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An unprecedented surge of Omicron infections appeared nationwide in China in December 2022 after the adjustment of COVID-19 response policy. In this study, we report the clinical and virological characteristics of SARS-CoV-2 Omicron BA.5 infections among children in Shanghai during the outbreak in late December 2022. We sequenced the 64 SARS-CoV-2 positive samples obtained from hospitalized children. The genomic monitoring revealed that the current outbreak was driven by the BA.5.2.48 and BF.7.14 subvariants. Additionally, children with BA.5.2.48 infection were more frequently observed to experience vomiting/diarrhea compared to those with BF.7.14 infection. The high-frequency unique non-synonymous mutations were present in BA.5.2.48 (N: Q241K) and BF.7.14 (nsp2: V94I, nsp12: L247F, S: C1243F, ORF7a: H47Y) with respect to their parental lineages. Of these mutations, C1243F mutation in S protein, L247F mutation in nsp12, and H47Y mutation in ORF7a protein were predicted to have a deleterious effect on the protein function. Besides, H47Y mutation was also found to increase the stability of ORF7a protein. Therefore, attention should be paid to these specific mutations, especially for H47Y mutation, which could serve as a viral immune escape strategy due to the potential immunomodulatory ability of the ORF7a protein. Continuous genomic monitoring and clinical manifestation assessments of the emerging variants will be crucial for effective responses to the ongoing COVID-19 pandemic.

This study aims to understand the epidemiological characteristics of SARS-CoV-2 infection in the paediatric population during the outbreak of the Omicron variant in Shanghai. We retrospectively analysed the population-based epidemiological characteristics and clinical outcome of SARS-CoV-2 Omicron variant infection in children in Minhang District, Shanghai, based on the citywide surveillance system during the outbreak period in 2022 (March to May). During this time, a total of 63,969 cases of SARS-CoV-2 infection were notified in Minhang District, out of which 4,652 (7.3%) were children and adolescents

This study aimed to understand the epidemiological and clinical characteristics of pediatric SARS-CoV-2 infection during the early stage of Omicron variant outbreak in Shanghai.This study included local COVID-19 caseslt;18 years in Shanghai referred to the exclusively designated hospital from March 7 to March 31, 2022. Clinical data, epidemiological exposure, and COVID-19 vaccination status were collected. Relative risks (RRs) were calculated to assess the effect of vaccination on symptomatic infection and febrile disease.A total of 376 pediatric cases of COVID-19 (median age: 6.0 ± 4.2 years) were referred to the designated hospital, including 257 (68.4%) symptomatic cases and 119 (31.6%) asymptomatic cases. Of the 307 (81.6%) children ≥3 years eligible for COVID-19 vaccination, 110 (35.8%) received two doses of vaccines. The median interval between the completion of two-dose vaccination and infection was 3.5 (interquartile range [IQR]: 3, 4.5) months. Compared with no vaccination, two-dose COVID-19 vaccination reduced the risks of symptomatic infection and febrile disease by 35% (RR 0.65, 95% confidence interval [CI]: 0.53-0.79) and 33% (RR 0.64, 95% CI: 0.51-0.81) among confirmed cases. Eighty-four percent of symptomatic cases had fever (mean duration: 1.7 ± 1.0.8 days), 40.5% had cough, and 16.4% had transient leukopenia. Three hundred and seven (81.6%) had an epidemiological exposure in household (69.1%), school (21.8%), and residential area (8.8%).The surge of pediatric COVID-19 cases and multiple transmission model reflect wide dissemination of Omicron variant in the community. Asymptomatic infection is common among Omicron-infected children. COVID-19 vaccination can offer some protection against symptomatic infection and febrile disease.

Objectives: To understand the epidemiological and clinical characteristics of pediatric SARS-CoV-2 infection during the early stage of Omicron variant outbreak in Shanghai. Study designs: This study included local COVID-19 cases

ObjectivesTo understand the epidemiological and clinical characteristics of pediatric SARS-CoV-2 infection during the early stage of Omicron variant outbreak in Shanghai.MethodsThis study included local COVID-19 cases ResultsA total of 376 pediatric cases of COVID-19 (median age:6.0±4.2 years) were referred to the designated hospital during the period of March 7-31, including 257 (68.4%) symptomatic cases and 119 (31.6%) asymptomatic cases. Of the 307 (81.6%) children;3 years eligible for COVID-19 vaccination, 110 (40.4%) received 2-dose vaccines and 16 (4.0%) received 1-dose vaccine. The median interval between 2-dose vaccination and infection was 3.5 (IQR: 3, 4.5) months (16 days-7 months). Two-dose COVID-19 vaccination reduced the risks of symptomatic infection and febrile disease by 35% (RR 0.65, 95% CI:0.53-0.79) and 33% (RR 0.64, 95% CI: 0.51-0.81). Two hundred and sixteen (83.4%) symptomatic cases had fever (mean duration: 1.7±1.0.8 days), 104 (40.2%) had cough, 16.4% had transient leukopenia; 307 (81.6%) had an epidemiological exposure in household (69.1%), school (21.8%) and residential area (8.8%).ConclusionThe surge of pediatric COVID-19 cases and multiple transmission model reflect wide dissemination of Omicron variant in the community. Asymptomatic infection is common among Omicron-infected children. COVID-19 vaccination can offer protection against symptomatic infection and febrile disease.

Supplemental Digital Content is available in the text., Background: Based on the impact public health of norovirus and the current progress in norovirus vaccine development, it is necessary to continuously monitor the epidemiology of norovirus infection, especially in children who are more susceptible to norovirus. Objectives: To monitor the activity and genotypes of norovirus infection in sporadic diarrhea in Shanghainese children during 2014–2018. Study design: Acute diarrheal cases were prospectively enrolled in the outpatient setting. Real-time reverse transcription-polymerase chain reaction was used for screening norovirus GI and GII genogroups. Dual norovirus genotypes were identified based on the partial capsid and polymerase gene sequences. Results: Of the 3422 children with diarrhea, 510 (14.9%) were positive for noroviruses with 13 (2.5%) strains being GI genogroup and 497 (97.5%) strains being GII genogroup. Five distinct capsid GII genotypes were identified, including GII.4-Sydney/2012 (71.8%), GII.3 (13.8%), GII.17 (7.8%), GII.2 (6.0%), GII.6 (0.3%) and GII.8 (0.3%). Seven polymerase GII genotypes were identified, including GII.Pe (77.0%), GII.P12 (11.0%), GII.P17 (9.0%), GII.P16 (2.1%), and GII.P7, GII.P8 and GII.P2 in each (0.3%). Eleven distinct polymerase/capsid genotypes were identified with GII.Pe/GII.4-Sydney/2012 (74.2%), GII.P12/GII.3 (11.7%) and GII.P17/GII.17 (7.7%) being common. GII.P17/GII.17 strains were detected since September 2014. Recombinant GII.P16/GII.2 strains were detected since December 2016. Conclusions: Norovirus is a major pathogen causing diarrhea in Shanghainese children. GII.Pe/GII.4-Sydney/2012 strains remained the predominant genotype. The emergence of GII.P17/GII.17 and GII.P16/GII.2 strains in sporadic diarrhea was consistent with norovirus-associated outbreaks attributable to these 2 novel variants in China. Continuous monitoring norovirus genotypes circulating in pediatric population is needed for current vaccine development.

Objective Scarlet fever epidemics caused by group A Streptococcus (GAS) have been ongoing in China since 2011. However, limited data are available on the dynamic molecular characterizations of the epidemic strains. Method Epidemiological data of scarlet fever in Shanghai were obtained from the National Notifiable Infectious Disease Surveillance System. Throat swabs of patients with scarlet fever and asymptomatic school-age children were cultured. Illumina sequencing was performed on 39emm1 isolates. Results The annual incidence of scarlet fever was 7.5–19.4/100,000 persons in Shanghai during 2011–2015, with an average GAS carriage rate being 7.6% in school-age children. The proportion ofemm1 GAS strains increased from 3.8% in 2011 to 48.6% in 2014; they harbored a superantigen profile similar to emm12 isolates, except for the speA gene. Two predominant clones, SH001-emm12, and SH002-emm1, circulated in 66.9% of scarlet fever cases and 44.8% of carriers. Genomic analysis showed emm1 isolates throughout China constituted distinct clades, enriched by the presence of mobile genetic elements carrying the multidrug-resistant determinants ermB and tetM and virulence genes speA, speC, and spd1. Conclusion A significant increase in the proportion ofemm1 strains occurred in the GAS population, causing scarlet fever in China. Ongoing surveillance is warranted to monitor the dynamic changes of GAS clones.

Hand, foot, and mouth disease (HFMD) is mainly epidemic in China and Southeast Asian countries. A novel enterovirus 71 vaccine has been available in China for preventing severe HFMD since 2016. Knowledge of the dynamic epidemiology of HFMD in different regions is necessary for appropriate intervention strategies. This study focused on the citywide surveillance data on the epidemiology and etiology of HFMD in Shanghai during 2014–2016. In these 3 years, the total numbers of reported HFMD cases were 65,018, 39,702, and 57,548, respectively; the numbers of severe cases (case-severity ratios) were 248 (0.38%), 35 (0.09%), and 59 (0.10%), respectively. Children

Background Non-polio enrerovirus causes a wide spectrum of neurologic syndromes. The epidemiological and clinical profiles of non-polio enrerovirus-associated central nervous system infections vary by regions and over year. Objectives This study aimed to understand the prevalence, serotypes and clinical characteristics of enterovirus-associated aseptic meningitis, encephalitis and meningo-encephalitis in children in Shanghai during 2016−2018. Methods We collected the clinical data and the cerebrospinal fluid specimens from the pediatric patients with aseptic meningitis, encephalitis and meningo-encephalitis during 2016−2018. The nested RT-PCR and sequencing were performed to identify enterovirus and serotypes. Results A total of 424 patients were included in this study and their non-duplicated cerebrospinal fluid specimens were collected during the acute stage of illness. Based on PCR assay, enterovirus was detected in 272 (64.15 %) patients, of whom, the ratio of male to female subjects was 1.99, and the mean age was 5.71 ± 3.55 years (range: 0.03−16 years). There were 17 serotypes identified. Echovirus 30 (24.63 %), Coxsackievirus A10 (20.96 %), Coxsackievirus A6 (18.01 %) accounted for 63.6 %, followed by Coxsackievirus B5 (7.72 %), Echovirus 6 (5.88 %), and other serotypes (22.8 %). Of the 10 (3.68 %) critically severe patients, all had refractory seizure, 8 required mechanical ventilation, 7 survivors had recurrent attacks of epilepsy and 3 abandoned treatment; Coxsackievirus A10, Echovirus 9, Coxsackievirus A2, Coxsackievirus A6 and Echovirus 6 were identified. Conclusions Non-polio enterovirus is the major pathogen causing aseptic meningitis, encephalitis and meningo-encephalitis in Chinese children and can cause life-threatening encephalitis and severe sequelae.

Prevention and control of childhood diarrhea is a global priority. We conducted a case-control study of childhood diarrhea in Shanghai.We prospectively recruited diarrheal children in an outpatient setting. Nondiarrheal controls were individually matched to cases. Rotavirus, norovirus and bacterial pathogens were examined. Clinical and epidemiologic data were obtained at enrollment and follow-up.Potential pathogens identified in 680 diarrheal cases and 680 controls were rotavirus (19.0% vs. 1.3%), norovirus (13.4% vs. 4.7%), nontyphoidal Salmonella (9.3% vs. 1.9%), enteropathogenic Escherichia coli (8.4% vs. 6.9%) and enteroaggregative Escherichia coli (7.2% vs. 6.2%) and Campylobacter (5.1% vs. 1.2%), enterotoxigenic Escherichia coli (1.2% vs. 0.6%), enterohemorrhagic Escherichia coli (0.3% vs. 0%) and Shigella (0.15% vs. 0%), respectively. The specificity and sensitivity of fecal leukocytes5 per high-power field for the diagnosis of bacterial diarrhea were 94.2% and 22.8%. Salmonella were susceptible to ciprofloxacin, ceftriaxone and amoxicillin-clavulanate and showed low frequency of resistance to azithromycin. Campylobacter showed low frequency of resistance to azithromycin and high frequency of resistance to ciprofloxacin. Diarrheagenic Escherichia coli was highly susceptible to ciprofloxacin and amoxicillin-clavulanate. Contact with diarrheal patients was a risk factor for rotavirus [adjusted odds ratio (aOR): 11.7], norovirus (aOR: 7.5) and Campylobacter (aOR: 27.1) infections. Mother's education was positively associated with Salmonella infection (aOR: 2.1). Good hand hygiene was protective against rotavirus (aOR: 0.6), norovirus (aOR: 0.5) and Salmonella (aOR: 0.3) infections.Rotavirus, norovirus, nontyphoidal Salmonella and Campylobacter are significantly associated with diarrhea in Chinese children. Fecal leukocytes5 per high-power field can predict bacterial diarrhea. Target prevention and appropriate treatment of diarrhea should consider the potential pathogen and resistance pattern.

To monitor the epidemic pattern of influenza in children during the 2011-2012 season in Shanghai and to evaluate the socioeconomic burden of influenza in children.We carried out a prospective surveillance program on influenza among children who visiting the outpatient clinic for influenza-like illness (ILI) between June 2011 and May 2012. Respiratory samples as well as related demographic and clinical data were obtained from the enrolled cases. Socio-economic burden was evaluated using the questionnaires for some of the confirmed cases during the outbreak.Out of the 1 119 enrolled cases, influenza viruses were virologically confirmed, using the RT-PCR in 370 (33.1%) otherwise healthy children. Among them, 109(9.7%) were positive for influenza A/H3N2 viruses, and 279 (24.9%) were positive for influenza B viruses. The 2011-2012 seasonal outbreak of influenza among children with Shanghai residency started with the major outbreak of influenza B during December 2011-Feburary 2012, followed by the smaller outbreak of influenza A/H3N2 during March-April, 2012. A total of 69 influenza A/H3N2-infected cases and 163 influenza B-infected cases were surveyed to evaluate the influenza-associated disease burden. The average costs per case were 706.10 Yuan and the average indirect costs per case incurred by the work loss of family members were 293.80 Yuan, with the total average costs per case were 999.90 Yuan. Mean visits to medical settings were 2.7, with antibiotics used in 67.2% of the cases. Secondary household cases were seen in 21.1% of the cases. Pneumonia was diagnosed in 5.6% of the cases. The burden of disease increased from both influenza A/H3N2 and influenza B but without significant differences between them.Influenza A/H3N2 and influenza B viruses caused outbreaks of influenza in children with Shanghai residency during the 2011-2012 season. Socioeconomic burden of influenza in children showed significantly direct impact on the sick children and an indirect impact on their families. Influenza vaccination should be recommended in children to reduce the disease burden.

Background In 2012 a large outbreak of hand, foot, and mouth disease (HFMD) widely spread over China, causing more than 2 million cases and 567 deaths. Our purpose was to characterize the major pathogens responsible for the 2012 HFMD outbreak and analyze the genetic characterization of the enterovirus 71 (EV71) strains in Shanghai; also, to analyze the dynamic patterns of neutralizing antibody (NAb) against EV71 and evaluate the diagnostic value of several methods for clinical detection of EV71. Methods Clinical samples including stool, serum and CSF were collected from 396 enrolled HFMD inpatients during the peak seasons in 2012. We analyzed the molecular epidemiology, clinical feature, and diagnostic tests of EV71 infection. Results EV71 was responsible for 60.35 % of HFMD inpatients and 88.46 % of severe cases. The circulating EV71 strains belonged to subgenogroup C4a. The nucleotide sequences of VP1 between severe cases and uncomplicated cases shared 99.2 ~ 100 % of homology. Among 218 cases with EV71 infection, 211 (96.79 %) serum samples showed NAb positive against EV71 and NAb titer reached higher level 3 days after disease onset. Of 92 cases with EV71-associated meningitis or encephalitis, 5 (5.43 %) of 92 had EV71 RNA detected in CSF samples. The blood anti-EV71 IgM assay showed a sensitivity of 93.30 % and a specificity of 50 %. Conclusions EV71 C4a remained the predominant subgenotype circulating in Shanghai. The severity of the EV71 infection is not associated with the virulence determinants in VP1. RT-PCR together with IgM detection can enhance the early diagnosis of severe EV71-associated HFMD. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0308-2) contains supplementary material, which is available to authorized users.

To monitor the epidemiology of norovirus infection in diarrheal children in Shanghai between 2009 and 2011 and characterize the genotypes of norovirus strains.The stool samples were collected from children visiting outpatient clinic for acute non-dysenteric diarrhea between 2009 and 2011.One step real-time RT-PCR was used for screening norovirus genogroups GI and GII. The genotypes of norovirus genogroup GII were classified based on the nucleotide sequences of both partial capsid and polymerase fragments.A total of 2 288 outpatient children with acute diarrhea were included in this study, out of whom, 531 (23.1%) were positive for norovirus in the fecal specimens based on real-time RT-PCR test.Norovirus was prevalent throughout the year and an increased activity of norovirus infection was usually observed between July and October. Children4 years of age accounted for 95.2% of norovirus-infected cases, and the detection rate of norovirus was significantly higher in diarrheal children4 years than in those ≥ 4 years (24.4% vs. 10.7%,χ(2) = 10.66, P0.05).Of 531 norovirus-positive specimens, 4 (1.7%) were positive for genogroup GI and 527 (98.3%) positive for genogroup GII. Seven distinct capsid genotypes were identified in 234 norovirus strains, including 153 (64.4%) GII.4 (9 belonging to 2010 variants and 145 belonging to 2006b variants), 66 (27.6%) GII.3, 7 (2.9%) GII.2, 6 (2.5%) GII.6, 4 (1.7%) GII.12, 1 (0.4%) GII.7 and GII.14 in each. Seven polymerase genotypes were identified in 244 norovirus strains, including 189 (77.5%) GII.4 (14 belonging to 2010 variants and 175 belonging to 2006b variants), 47 (19.3%) GII.12, 2 (0.8%) GII.16, GII.b and GII.g in each, 1 (0.4%) GII.2 and GII.6 in each. A new GII.4-2010 (New Orleans) variant was first detected in June 2010 and sporadically circulated afterwards.Of 198 norovirus strains in which both polymerase and capsid genotypes were determined, 56 showed discordant results, indicating potential norovirus recombinants. The common discordant combinations of the polymerase and capsid genotypes were GII.12/GII.3 (69.6%) and GII.4/GII.3 (8.9%).Norovirus is a common causative agent responsible for diarrhea in Shanghai children over the three years and norovirus-associated diarrhea was epidemic year round with high activity in late summer and autumn in Shanghai.Infants and young children are susceptible to norovirus infection. The circulating norovirus showed genetic diversity. The GII.4-2006b variant continued to predominate in Shanghai during the period of 2009-2011 despite the emergence of the novel GII.4-2010 (New Orleans) variant.

Influenza is a common cause of outpatient visits in childhood. Influenza vaccine has been widely used for children ≥ 6 months of age in developed countries based on accumulating evidence on the substantial socioeconomic burden of influenza in children. However, the data of childhood influenza in China are scarce.We carried out a prospective surveillance of influenza among children visiting outpatient clinic for influenza-like illness between June 2009 and May 2011. Respiratory samples were obtained from the enrolled cases and the demographic and clinical data were collected.Of 2356 enrolled cases, influenza was virologically confirmed in 608 (25.81%) otherwise healthy children. Four hundred sixty-eight (76.97%) were influenza A positive (A/H3N2:236, pandemic A/H1N1:219, seasonal A/H1N1:4, A/H3N2 coinfected with pandemic A/H1N1:3, untyped:6) and 142 (23.35%) were influenza B positive (2 coinfected with pandemic A/H1N1). The outbreaks of A/H3N2, pandemic A/H1N1 and influenza B took place in fall, winter and spring, alternatively. More institutionalized children were affected when the outbreaks overlapped with school opening. Among 603 children with a single influenza virus infection, 289 (47.93%) were3 years old and 283 (46.93%) had close contact with persons who had fever or respiratory infection, of whom, 192 (67.84%) contacts were family members.The annual outbreak of influenza led to a high rate of outpatient visits among children in Shanghai. Outbreaks occurred in younger and institutionalized children. Household members were the main disseminators to spread influenza among children.