Epidemiological and molecular characteristics of SARS-CoV-2 Delta variant-caused pneumonia in Henan Province in 2021 / 中华微生物学和免疫学杂志

Objective:To analyze and summarize the epidemiological and molecular characteristics of SARS-CoV-2 Delta variant, a variant of concern (VOC), in Henan Province in 2021 in order to provide a basis for epidemic prevention and control.Methods:According to the feedback of sequencing results from Chinese Center for Disease Control and Prevention, 111 patients infected with SARS-CoV-2 Delta VOC were selected from the Henan imported and local cases in 2021. Basic patient information was obtained from the pandemic website. The differences in age, gender, vaccination history, the number of vaccine doses and different clinical types were analyzed. Moreover, the differences in RT-qPCR results of ORF1 ab gene and N gene Ct values between cases of different genders and symptoms were analyzed statistically. Sequencing results of the nucleotide and S protein mutation sites were analyzed. Results:There was no significant difference in the gender distribution of 111 cases between different age groups (χ 2=2.217, P=0.529). There was also no significant difference in clinical types between patients with different vaccination history (χ 2=12.074, P=0.209). The Ct values of most SARS-CoV-2 nucleic acid-positive specimens were distributed in the lower range and the viral loads were higher. The difference in the Ct value of ORF1 ab gene between different gender groups was not statistically significant (χ 2=1.646, P=0.439), but were significantly different among asymptomatic, mild, normal, and severe cases (χ 2=13.257, P=0.039). There was no significant difference in N gene Ct value among cases of different genders or different symptoms (all P>0.05). The 111 patients in this study were mainly found through close-contact screening and full-staff nucleic acid screening and accounted for 62.2% (69 cases) of the total. The sequencing length coverage was basically greater than 99% (accounting for 90.1%, 100/111); the total number of nucleotide mutation sites was mostly in the range of 46-50 (86.4%, 89/103); the total number of S protein mutation sites was mostly 12 (82.5%, 85/103). The 103 Delta mutants all contained nine mutation sites, which were T19R, R158G, L452R, T478K, D614G, P681R, D950N, E156del and F157del, with a mutation rate of 100%. Conclusions:People were highly susceptible to the SARS-CoV-2 Delta in Henan Province in 2021. High viral load and increase in the ORF1 ab gene load would aggravate the clinical symptoms.

Detection of measles virus infection and proliferation by real-time quantitative PCR / 上海预防医学

Objective A SYBR-Green real-time quantitative PCR(RT-qPCR)method was set up to detect the infection and proliferation of measles virus, which could be useful in virus titer determination. Methods In this project, we used a 405 bp fragment of the N gene of measles virus as a target sequence and constructed a plasmid to establish the standard curve in absolute quantitative experiment. We then used this method to obtain the proliferation curve of measles virus and to detect the virus proliferation at different MOI. Results There was a linear relationship between the virus copy number and the titer of the measles virus reference at the range of 6 to 2 lgCCID50/mL, with a correlation coefficient (r) of 0.991(P < 0.01). Based on the analysis of virus proliferation curve, measles virus mainly proliferated intracellularly within 48 h after its entering the cell. There was no detected increase in viral RNA level in the first 24 h, suggesting the virus was in a silent period in the cell. After 24 h, the virus expanded in large numbers and entered the exponential growth phase. The intracellular viral RNA level reached the plateau phase after its peak at 96 h. The virus secreted to the outside of the cell entered the exponential growth phase starting from 48 h, peaked at 144 h, then followed by plateau phase. Conclusion A SYBR-Green RT-qPCR method is established and used to monitor virus proliferation. Our result is helpful in understanding of the proliferation and secretion of measles virus in cells and provides experimental basis for detection of live attenuated virus titers.

Phylogenetic analysis of nucleoprotein gene of Rabies virus in Malaysia from 2015 to 2018

@#Rabies is a fatal zoonotic disease caused by rabies virus (RABV) and remains a public health problem in Malaysia. Malaysia was declared rabies-free in 2012, however rabies outbreaks occurred at few states in Peninsular Malaysia three years later; and for the first time, in Sarawak (East Malaysia) in 2017 which has caused more than 20 human deaths. This study describes the phylogenetic analysis of the complete nucleoprotein (N) gene of RABV from animal samples in Malaysia from year 2015 to 2018. The N gene of 17 RABVs from Perlis, Kedah and Sarawak were amplified and sequenced. The nucleotide and deduced amino acid similarities of N gene analysis indicated that there is high similarity among the local RABVs. Phylogenetic analysis of the N gene revealed that all Malaysia RABVs belonged to the Asian clade. Among these, RABVs from Peninsular Malaysia were clustered together with RABVs from Thailand, Vietnam and other Southeast Asia countries except Indonesia. However, RABVs from Sarawak were grouped together with Indonesian strains from Kalimantan. Our study provides baseline genetic information of the potential origins of the circulating RABVs in Malaysia. This crucial information helped the authority in policies making and strategies to be taken in outbreak control. Continuous surveillance program to monitor the disease trend, strict border control, vaccination of dog and cat population and public awareness are important steps to control the spread of the RABV.

Optimization of a fluorescent qPCR detection for RNA of SARS-CoV-2 / 生物工程学报

We optimized a fluorescent quantitative polymerase chain reaction (qPCR) assay system for rapid and real time detection of SARS-CoV-2 RNA. The results show that the lowest dilution of RNA samples used for the detection of SARS-CoV-2 RNA could reach 1/10 000 (the initial value is set as 10 ng/μL). Moreover, the cycle threshold (Ct) for samples of clinically diagnosed COVID-19 was lower than 35 or 40. The sensitivity of this method was satisfactory. The results were consistent with those of the COVID-19 detection kit on the market under the same conditions, but the number of cycles required was shortened by about 2. Therefore, the optimized assay developed in this study can be used in screening and early clinical diagnosis. Our work provides a tool to facilitate rapid clinical diagnosis of COVID-19.

Confirmation and Sequence analysis of N gene of PPRV in South Xinjiang, China / Confirmação e análise de sequência do gene N de PPRV em Xinjiang do Sul, China

In China, Peste des petits ruminants (PPR) was officially first reported in 2007. From 2010 until the outbreak of 2013, PPRV infection was not reported. In November 2013, PPRV re-emerged in Xinjiang and rapidly spread to 22 P/A/M (provinces, autonomous regions and municipalities) of China. In the study, suspected PPRV-infected sheep in a breeding farm of South Xinjiang in 2014 were diagnosed and the characteristics of complete sequence of N protein gene of PPRV was analyzed. The sheep showed PPRV-infected signs, such as fever, orinasal secretions increase, dyspnea and diarrhea, with 60% of morbidity and 21.1% of fatality rate. The macroscopic lesions after autopsy and histopathological changes were observed under light microscope including stomatitis, broncho-interstitial pneumonia, catarrhal hemorrhagic enteritis and intracytoplasmic eosinophilic inclusions in multinucleated giantcell in lung. The formalin-fixed mixed tissues samples were positive by nucleic acid extraction and RT-PCR detection. The nucleotide of N protein gene of China/XJNJ/2014 strain was extremely high homology with the China/XJYL/2013 strain, and the highest with PRADESH_95 strain from India in exotic strains. Phylogenetic analysis based on complete sequence of N protein gene of PPRV showed that the China/XJNJ/2014 strain, other strain of 2013-2014 in this study and Tibetan strains all belonged to lineage Ⅳ, but the PPRV strains of 2013-2014 in this study and Tibetan strains were in different sub-branches.(AU)

Na China, Peste des petits ruminants (PPR) foi relatado oficialmente em 2007. De 2010 até o surto de 2013, não houve relato de infecção por PPRV. Em Novembro de 2013, PPRV ressurgiu em Xinjiang e rapidamente se espalhou para 22 P/A/M (províncias, regiões autônomas e municípios) da China. No estudo, ovelhas com suspeita de infecção por PPRV em uma fazenda de reprodução no sul de Xinjiang form diagnosticadas em 2014 e as características da sequência completa da proteína N do gene do PPRV foi analisada. As ovelhas tinham sinais de infecção pelo PPRV, como febre, aumento de secreções oro-nasais, dispneia e diarreia, com 60% de morbidade e 21.1% de fatalidade. As lesões macroscópicas após mudanças histopatológicas foram observadas sob microscópio, incluindo estomatite, pneumonia bronco-intersticial, enterite hemorrágica catarral e inclusões eosinofílicas intracitoplasmáticas em células gigantes multinucleares no pulmão. As amostras de tecido fixadas em formalina testaram positivo para detecção de RT-PCR por extração de ácido nucleico. Os nucleotídeos da proteína N do gene da linhagem China/XJNJ/2014 apresentou extrema homologia com o China/XJYL/2013, e homologia ainda maior com a variedade PRADESH-95 da Índia. Análise filogenética baseada na sequencia completa da proteína N do gene de PPRV mostrou que as variedades China/XJNJ/2014, outra de 2013-2014 mostrada nesse estudo e as Tibetanas todas pertenciam à linhagem Ⅳ, mas as PPRV de 2013-2014 nesse estudo e as Tibetanas estavam em diferentes agrupamentos.(AU)

Molecular genotyping of measles viruses in Yancheng area in 2016 and analysis of the genetic characterization of hemagglutinin genes / 中华实验和临床病毒学杂志

Objective@#To analyze the genotypes and the genetic evolution of the hemagglutinin genes of measles viruses in the city of Yancheng in 2016.@*Methods@#Using a set of primers and probes for screening positive for measles viruses, specimens of throat swab were detected using the method of real time RT-PCR. The sequences of the nucleoprotein and hemagglutinin genes of measles viruses were amplified through one step RT-PCR method and the PCR products were sequenced. The sequences of nucleotide and amino acid of the nucleoprotein and hemagglutinin genes of measles viruses were analyzed and the evolutional trees were generated using bioinformatics software.@*Results@#The genotypes of measles viruses in the Yancheng area in 2016 included subgenotype H1a and genotype D8. Phylogenetic trees analysis showed that the five representative strains of subgenotype H1a in Yancheng area and Jiangxi representative strain (KJ136545) clustered into independent evolutionary branches, belonged to the clade of H1a -1 evolutionary genes. The seven representative strains of genotype D8 in Yancheng area were clustered with the American representative strain in 2009 (JN635404), belonged to the D8-3-2 small clade genes. Compared with vaccine strain of Shanghai S191, the amino acid site in 240thof the five representative strains of subgenotype H1a in Yancheng area mutated from serine to asparagine, leading to a loss of the N-glycosylation site NLS238-240. The seven representative strains of genotype D8 in Yancheng area had no change in N-glycosylation.@*Conclusions@#In 2016, the prevalent strains of measles viruses in Yancheng area were mainly Chinese H1a dominant subgenotype and D8 imported genotype. In addition to a loss of the N-glycosylation site NLS238-240in 240thof the five representative strains of subgenotype H1a, most of the major neutralizing antigen sites of hemagglutinin gene of measles viruses in Yancheng area did not mutate. The Chinese vaccine of Shanghai S191 can effectively prevent infection caused by subgenotype H1a and subgenotype D8 strains.

Production and characterization of monoclonal antibodies to Newcastle Disease Virus.

Newcastle Disease (ND) is one of the major causes of economic loss in the poultry industry. Newcastle Disease Virus (NDV) is a single-stranded, negative-sense enveloped RNA virus (Fam. Paramyxoviridae; Order Mononegavirales). In the present study three monoclonal antibodies (MAbs) were produced by polyethyleneglycol (PEG)-mediated fusion of lymphocytes sensitized to NDV Bareilly strain and myeloma cells. NDV possesses ability to agglutinate erythrocytes of avian species. All the three MAbs designated as 2H7, 3E9 and 3G6 caused hemagglutination inhibition of NDV by specifically binding to NDV. The reactivity for all the 3 MAbs on indirect ELISA was found to be significantly higher than the antibody and antigen controls. On flowcytometry of HeLa cells infected with NDV using the MAbs as primary antibodies, there was a significant difference in the percentage of cells showing positive fluorescence compared to the mock control. One of the MAbs (3E9) was found to react with hemagglutinin-neuraminidase (HN) protein on western blot.

Genetic diversity of nucleocapsid genes of recent porcine epidemic diarrhea viruses isolated in Korea

Porcine epidemic diarrhea virus (PEDV), a porcine enteropathogenic coronavirus, causes lethal watery diarrhea in piglets, resulting in large economic losses because of high mortality. In November 2013, PEDV reemerged in Korea, and these outbreaks have since continuously occurred. In the present study, we determined the full-length nucleocapsid (N) gene sequences of three Korean PEDV field isolates collected in 2014-2015. Sequence and phylogenetic analysis of N genes revealed that recent prevalent Korean PEDV isolates were very closely related to the US PEDV isolates in 2013. Interestingly, the phylogenetic tree based on the nucleotide sequencing of the PEDV N gene was similar to the tree topology of the PEDV complete genomes. Therefore, our data provide a better understanding of the genetic diversity and contribute to the accurate diagnosis and development of vaccines against PEDV.

Calcitonin gene-related peptide / 中国小儿急救医学

Calcitonin gene-related peptide( CGRP) is the strongest vasodilator discovered to date,the synthesis and release of CGRP are regulated by multiple factors.CGRP possesses multiple biological func-tions,such as vasodilator,myocardial strengthener,lung protector,brain protector,immunomodulator.It plays an important role in regulating the function in the body.

Etiologic and viral gene analysis on a case of human rabies caused by the wounding of a dog in Guizhou province / 中华微生物学和免疫学杂志

Objective To confirm the death of a child injured by a dog was due to rabies and to understand the molecular biologic features of rabies virus in Kaili,Guizhou province.Methods Brain tissue samples of patient and dog were collected to detect the rabies virus by direct immunofluorescence assay (DFA) and RT-nested PCR assay.Homology and phylogenetic tree were analyzed based on the whole nucleotide and deduced amino acid sequence of N gene of rabies virus followed by molecular epidemiological analysis.Results Both the human and dog brain tissue samples were confirmed positive by DFA and RT-nested PCR assay.The homology analysis of N gene sequences among GZH,GZD and other epidemic and vaccine rabies strains isolated from other provinces and other countries indicated that the detected samples shared the highest homology with the strain detected in Anlong prefecture in Guizhou in the year of 2006,and the homology between GZH and GZD was as high as 100％.Besides,among the vaccine strains,GZH and GZD showed the highest homology with strain CNT.Phylogenetic analysis indicated that the two samples were very close and belonged to genetype 1 lyssavirus,with the closest relationship between samples reported in Guizhou and Beijing.Conclusion It was confirmed on the viral molecular level that both the human and dog in Kaili were suffered from rabies,and the pathogens were genetype 1 lyssavirus.The prevalent strains in Kaili city was probably imported from other prefectures of Guizhou province,suggesting that prevention and control measures on rabies in Guizhou province should be strengthened.

Prokaryotic expression of the nucleocapsid protein gene in bovine coronavirus and its preliminary application / 中国人兽共患病学报

To obtain and analyze the sequence of the nucleocapsid gene from bovine coronavirus, and to produce the fusion protein of the N gene in E.coli in order to use this recombinant protein for the study of bovine coronavirus. The N gene of BCV-DQ strain was amplified by RT-PCR, in which the primers were designed on the basis of N gene sequence of BCV-Mebus strain. The PCR products of 1 347 bp in length were cloned and sequenced, and then inserted into the prokaryotic vector pET30a. The recombinant plasmids were then transformed into Escherichia coli BL21 and identified by SDS-PAGE and Western blot assay. ELISA assay was optimized of N protein as the coating antigen to detect the viruses in the clinical samples. In comparison with 6 BCV strains in GenBank, the sequence identity was proved to be more than 98.3%. Result in SDS-PAGE showed that the fusion protein had a molecular weight of 60 ku, and could be specifically recognized by mouse serum against BCV. The indirect ELISA was used to test 256 serum samples collected from Heilongjiang province and 65.23% samples were positive. On testing field samples, an overall agreement of 95.31% was generated between the the neutralization test of viruses (VN) and indirect ELISA. It is apparent that the N gene was highly conservative and is expressed in E. coli in high level,also the prokaryotic expression products of this gene show a fine reactiongenicity in immune responses. It was also suggested that the N protein may be a useful antigen for sero-diagnosis and epidemiological investigation of BCV.

Cloning the Structure Genes and Expression the N Gene of Porcine Epidemic Diarrhea Virus DX / 中国病毒学·英文版

The structure genes spike (S), nucleocapsid (N), membrane (M), small membrane (sM) of a porcine epidemic diarrhea virus (PEDV) strain DX isolated in Gansu province, North-west of China, were cloned, sequenced and compared with published sequences of PEDV strains. The nucleotide sequences encoding the entire S, sM, M and N genes open reading frame (ORF) of DX were 4 152, 231, 681 and 1 326 bases long respectively. There were transcription regulatory sequences (TRSs) upstream of the initiator ATG of the S, N and M genes. The amino acids sequences of S, M and N contained 30, 3 and 7 potential asparagine (N)-linked glycosylation sites. Homologous analysis and phylogenetic trees showed that DX had the closest relationship with strains LJB/06, JS-2004-2Z and CH/HLJH/06 that were also isolated from China and indicated the prevalence of some PEDV isolates in China were widespread since the JS-2004-2Z strain originated from the south of the China, and LJB/06 and CH/HLJH/06 were isolated from northeast China. The N gene was cloned using two primers which contained Nco I and BamH I restriction enzyme sites and subcloned into expression vector pET30a. The recombinant plasmid was then transformed into E.coli Rossta. SDS-PAGE showed there was a protein of about 55kDa as expected and Western blot indicated the N protein had biological activity.

Live-attenuated Salmonella typhimurium as a Oral Delivery Vehicle for SARS-CoV N DNA Vaccine / 中国生物工程杂志

Objective:To investigate the immunogenicity of SARS-CoV N DNA vaccine and the feasibility of live-attenuated Salmonella typhimurium as the carrier to deliver the N DNA vaccine.Method:The recombinant attenuated salmonella strain CS022 harboring the pcDNA-N DNA vaccine was constructed.And mouse was immunized with the recombinant strain via intranasal and oral routes.Cellular and humoral immune responses were assessed by ELISA,lymphocyte proliferation assays,ELISPOT and FACS.Result:The oral immunization with the transformed salmonellae elicited strong immune responses mainly including high level of N-specific antibody,a dramatic activation of IFN-?-secreting cells,a high level of lymphocyte proliferation,and a high level of activated CD8+ T cells.Conclusion:Live-attenuated Salmonella typhimurium could effectively deliver the SARS-CoV N DNA vaccine in vivo.These encouraging pre-clinical data provide a rational basis for undertaking a new immune style to investigate SARS vaccine.

Effects of Kangliyin on N Gene Relative Expression in the Infectious Bronchitis Virus Infected Model / 中药新药与临床药理

Objective To observe the therapeutic effect of Kangliyin(KLY,the compound Chinese herbal formulation with the functions of clearing heat and damp elimination,regulating stomach and dissipate phlegm) on the models with infection of infectious bronchitis virus(IBV),and to evaluate its effect on the IBV N gene relative expression by using real-time florescent quantitative polymerase chain reaction(PCR).Methods Seven-day-old chicks were inoculated with IBV by the nasal and ocular administration.The chicks were divided into 6 groups by stratified random sampling according to the body weight.The 6 groups were blank control group,model group,three KLY treatment groups(receiving KLY at the dosage of 10 g/kg? d-1,20 g/kg? d-1 or 40 g/kg? d-1,respectively),and positive control group(ganciclovir at the dosage of 0.004 g/kg? d-1).The chicks in the model group and blank control group received normal saline,and the medication groups received the corresponding medicine according to the experimental design from the next day of inoculation,and the treatment lasted 5 days.The relative quantity of IBV N gene expression in the lung and bronchial tissues were assayed by real-time florescent quantitative PCR,and the clinical manifestations and the pathological changes of all groups were also examined.Results Compared with the model group,KLY could significantly inhibit the IBV N gene expression,improve the general clinical symptoms and respiratory symptoms,and improve the pathological changes in the bronchus and lung of the IBV infected model.Conclusion KLY could effectively inhibit the viral replication,repair the pathological damage in the bronchus and lung,and improve the general clinical symptoms in the IBV infected model,which is beneficial to the recovery of the chicks from IBV infection.