国人兽共患病学报

This study determined the whole genome sequence and phylogenetic characteristics of a rat coronavirus.Nucleic acids were extracted from rat intestinal tissues collected in Inner Mongolia,and high-throughput sequencing was performed.A novel alphacoronavirus was present in the samples.The complete genome was amplified with PCR and RACE.Multiple se-quence alignment and a phylogenetic tree were constructed in MEGA.The whole genome of the rat coronavirus,denoted NMR-13,was 27 674 bp and included two non-coding regions and eight open reading frames,successively 5'UTR-ORF1ab-S-ORF3-E-M-ORF6-N-ORF8-3'UTR.Sequence identity analysis indicated that NMR-13 was most closely related to alphacoronavirus,which shared 91.3％nt identity with strain FiCoV/UMN2020.NMR-13h shared the next highest-sequence identitywiththe strains Lucheng/Lijiang-170,Lucheng/Ruian-83 and Lucheng/Lijiang-71 found in Zhejiang Province,China(79.49％,80.6％and 81.0％,respectively).Phylogeneticanalysis indicated that NMR-13 clustered with FiCoV/UMN2020.Recombination analy-sis indicated no recombination phenomenon.A rat coronavirus was isolated in this study,thus enriching the diversity of known alphacoronaviruses,and providing a reference for understanding the molecular genetic characteristics and molecular evolution of mouse coronaviruses in China.

Three-dimensional Culture of Human Airway Epithelium in Matrigel for Evaluation of Human Rhinovirus C and Bocavirus Infections / 生物医学与环境科学（英文）

OBJECTIVE@#Newly identified human rhinovirus C (HRV-C) and human bocavirus (HBoV) cannot propagate in vitro in traditional cell culture models; thus obtaining knowledge about these viruses and developing related vaccines are difficult. Therefore, it is necessary to develop a novel platform for the propagation of these types of viruses.@*METHODS@#A platform for culturing human airway epithelia in a three-dimensional (3D) pattern using Matrigel as scaffold was developed. The features of 3D culture were identified by immunochemical staining and transmission electron microscopy. Nucleic acid levels of HRV-C and HBoV in 3D cells at designated time points were quantitated by real-time polymerase chain reaction (PCR). Levels of cytokines, whose secretion was induced by the viruses, were measured by ELISA.@*RESULTS@#Properties of bronchial-like tissues, such as the expression of biomarkers CK5, ZO-1, and PCK, and the development of cilium-like protuberances indicative of the human respiration tract, were observed in 3D-cultured human airway epithelial (HAE) cultures, but not in monolayer-cultured cells. Nucleic acid levels of HRV-C and HBoV and levels of virus-induced cytokines were also measured using the 3D culture system.@*CONCLUSION@#Our data provide a preliminary indication that the 3D culture model of primary epithelia using a Matrigel scaffold in vitro can be used to propagate HRV-C and HBoV.

Norovirus Infection and Histo-blood Group Antigens in Children Hospitalized with Diarrhea in Lulong and Chenzhou in China / 生物医学与环境科学（英文）

Norovirus (NoV) is a pathogen that commonly causes viral diarrhea in children. Studies indicate that NoV recognizes human histo-blood group antigens (HBGAs) as cell attachment factors. In order to explore the correlation between of NoV infection and HBGAs, a cross-sectional study was conducted in children less than five years old who were hospitalized with diarrhea in two areas of China between November 2014 and February 2015. Of the paired stool and saliva samples taken from 424 children, NoV was detected in 24 (6%) children, with viral genotypes GII.3 (n=5), GII.4 (n=14), GII.12 (n=1), and GII.17 (n=4). All of the individuals having NoV infection were either secretors (Lea-b+/Lex-y+) or partial secretors (Lea+b+/Lex+y+) except one GII.3 infection of a non-secretor (Lea+b-/Lex+y-). These results suggest that secretor positive is associated with NoV infection, although non-secretors are not absolutely protected from NoV infection.

Gene Knockdown in Human Rhinovirus 1B Using 2'-OMe-modified siRNAs Results in the Reactivation of the Interferon Response / 生物医学与环境科学（英文）

The aim of this study was to investigate the knockdown efficiency of 2'-O-methylated (2'-OMe)-modified small interfering RNAs (siRNAs) on human rhinovirus 1B (HRV1B) replication and the interferon response. Thus, 24 2'-OMe-modified siRNAs were designed to target HRV1B. The RNA levels of HRV1B, Toll-like receptor 3, melanoma differentiation-associated gene 5, retinoic acid inducible gene-I, and interferons were determined in HRV1B-infected HeLa and BEAS-2B epithelial cells transfected with 2'-OMe-modified siRNAs. The results revealed that all 2'-OMe-modified siRNAs interfered with the replication of HRV1B in a cell-specific and transfection efficiency-dependent manner. Viral activation of Toll-like receptor 3, melanoma differentiation-associated gene 5, retinoic acid inducible gene-I, and the interferon response was detected. In conclusion, the 2'-OMe-modified siRNAs used in this study could interfere with HRV1B replication, possibly leading to the reactivation of the interferon response.

Viral etiology in children with acute lower respiratory tract infections plus platelet disorders in Changsha, China: an analysis of 255 cases / 中国当代儿科杂志

<p><b>OBJECTIVE</b>To investigate the viral etiology in hospitalized children with acute lower respiratory tract infections (ALRTI) plus platelet disorders.</p><p><b>METHODS</b>A total of 255 children with ALRTI plus platelet disorders and 442 children with ALRTI and normal platelets, all of whom were hospitalized between March 2010 and February 2011, were included in the study. Their nasopharyngeal aspirate samples were collected, and RT-PCR or PCR was performed to detect 14 viruses.</p><p><b>RESULTS</b>Of 255 ALRTI patients with platelet disorders, thrombocytosis was found in 253 cases (99.2%) and thrombocytopenia in 2 cases (0.8%). Among ALRTI patients with platelet disorders, 173 (67.8%) were infected with at least one virus, with human rhinovirus as the most common one, followed by parainfluenza virus type 3 (PIV3) and respiratory syncytial virus (RSV). The detection rate of PIV3 in the abnormal platelet group was significantly higher than in the normal platelet group (P<0.05). In contrast, the detection rate of influenza virus B (IFVB) in the abonormal platelet group was significantly lower than in the normal platelet group (P<0.05). The age distribution showed significant difference between the abnormal and normal platelet groups (P<0.01). Platelet disorders were mainly found in children under one year of age (P<0.01).</p><p><b>CONCLUSIONS</b>Thrombocytosis is often found in children with ALRTI caused by viruses, especially PIV3, but infection with IFVB seldom causes platelet disorders. Hospitalized children with ALRTI under one year tend to develop platelet disorders.</p>

Detection of human bocavirus in children with acute respiratory tract infections in Lanzhou and Nanjing, China / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>The aim of this study was to explore the prevalent characteristics of HBoV1 and its co-infection.</p><p><b>METHODS</b>PCR was used to detect HBoV1-DNA (HBoV1) and other viruses. A multivariate logistic regression model was used to explore possibility of co-detected for related viruses.</p><p><b>RESULTS</b>The positivity rates in Nanjing and Lanzhou were 9.38% (74/789) and 11.62% (161/1386), respectively (P>0.05). The HBoV1 positive group was younger than negative group (P<0.05). Seasonal differences were noted, with a higher frequency of infection in December and July. HBoV1-positive children [72.34% (169/235)] were co-infected with other respiratory viruses. Multifactorial analysis showed no correlations between HBoV1 and the clinical classification, region, gender, age, or treatment as an outpatient or in a hospital. Correlations were identified between HBoV1 infections with ADV (OR=1.53, 95% CI 1.03-2.28), RSV (OR=0.71, 95% CI 0.52-0.98), and IFVA (OR=1.77, 95% CI 1.00-3.13).</p><p><b>CONCLUSION</b>Presence of HBoV1 in nasopharyngeal aspirates did not correlate with region or gender, although the prevalence of HBoV1 was higher in younger children. There were no correlations between HBoV1 and other variables, except for the season and ADV, RSV, or IFVA infections.</p>

Research progress in receptors involved in rotavirus infection / 病毒学报

Rotaviruses, which are recognized as one of the major etiological agents among infants and young children with diarrhea, consist of three concentric layers of protein capsid with the enclosed double-stranded RNA genome. Rotaviruses infect host cells mainly by identifying the specific receptors on cell surfaces and binding to them. Therefore, receptors are important factors for viruses infecting cells. So far, there have been many receptors found to be involved in rotavirus infection, including sialic acid, integrin, Toll-like receptor, and blood group antigen. This article provides an overview of receptors involved in rotavirus infection.

A review of detection methods for human bocaviruses / 病毒学报

Human bocavirus (HBoV) 1-4 have been detected both in respiratory and stool samples since the first HBoV was discovered in 2005. HBoV-1 is mostly associated with respiratory infection, while HBoV 2-4 are usually associated with intestinal tract infection. A variety of signs and symptoms have been described in patients with HBoV infection, including cough, wheezing, pneumonia, and diarrhea, but the research on pathogenic mechanism of HBoV is limited because HBoV cannot be cultured in vitro due to the lack of appropriate host cells. Three-dimensional epithelial cell culture, reverse genetics, and viral metagenomics are identified as novel tools that may promote the research on pathogenic mechanism of HBoV and the discovery of new viruses. This review summaries currently available diagnostic approaches such as electron microscopy, cell culture, PCR, and immunoassay in order to provide a method reference for indepth research on HBoV.

Genome amplification and sequence analysis of human bocavirus 2 / 病毒学报

To obtain the genome sequence of human bocavirus 2 (HBoV2), different regions of HBoV2 genome were amplified through PCR in fecal specimens which had been identified as single-positive for HBoV2 in 2010. A genome sequence of HBoV2 (HBoV2-NC, 5444 bp) was obtained after sequence assembly. The phylogenetic analysis showed that HBoV2-NC had the closest evolutionary relationship with HBoV2 Lanzhou strain. The predication of inverted terminal repeats of HBoV2-NC by DINAMelt showed that inverted terminal repeats were contained in HBoV2-NC 5' terminal, which had the typical stem-loop structure in other parvoviruses. Finally, some flanking sequences of HBoV2-NC were amplified by linker-PCR.

Research progress in human adenovirus / 病毒学报

Human adenovirus (HAdV) is one of the most important pathogens in infants and young children with acute respiratory infections and other diseases. This article reviews the literature on HAdV, including its molecular biological characteristics, detection and typing, and pathogenic mechanism, the clinical features and epidemiological characteristics of HAdV-related diseases, and the prevention and control of HAdV infections. So far, 67 types of HAdV have been identified, including recombinant variants discovered in recent years. The major epidemic strains that cause acute respiratory infections are HAdV-3 and HAdV-7, both of which belong to the subgroup B. HAdV often leads to acute respiratory infections, but it also causes diseases of other systems. HAdV-related diseases have similar clinical manifestations as those caused by other respiratory viruses, but often accompanied by gastrointestinal symptoms. The pathogenic mechanism of HAdV remains unclear, especially for the new recombinant variants, due to few studies on their association with diseases. Because there are no prospective, large randomized controlled trials of HAdV infections, the treatment of HAdV infections is controversial. Vaccine is the most effective measure to reduce respiratory HAdV infections, but it is still not commercially available.

Establishment and primary application of a novel resequencing pathogen microarray-based assay for detecting pathogens in patients with unexplained diarrhea / 病毒学报

In this study, a novel resequencing pathogen microarray (RPM)-based multi-pathogen detection assay was developed to simultaneously detect 14 rotaviruses, 7 caliciviruses, 8 astroviruses, 28 enteroviruses, and 16 rare diarrhea viruses in patients with diarrhea syndrome. The specificity of the assay was examined using confirmed virus-positive specimens, and the sensitivity was evaluated by serial ten-fold dilutions of in vitro transcribed RNA. RPM assay could detect and differentiate virus types/subtypes at 20-2000 copies/microL. The detection threshold of RPM was determined by adjusting the reference concentration, and the detection steps were optimized to type Enterovirus. The nucleic acids of 10 stool samples from patients with unexplained diarrhea were screened, and 6 of them showed positive results. The RPM results were further verified by singleplex PCR followed by sequencing, and no difference was found between the two assays. In conclusion, we have established a high-throughput RPM assay with high specificity and sensitivity, which demonstrates a great potential for the identification of pathogens in patients with unexplained diarrhea and the management of emerging epidemic.

Whole genome analysis of human group A rotavirus G9p8 strains in Hebei lulong region, 2009-2011 / 病毒学报

Abstract:This study aims to investigate the genetic characteristics of group A rotavirus (GARV) G9P[8] strains from infantile diarrhea samples in Hebei Lulong region from 2009 to 2011. We randomly selected five GARV G9P[8] strains in Hebei Lulong region from 2009 to 2011, amplified the 11 gene fragments of GARVs by RT-PCR, and analyz their full-genome sequences by homology and phylogenetic analysis with DNAStar and MEGA. The nucleotide homology between strains LL11131077 and LL11131083 in 2011 was significantly higher than hat etween them and the other three strains in 2009 and 2010. The G9P[8] GARVs circulating in Hebei Lulong region from 2009 to 2011 elenged to the same genotype as the prevalent G9P[8] GARVs in other parts of the world. However,the two strains in 2011, compared with those in 2009 and 2010, were located in a different sub-branch of the phylogenetic tree and had amino acid mutations at many sites.

Progress on development and research of human bocavirus 1 / 病毒学报

Human bocavirus 1 (HBoV1) is a novel virus that mainly causes respiratory tract infection, and it has the characteristic of genome of Parvovirus, containing three open reading frames that encode non-structural proteins NS1 and NP1 and structural proteins VP1 and VP2. Circular episome is present during the rolling circle replication of HBoV1, which provides the possibility of full genome amplification and infectious clone construction to save HBoV1. The recombination between HBoV1 and HBoV2-4 occurs frequently. With the three-dimensional culture, in vitro culture of HBoV1 provides a powerful tool for research on the pathogenesis of HBoV1. This review focuses on the molecular characteristics, association with diseases, in vitro culture, diagnosis and treatment of HBoV1.

Current research on picornavirus 3C protease / 病毒学报

The picornavirus family comprises many small viruses, several of which are important pathogens of humans and livestock. The 3C protease (3Cpro) of different species and genera of picornavirus contains the classic G-X-C-G motif and Cys-His-Asp/Glu catalytic triad. 3Cpro conducts maturation cleavage in the regions of VP2-VP3 and VP3-VP1 in P1, 2A-2B and 2B-2C in P2 and the whole P3. Picornavirus 3Cpro has been shown to have significant substrate preference in Q-G/S/A/V/H/R and E-S/G/R/M as well as species and genera specificity through analyses of the maturation cleavage of picornavirus polyproteins. Innate immune adaptors such as TRIF, MAVS, IRF3, IRF7 and NEMO have various potential cleavage sites in picornavirus 3Cpro (TRIF and NEMO show considerable diversity in their cleavage sites). Useful information will be provided for the development of broad-spectrum antiviral agents as well as evasion mechanisms of the innate immune system against picornavirus 3Cpro through continued research of picornavirus 3Cpro.

Evolutionary relationships of G3 GARV isolated from pigs and humans in Lulong County, Hebei Province, China / 病毒学报

This study aimed to amplify major genome segments (VP7, VP4, VP6, VP2 and NSP2-5) of porcine G3 group A rotavirus (GARV) LLZ212 isolated in our laboratory, determine their genotypes, and explore the evolutionary relationships between G3 GARV strains isolated from humans and pigs in Lulong County, Hebei Province, China. Major genome segments of seven GARV strains were amplified by reverse transcription-polymerase chain reaction (RT-PCR) and the segments were sequenced. The genome segments of seven GARV strains were determined by the online RotaC genotyping tool (RotaC v2.0). The reference sequences of each GARV genome segment were downloaded from GenBank. Homology and phylogenetic evolutionary analyses were conducted using the MEGA 5.0 and DNAStar software packages. LLZ212 isolated from pigs in Lulong had the following genotype: G3-P[8]-I5-C1-N1-T1-E1-H1. All human GARV strains had the following genotype: G3-P[8]-I1-C1-N1-T1-E1-H1. The VP7, VP4, NSP4 and NSP5 genes of the LLZ212 strain had the highest nucleotide identities with the human GARV E885, CMH014/07, Wa and RMC321 strains, respectively, and these clustered together in a sublineage. The VP6, NSP4 and NSP5 genes of the LLZ212 strain shared the highest nucleotide identities with the porcine GARV PRG921 strain, while VP2 associated most closely with porcine GARV OSU strain, and these also clustered in a sublineage. A rare porcine G3-P[8]-I5-C1-N1-T1-E1-H1 GARV strain was identified, which may represent a reassortment between porcine and human viruses. In conclusion, the VP7, VP4, NSP4 and NSP5 genes of LLZ212 share high levels of sequence identity with human GARV, while VP2, VP6, NSP2 and NSP3 cluster with porcine GARV.

Etiological study of human bocavirus 1-4 in children with acute diarrhea in Lanzhou, China / 病毒学报

This study aimed to study the epidemiological and clinical characteristics of human bocavirus 1-4 (HBoV1-4) in children with acute diarrhea in Lanzhou and to investigate the association between HBoV and acute gastroenteritis. A total of 331 stool samples were collected from children aged under 5 years with acute diarrhea at the Department of Pediatrics, the First Hospital, Lanzhou University, between July 2012 and June 2013. Nested PCR was used to screen for HBoV and a general PCR was employed to screen other common diarrhea viruses. We found human bocavirus 1, 2, 3 and 4 in 26, 15, 7 and 1 cases, respectively. There was no specific seasonal distribution of HBoV, with infections occurring throughout the year. HBoV was mostly found in children aged between 7 and 12 months, with a mean age of 11.04 months (+/- 6.92 months), and 93.88% of affected children were aged under 2 years. Overall, 71.3% of mixed infections were mixed and the majority of other infections were caused by rotavirus. There was no statistical difference in the incidence of fever and vomiting associated with HBoV infection. A rare virus strain, HBoV4 (LZFB086), was identified, which showed highest levels of nucleotide sequence identity (99.0%) with a single Thai HBoV strain (JQ267789). No case of HBoV2B was found. In conclusion, HBoV1 was a major etiological pathogen of HBoV in pediatric cases in Lanzhou. HBoV4 was detected in feces for the first time in China. The rate of mixed infections was high and rotavirus was dominant. The data presented suggests that HBoV is not a major causative agent of gastroenteritis.

The effects of recombinant human beta-defensin-3 on expression of interleukin-17A and interleukin-22 in BEAS-2B cell / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To research the effects of recombinant human beta-defensin-3 (hBD-3) on expression of interleukin-17A (IL-17A) and interleukin-22 (IL-22) in BEAS-2B cell.</p><p><b>METHODS</b>The BEAS-2B cells were stimulated with different concentrations of hBD-3 for 6 hours and 24 hours, respectively. Toll-like receptor 2 (TLR2), IL-17A and IL-22 mRNA expression levels were determined by real-time PCR, and the expression levels of IL-17A and IL-22 protein were examined by enzyme linked immune-sorbent assay.</p><p><b>RESULTS</b>TLR2 mRNA in BEAS-2B cells were significantly increased in a concentration-and time-dependent manner after stimulating by hBD-3 for 24 hours compared to 6 hours. The IL-17A has significantly increased in mRNA and protein levels stimulated 24 hours in a concentration of 100 ng/ml, however, IL-17A mRNA expression has increased while protein didn't change stimulated 6 hours in a concentration of 50 ng/ml. The IL-22 mRNA and protein expression reached peak levels after stimulating in a concentration of 50 ng/ml of hBD-3 while IL-22 expression declined in mRNA and protein levels as the concentration of hBD-3 increased.</p><p><b>CONCLUSIONS</b>Recombinant hBD-3 can up-regulated the expression of TLR2, IL-17A and IL-22, lower concentration of hBD-3 mainly increased the expression of IL-22 while higher concentration of hBD-3 mainly increased the expression of IL-17A. These results show that different concentrations of hBD-3 maybe activate different transcription factors which was mediated by TLR2, initiating host immune response.</p>

Genetic characterization of G II.12 norovirus in Beijing from 2008 to 2009 / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To reveal the genetic characteristics of GII.12 Norovirus strains isolating from stool samples of adults with diarrhea in Beijing during 2008-2009.</p><p><b>METHODS</b>RdRp, ORF2, ORF3 and ORF1/ORF2 overlap region were respectively amplified by primers using RT-PCR. The products were purified, cloned, sequenced and then aligned, phylogenetic and recombinant analyzed by softwares of DNAStar, MEGA and SimPlot.</p><p><b>RESULTS</b>According to the phylogenetic analysis, 11 strains belonged to G II.g in the RdRp region,while GII.12 in the ORF2 and ORF3. SimPlot analysis further confirmed the 11 strains were recombinant strains ( G II.g [RdRp]/G II.12 [capsid]).</p><p><b>CONCLUSION</b>G II.12 Norovirus prevailing in Beijing and other regions of the world belonged to the same strain, and we identified the genetic characteristics of G II.12 Norovirus in Beijing.</p>

Full sequence analysis and characterization of the Shenzhen Norovirus strain SZ2010422 / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To obtain information on viral molecular structural and evolutionary characteristics, we conducted the SZ2010422 full-length genomic analysis.</p><p><b>METHODS</b>Primers were designed by New Orleans full sequence, SZ2010422 full genome was amplified by RT-PCR, the whole genome sequence and the capsid domain amino acid sites was analysised after cloned and sequenced.</p><p><b>RESULTS</b>The genome of G II-4 Norovirus SZ2010422 strain was consist of 7559 bp, it revealed three ORFs composites of the whole genome, ORF1 (5100 bp), ORF2 (1623 bp), ORF3 (807 bp) respectively, ORF1 and ORF2 had 19 nucleotide overlap. By evolutionary comparative analysis found SZ2010422 genomic nucleotide sequences with reference strains of G II-4 New Orleans1805 strains the highest homology with a total length of homology was 99.3%, of ORF1 (99.5%), ORF2 (99.2%), ORF3 (98.6%). Phylogenetic analyses showed SZ2010422 belonging to G II-4 New Orleans variant. Date of 541 amino acid analyses showed: New Orleans variant strains of popular sites: aa310N or K, --> S aa341D --> of N, aa359T--> S, aa396H --> P, aa460H --> Y.</p><p><b>CONCLUSION</b>Norovirus SZ2010422 belonged to the G II-4 New Orleans variant. In This study, SZ2010422 full sequence can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants. Noroviruses; Genes; Sequence analysis</p>

Molecular and epidemiological study of human adenovirus among infants with diarrhea in Nanjing / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To study the prevalence, clinic features and epidemiologic characteristics of human adenovirus diarrhea in Nanjing.</p><p><b>METHODS</b>730 stool specimens were collected from children with diarrhea in Nanjing Children's Hospital of Nanjing Medical University from June 2009 to June 2011. Polymerase chain reaction (PCR) was employed to detect human adenovirus. The total positive PCR products were typed by nest-PCR or multiple PCR.</p><p><b>RESULTS</b>21 samples (21/730) were positive for human adenovirus of all 730 samples from June 2009 to June 2011 and enteric HAdV-41 is the predominant stain.</p><p><b>CONCLUSION</b>Enteric HAdV-41 and non-enteric adenovirus were the major etiological agents of viral diarrhea among infants and children in Nanjing from 2009 to 2011. We should take the long-term systematic surveillance seriously.</p>