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ObjectiveTo determine the genomic characteristics of a subgenus B human adenovirus strain isolated in Shanghai in 2021. MethodsAn adenovirus type 55 strain was isolated and identified from a patient with acute hemorrhagic conjunctivitis （AHC）. Complete genome of the strain was obtained using the next-generation sequencing （NGS）. Phylogenetic trees were reconstructed based on the sequences of Hexon， Fiber， Penton and complete genome to genomically characterize this strain. ResultsPhylogenetic analysis based on the complete genome classified this strain （MH2021001） into subgenus B， subspecies B2 of HAdV-55. Hexon gene of MH2021001 had close phylogenetic relationship with HAdV-11， while Fiber and Penton genes had close relationship with HAdV-14. The MH2021001 showed high nucleotide identity with currently prevalent HAdV⁃55 strains （>99.90%）. The complete genome had 99.96% nucleotide identity to the 73-GD_CHN_2016 strain isolated in Guangdong. In addition， the amino acid sequence of MH2021001 had several substitutions in regions coding for E1B， L4， E3 and L5. ConclusionThis strain has been classified to HAdV-B55. No recombination event is identified in the complete genome. Due to multiple amino acid substitutions， the biological characteristics of the strain need to be further identified.
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Objective:To analyze the features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected with other common respiratory pathogens among coronavirus disease 2019 (COVID-19) patients in Shanghai City, and to provide a reference for scientific prevention and control of COVID-19 and other respiratory infectious diseases.Methods:Descriptive epidemiological approaches were used to analyze the data of COVID-19 reported cases in Shanghai City from January 2020 to February 2021 in the information system of Chinese Disease Prevention and Control. Clinical data of the participants were collected, and their SARS-CoV-2 nucleic acid-positive respiratory specimens were collected at the time of illness onset or admission. Multiplex reverse transcription-polymerase chain reaction (RT-PCR) was performed to detect the 22 respiratory pathogens. Independent-samples t test was used for statistical analysis. Results:Of the 272 patients with COVID-19, 15(5.5%) had co-infection of SARS-CoV-2 with other respiratory pathogens, all of which were double infection. There were three cases infected with enterovirus/rhinovirus, two of each with adenovirus, human metapneumovirus and coronavirus NL63/HKU1, and one of each with coronavirus 229E, influenza A virus H1N1, parainfluenza virus 1 and respiratory syncytial virus B. Two cases infected with Mycoplasma pneumoniae. Among the 272 COVID-19 patients, 212(77.9%) had fever, 117(43.0%) had cough, 46(16.9%) had fatigue, and 35(12.9%) had sore throat. The white blood cell count of co-infection cases was higher than that of non-co-infection cases ((6.8±1.7)×10 9/L vs (5.3±1.6)×10 9/L), and the difference was statistically significant ( t=3.09, P=0.008). Conclusions:There is a certain proportion of co-infection of SARS-CoV-2 with other respiratory pathogens among the COVID-19 cases in Shanghai City, mainly viral pathogens, especially enterovirus/rhinovirus. A rational combination of drugs was recommended to improve the cure rate. Surveillance of acute respiratory infection should be further strengthened as well.
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ObjectiveTo isolate and study the biological characteristics of severe acute respiratory syndrome coronavirus 2 （SARS-CoV-2） from feces of coronavirus disease 2019 （COVID-19） patients. MethodsVero E6 cells were used for virus isolation and the isolated strains were tested by nucleic acid test， immunofluorescence test， virulence test and whole genome sequencing. 50% tissue culture infective dose （TCID50） was calculated after the cell cultures of each generation were collected ResultsEight fecal specimens were inoculated with Vero E6 cells after treatment and cultured for 48 h. One specimen showed obvious cytopathic effect on Vero E6 cells. One SARS-CoV-2 out of 8 fecal samples from COVID-19 patients were isolated， and separation rate was 12.5%. The TCID50 of P1， P2 and P3 were 104.0/0.2 mL， 104.5/0.2 mL and 104.75/0.2 mL， respectively. Only one of the 8 stool samples had SARS-CoV-2 virus replication and amplification， and the Ct value of the nucleic acid detection was about 10. The sequence of the isolation was more than 99.99% homologous with that of Wuhan-Hu-1（GenBank MN908947）. ConclusionThe SARS-CoV-2 strain is isolated from the fecal samples of COVID-19 cases and is confirmed by genomic sequencing and immunofluorescence test， which indicates the presence of live virus in feces of COVID-19 cases.
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In order to meet the needs of prevention and control of intestinal infectious diseases， a comprehensive surveillance for diarrheal diseases has been innovated and explored in Shanghai since 2012. The surveillance has extensive distribution of sentinel hospitals， systematic sampling， multi-pathogen collection， and hospital information system （HIS） as the basis， which has achieved “One system for surveillance of multiple diseases and one sample for detection of multiple pathogens". Continual active surveillance for the whole population has been conducted， covering demography， clinical information， epidemiology， pathogen detection， and drug sensitivity test for diarrhea cases. The surveillance has obtained preliminary achievements as follows. First， diarrheal diseases and their periodic changes have been characterized， in which the most prevalent pathogen of diarrhea is determined to be norovirus in Shanghai. Second， some rare pathogens and serotypes have been identified that may provide clues to the sources of outbreaks. Third， it facilitates the information sharing between public health institutions and clinical institutions， and provides scientific evidence for clinical diagnosis and treatment. In the future， Shanghai diarrhea comprehensive surveillance will be improved for expanding range and depth of surveillance， artificial intelligence assisted diagnosis and treatment， early warning of outbreaks， prediction of epidemic trends， and application of new detection technologies.
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Objective:To observe the stability of severe acute respiratory syrdrome coronavirus （SARS-CoV-2） in cell cultures at different temperatures so as to provide basic data and scientific basis for the research and control of COVID-19 epidemic. Methods:The Vero E6 cells inoculated with SARS-CoV-2. According to TCID50， SARS-CoV-2 with different dilution （10-1， 10-3， 10-5， 10-6）were stored at 37 °C， 22.5 °C， and 4 °C for one to seven days， and then infectious titer was determined by micro cytopathogenic effect assay， observing cytopathic effect （CPE）， and real-time fluorescence quantitative testing. Results:SARS-CoV-2 was stable under 4 °C. The infectivity of high concentration （10-1 dilution） under 22.5 °C for seven days gradually decreased， while lower concentration completely lost infectivity after one day. The virus lost infectivity when stored at 37 °C for more than one day. Conclusion:SARS-CoV-2 is highly stable at 4 °C， sensitive to heat， and related to virus concentration.
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Objective A/H1N1(pdm09) viruses were the dominant strains in Shanghai during 2018-2019 influenza surveillance year.This study is to provide a scientific reference for clinical drug use by investigating the susceptibility of A/H1N1(pdm09) viruses to neuraminidase inhibitors(NAIs). Methods Sixty strains of A/H1N1(pdm09) viruses were randomly selected for testing the susceptibility and drug resistance to Oseltamivir and Zanamivir by means of neutaminidase inhibition and neuraminidase (NA) gene sequencing. Results The 60 epidemic strains all proved to be susceptible to Oseltamivir and Zanamivir and the susceptibility was not observed to be decreased or remarkably decreased.In genetic sequencing, NA was not observed to present amino acid mutation at the key sites and auxiliary sites in catalytic activity, which confirmed the results of the phototypic detection of neuraminidase inhibition. Conclusion The subtype influenza viruses A/H1N1(pdm09) circulating in Shanghai during 2018-2019 surveillance year are still sensitive to NAIs, which provides a scientific reference for clinical use of drugs.However, we monitored only a number of strains and think that the work monitoring antiviral susceptibility should be continued with the wide use of the drugs.
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Objective@#To understand the epidemiological and pathogenic characteristics of hospitalized severe acute respiratory infections (SARI) in Shanghai, China.@*Methods@#From 2015 to 2017, one Tertiary hospital and one Secondary hospital were chosen as the surveillance sites. Two respiratory tract specimens per case were collected from SARI cases aged 15 years and older. One specimen was tested for 22 respiratory pathogens by RT-PCR, and the other specimen was cultured for 6 respiratory bacteria.@*Results@#A total of 287 SARI cases were enrolled for sampling and lab testing. 70.73% of the cases were aged 60 years and older, with 41.46% (119/287) were positive for at least one pathogen. Influenza virus was the predominant pathogen, accounting for 17.77% (51/287) of all SARI cases. Human rhinovirus/Enterovirus and Coronavirus were both accounting for 7.32% (21/287), followed by Mycoplasma pneumoniae (5.57%, 16/287). The positive rates of parainfluenza virus, bocavirus, adenovirus, respiratory syncytial virus and human metapneumo virus were all less than 5%. Bacterial strains were identified in seven SARI cases, including Klebsiella pneumoniae (3 strains), Staphylococcus aureus (2 strains), Streptococcus pneumoniae (1 strain) and Pseudomonas aeruginosa (1 strain). Two or Three pathogens were co-detected from 40 cases, accounting for 33.61% of 119 positive cases. The most common co-detected pathogens were influenza virus and Mycoplasma pneumoniae (10 cases). Influenza cases peaked in winter-spring and summer. Mycoplasma pneumoniae peaked in winter-spring season and overlapped with influenza. The positive rates of pathogens were not significantly different between different age groups.@*Conclusions@#Various respiratory pathogens can be detected from SARI cases aged 15 years and older. Influenza virus was the predominant pathogen and the co-detection of influenza virus with Mycoplasma pneumoniae the most common one.
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Objective@#To conduct a viral pathogen surveillance program on pediatric inpatients less than five years old with acute gastroenteritis in Shanghai and to better understand the pathogenic spectrum and molecular features in the target population, for setting up programs on control, prevention, medication and vaccine applications of the diseases.@*Methods@#Fecal samples were collected from inpatients less than 5 years old who were admitted to a pediatric hospital for having acute gastroenteritis. Information related to demographic, clinical and epidemiological features of the patients was also collected. Laboratory assays including ELISA, real-time PCR and nested PCR, were performed to detect the presence of pathogens as rotavirus, calicivirus, astrovirus and adenovirus.@*Results@#A total of 1 018 samples were collected (male 671 and 347 female), with the positive detection rate as 40.57% which peaked from autumn till winter, annually. Calicivirus and rotavirus A presented with the highest detection rates (24.75% and 13.95% respectively). The lowest detection rate was found in the 0-6 month-olds (32.20%). 65% of the patients with positive virus had received antibiotic treatment prior to the hospitalization. However, no statistically significant difference was seen, regarding the rates of antibiotic medication in the virus positive or negative populations (P>0.05). Data from the Rotavirus genotype analysis revealed that G9P[8] genotype was the predominant strain, and causing majority of rotavirus infections in all the age groups.@*Conclusions@#Among the inpatients under 5 years of age in Shanghai, the positive detection rate for Calicivirus was higher than that for rotavirus group A, suggesting the necessity to carefully monitor the changes regarding the pathogenic spectrum and subtypes of the virus. Antibiotics should also be attentively administered, together with the development of suitable vaccine.
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Objective@#To investigate the epidemiologic characteristics of Norovirus among adult patients suffering from infectious diarrhea in Shanghai, so as to provide evidence for developing related strategies on prevention and control of the disease.@*Methods@#Diarrheal outpatients were monitored at the 'Intestinal clinic’ from 22 hospitals involved in the sentinel surveillance program in Shanghai. Information on demographic and epidemiologic features of the patients was collected while data and clinical, fecal specimens were collected and sent to the district CDC for Norovirus detection. Positive rates of Norovirus were also compared in various populations and seasons during 2013-2018. Multivariate logistic regression model was adopted to fit into the comparisons between non-Norovirus and Norovirus groups.@*Results@#19.28% of the 12 083 diarrheal cases were found to have carried the Norovirus, with GⅡgroup the most commonly identified genotype. Rates of detection was seen higher in males (20.78%) than in females (17.73%). 30-44 year-old were found having the highest positive rate (21.51%). The positive rates were found the highest (23.60%) in the year of 2015. All the above shown differences were statistically significant (P<0.05). Diarrheal patients affected with Norovirus would present watery stool (75.94%) and vomiting (35.84%). Data from the multivariate logistic analysis showed that factors as: being males, 30-44 years old, officials/clerks, in winter season and with histories of travelling etc., were related to higher risks on Norovirus infection.@*Conclusions@#Infectious diarrhea caused by Norovirus occurred all year round, with seasonal peaks seen in winter and spring, in Shanghai. Specific prevention and control measures should be taken on Norovirus- caused infectious diarrhea, according to the difference on age, gender and season.
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Objective To introduce the establishment of Shanghai Diarrhea Comprehensive Surveillance System ,and to analyze the epidemiological and etiological characteristics of infectious diarrhea outpatients in Shanghai based on data of Shanghai Diarrhea Comprehensive Surveillance System .Methods Diarrhea patients were surveyed according to a unified designed questionnaire ,who visited one of 22 adult sentinel hospitals and 4 children sentinel hospitals of Shanghai Diarrhea Comprehensive Surveillance during September 2013 to August 2016 .Stool specimens were collected according to different sampling intervals and detected for 12 bacteria and 5 viruses .Characteristics of diarrhea patients were compared and analyzed .Chi-square test was used for statistical analysis .Results Of 4497 infectious diarrhea patients ,the detection rate of viral infection was 29 .77％ ,of which norovirus infection (16 .33％ ) , rotavirus infection (7 .90％ ) and sapovirus infection (1 .90％ ) were dominated . The detection rate of bacterial infection was 15 .38％ ,diarrheagenic E .coli (DEC) infection (5 .25％ ) ,V . parahaemolyticus infection (4 .27％ ) and Salmonella spp .infection (3 .13％ ) .Mixed infection accounted for 11 .07％ .The detection rate ,the infection types and the predominant pathogens in different age groups were statistically different (χ= 18 .11 ,61 .86 and 449 .52 ,respectively ,all P< 0 .01) .DEC ranked first in 3 - 14 years age group , and norovirus ranked first in all other age groups .The pathogen spectrum of infectious diarrhea patients≥ 15 years old showed obvious seasonal changes ,with mainly bacterial infection in summer (peaked in August ,accounting for 81 .56％ ) and mainly viral infection in winter (peaked in January ,accounting for 95 .27％ ) .Norovirus ranked first through the year ,except January ,June ,July and August .Among patients ≥ 15 years old , abdominal pain , fever and loose stools were main symptoms in bacterial infections .Vomiting and watery stool were main symptoms in viral infections . Loose stools appeared frequently in patients ≤ 14 years old .Conclusions Diarrhea Comprehensive Surveillance System based on scientific design and rational distribution is beneficial for understanding the epidemic trends and pathogen characteristics of diarrhea .Viral infections are predominant in infectious diarrhea patients in Shanghai . Norovirus and rotavirus are the most common diarrheal pathogens .The pathogen spectrum of infectious diarrhea patients shows obvious seasonal changes .DEC is common in diarrhea patients ≤ 14 years old . The clinical symptoms of infectious diarrhea caused by different pathogens are different . Targeted preventive measures should be taken for infectious diarrhea of different ages ,different pathogens ,and in different seasons .
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This research aims to evaluate the application of Real - time cell assay (RTCA) based on microelectronics sensor technology in the detection of HEV71 induced cell lesion. Growth indexes of RD cells at different stages were observed dynamically, appropriate cell concentration was selected to test HEV71 infectivity and to determine the HEV71 neutralizing antibody titer in serum. The traditional microplate test was used as methodology comparison and results validation at the same time. Cell impedance was transformed to cell index (CI) value and visual dynamic curve through software, and the result showed that the observation of HEV71 infectivity was more than 5d when the RD cells concentration was 1. 5 X 10(4) hole on the 96 electronic orifice plate. Compared with the traditional cytopathic effect (CPE) through microscope observation method, the end point judgment results were consistent between these two methods at 132h (about 5. 5d) post virus inoculation. In the neutralization tests, three CI values of neutralizing antibody titers against HEV71 in human serum were correspond to those obtained from traditional 96 microplate microscopy. RTCA also suggested that the presentation time of CPE induced by the i virus could be different even the end point judgment was the same with the same neutralization antibody titer. Compared with the traditional microplate monitoring method, RTCA can save labor and eliminate the hands-on error in the monitoring HEV71 infectivity and antibody titer detection in serum. RTCA can be served as one of the supplementary methods of traditional detection method, with the advantages of dynamically observing the occurrence and development of cell pathological changes, and the variation of virus infectivity and serum neutralizing antibodies.
Subject(s)
Humans , Antibodies, Neutralizing , Blood , Antibodies, Viral , Blood , Cell Line, Tumor , Cytopathogenic Effect, Viral , Electric Impedance , Enterovirus A, Human , Allergy and Immunology , Virulence , Enterovirus Infections , Virology , Microelectrodes , Neutralization Tests , MethodsABSTRACT
To analyze the epidemiological and etiological characteristics of Hand-Foot-and-Mouth disease (HFMD) in Shanghai in 2009, epidemiological data was retrieved from the National Notifiable Disease Report System (NNDRS). Nucleic acid of enterovirus (EV) was detected by real-time RT-PCR from 799 HFMD cases from 15 districts/counties in Shanghai; the complete sequences of VP1 encoding region of several identified EV71 strains and sequences of VP4 encoding region of several untyped EV were determined and analyzed. Analysis and summary of the epidemiological data was conducted with Microsoft Excel, and sequence analyses were conducted with both BioEdit and MEGA software. Untyped EV was identified through comparing the VP4 sequence to sequence database using BLAST online service. It was showed that all the 18 districts/counties had reported HFMD cases; children less than 6 years old were the most susceptible population group; the peak of epidemics of HFMD was from April to July; EV71 and Coxsackievirus A16 (CA16) were the major pathogens for this epidemic, but the constituent ratio of EV71 and CA16 was different in different months and regions; CA16 infection was mainly responsible for the mild HFMD, but EV71 for most of the severe cases; EV71 strains of Shanghai were clustered with representatives of subgenotype C4a and showed the highest identity to them, based on the sequence analyses of VP1 encoding region; 2 of the untyped EV were identified as CA2 and CA10 respectively. All the results indicated that EV71 and CA16 were the major pathogens for the epidemic of HFMD in Shanghai, 2009; the circulating EV71 belonged to subgenotype C4a. Besides, other types of EV (for example: CA2 and CA10) were also responsible for a few of the HFMD cases.