Norovirus remains a leading cause of foodborne gastroenteritis globally. While isothermal amplification technologies offer advantages over traditional reverse transcription quantitative PCR (RT-qPCR) in terms of speed and portability, there is a lack of domestically developed isothermal amplification systems for norovirus in China. Using a domestic patented cross-priming amplification (CPA) technology, we established CPA systems targeting the predominant norovirus genotypes GII.3, GII.4, and GII.17. The systems were evaluated using 224 fecal samples with confirmed genotypes via sequencing. Our lab-developed CPA (Lab-CPA) systems demonstrated high sensitivity, detecting 98.0% (49/50) of GII.3, 100% (80/80) of GII.4, and 96.9% (31/32) of GII.17 samples, with 100% specificity across all genotypes. Compared to certified clinical RT-qPCR kits, the total percent agreement was 98.7%, 99.3%, and 96.9% for GII.3, GII.4, and GII.17, respectively, accompanied by a significant linear correlation in threshold times. Crucially, the Lab-CPA systems reduced processing time by 44-60 min compared to RT-qPCR. Successful integration into the commercial EasyNAT platform using all-in-one cartridges further streamlined the workflow while maintaining accuracy. Our CPA systems offer a rapid, cost-effective, and streamlined diagnostic solution, ideally suited for point-of-care testing in resource-limited primary healthcare environments.IMPORTANCENorovirus remains a critical public health threat, driving demand for rapid, deployable diagnostics. While isothermal amplification offers theoretical advantages over reverse transcription quantitative PCR, the absence of domestically developed systems in China has created a reliance on imported assays, limiting point-of-care testing capabilities. This study addresses that gap by establishing a novel cross-priming amplification system tailored to China's predominant norovirus genotypes. Achieving high sensitivity/specificity and significantly reducing processing time, this work validates a robust, field-adaptable alternative to conventional methods. Furthermore, successful integration with the commercial EasyNAT platform demonstrates immediate translational potential. By providing a cost-effective, high-performance domestic solution, these findings significantly enhance decentralized surveillance and emergency response capacity for norovirus infections in resource-limited settings.

OBJECTIVE:Brainstem encephalitis (BE) can cause sudden death in children. Fewer studies have been conducted on the incidence, clinical manifestations, pathogens and post-infectious sequelae of pediatric infectious BE. METHODS:Pediatric patients diagnosed with BE in our Medical Center from 01 January 2015 to 31 July 2024 were retrospectively reviewed. The clinical data of these children were obtained from the hospital's medical database on 15 August 2024. The number of outpatient and inpatient patients at our Medical Center during that period were provided by the hospital data center. Data analysis was conducted using Excel 2019. RESULTS:A total of twenty-eight cases were diagnosed with BE in our National Children's Medical Center over the past decade. Among them, 57.1% (16/28) cases were diagnosed with infectious BE. The incidence of infectious BE was estimated to be 16 cases per 30 million outpatient visits and 13 cases per 500,000 hospitalized patients. Fever, consciousness disorders and seizures were observed in 75.0% (12/16), 68.8% (11/16) and 62.5% (10/16) of the cases, respectively. Among them, 31.3% (5/16) cases were diagnosed as human enterovirus infections, 12.5% (2/16) cases were confirmed to be influenza B virus infections, while one case each was diagnosed with herpes simplex virus 1 and human herpesvirus 6 infection. The mortality rate during hospitalization was 12.5% (2/16). Among the surviving patients, 50.0% (7/14) of them had follow-up records, 85.7% (6/7) of the survivors suffered from sequelae such as motor disorders. CONCLUSION:Fever, consciousness disorders and seizures were the major clinical manifestations in patients with infectious BE visited our Medical Center. These rare cases exhibited a notably high mortality rate and a significant frequency of long-term complications.

BACKGROUND:The immature and suppressed immune response makes transplanted children a special susceptible group to Parvovirus B19 (PVB19). However, the clinical features of transplanted children with PVB19 infection haven't been comprehensively described.METHODS:We searched the medical records of all the transplant recipients who attended the Children's Hospital of Fudan University from 1 Oct 2020 to 31 May 2023, and reviewed the medical literature for PVB19 infection cases among transplanted children.RESULTS:A total of 10 cases of PVB19 infection were identified in 201 transplanted children at our hospital, and the medical records of each of these cases were shown. Also, we retrieved 40 cases of PVB19 infection among transplanted children from the literature, thus summarizing a total of 50 unique cases of PVB19 infection. The median time to the first positive PVB19 DNA detection was 14 weeks post-transplantation. PVB19 IgM and IgG were detected in merely 26% and 24% of the children, respectively. The incidence of graft loss/dysfunction was as high as 36%. Hematopoietic stem cell transplant (HSCT) recipients showed higher PVB19 load, lower HGB level, greater platelet damage, lower PVB19 IgM/IgG positive rates, and more graft dysfunction than solid-organ transplant (SOT) recipients, indicating a more incompetent immune system.CONCLUSIONS:Compared with the published data of transplanted adults, transplanted children displayed distinct clinical features upon PVB19 infection, including lower PVB19 IgM/IgG positive rates, more graft dysfunction, and broader damage on hematopoietic cell lines, which was even more prominent in HSCT recipients, thus should be of greater concern.

BackgroundDuring the coronavirus disease 2019 (COVID-19) pandemic, the infection of Mycoplasma pneumoniae (MP) decreased significantly. At the beginning of the summer of 2023, there was an increasing trend of MP infection in China and the MP pneumonia (MPP) is surging when it comes to the school season and lasts for several months which has attracted widespread attention.ObjectiveThis study aims to investigate the prevalent characteristics of the MP and the difference between the COVID-19 pandemic and the post in Shanghai, China.MethodsThe demographic information and the results of laboratory pathogen detection from July 2021 to May 2024 were collected and analyzed to find out the prevalent characteristics of MP. Two periods, during the COVID-19 pandemic and the post-pandemic, were divided and compared. The P1 genotyping and macrolide resistance-associated gene of 23 s rRNA were detected using the remaining MP-positive samples.ResultsDuring the COVID-19 pandemic, the prevalence of the MP has significantly decreased. Female children are more susceptible to MP infection than the male. The school-aged group (>6 years) had the highest infection rate. The rate of MP P1 genotype during post panel is higher than that during COVID-19 pandemic, which is dominant from July 2021 to May 2024, while the macrolide-resistant associated mutations (A2063G) keep high percentage during or post pandemic.ConclusionAfter the COVID-19 pandemic, an outbreak of MP infection occurred from summer onwards in 2023 with children in Shanghai, China. Immunity debt and high rate of macrolide-resistance may take effects in this MP epidemic. Continuous surveillance of MP is necessary to help to alert the prevalence of MPP.

Group A rotavirus (RVA) is considered an important cause of acute gastroenteritis (AGE) in all age groups, especially in children. We investigated the epidemiology of RVA in outpatients aged ≤16 years at the Children’s Hospital of Fudan University, Shanghai, China. In this study, 16.6% (246/1482) were infected with RVA. The detection rate of RVA was significantly higher in the year of 2021 (20.3%, 147/725) compared to the year of 2020 (14.5%, 77/531) and 2022 (9.7%, 22/226) ( p =0.000). RVA infection was prevalent in all seasons from 2020 to 2022, with a different monthly distribution observed in different years. Among 246 RVA-positive samples, 14 different RVA genotypes were detected with different frequencies. Overall, G9P[8] (45.5%, 112/246) was the most common RVA genotype, followed by G8P[8] (37.4%, 92/246) and G3P[8] (4.1%, 10/246). The prevalence of G/P combinations varied from 2020 to 2022. G9P[8] was the most circulating genotype in 2020 (68.2%, 15/22) and 2021 (57.8%, 85/147). However, G8P[8] (68.8%, 53/77) suddenly became the most prevalent genotype in 2022 after being first identified in 2020 and prevalent in 2021. The G8 strains detected in the study were all clustered to DS-1-like G8 strains with the closest genetic distance to strains circulating in Southeast Asia. Our study demonstrated the diversity of circulating RVA genotypes in Shanghai. The sudden emergence and high prevalence of unusual G8P[8] strains deserve more concern and indicate the need for continuous surveillance of RVA in children with AGE in the future to refine future vaccine strategy.

Respiratory syncytial virus (RSV) is a significant cause of acute lower respiratory tract infection (ALRTI) in children under five years of age. Between 2017 and 2021, 396 complete sequences of the RSV F gene were obtained from 500 RSV-positive throat swabs collected from ten hospitals across nine provinces in China. In addition, 151 sequences from China were sourced from GenBank and GISAID, making a total of 549 RSV F gene sequences subjected to analysis. Phylogenetic and genetic diversity analyses revealed that the RSV F genes circulating in China from 2017 to 2021 have remained relatively conserved, although some amino acids (AAs) have undergone changes. AA mutations with frequencies ≥ 10% were identified at six sites and the p27 region: V384I (site I), N276S (site II), R213S (site Ø), and K124N (p27) for RSV A; F45L (site I), M152I/L172Q/S173L/I185V/K191R (site V), and R202Q/I206M/Q209R (site Ø) for RSV B. Comparing mutational frequencies in RSV-F before and after 2020 revealed minor changes for RSV A, while the K191R, I206M, and Q209R frequencies increased by over 10% in RSV B. Notably, the nirsevimab-resistant mutation, S211N in RSV B, increased in frequency from 0% to 1.15%. Both representative strains aligned with the predicted RSV-F structures of their respective prototypes exhibited similar conformations, with low root-mean-square deviation values. These results could provide foundational data from China for the development of RSV mAbs and vaccines.

BACKGROUND:Stringent nonpharmaceutical interventions (NPIs) have been implemented worldwide to combat the COVID-19 pandemic, and the circulation and seasonality of common respiratory viruses have subsequently changed. There have been few multicentre studies or comparisons of the prevalence of respiratory viruses accounting for community-acquired pneumonia (CAP) in hospitalized children between the pre-COVID period and the period after community and school reopening in the setting of the zero-COVID policy.METHODS:We included 1543 children with CAP who required hospitalization from November 1, 2020 to April 30, 2021 (period 1), and 629 children with the same conditions from November 1, 2018, to April 30, 2019 (period 2), in our study. All respiratory samples from these patients were screened for six respiratory viruses (respiratory syncytial virus [RSV], adenovirus [ADV], influenza A virus [Flu A], influenza B virus [Flu B], parainfluenza virus type 1 [PIV1], and parainfluenza virus type 3 [PIV3]) using a multiplex real-time PCR assay.RESULTS AND CONCLUSIONS:The median ages of the enrolled patients at the time of diagnosis were 1.5 years and 1.0 years for period 1 and period 2, respectively. In period 1, viral pathogens were detected in 50.3% (776/1543) of the enrolled patients. The most frequently identified viral pathogen was RSV (35.9%, 554/1543), followed by PIV3 (9.6%, 148/1543), PIV1 (3.6%, 56/1543), ADV (3.4%, 52/1543), Flu A (1.0%, 16/1543), and Flu B (0.8%, 13/1543). The total detection rates of these six viruses in the peak season of CAP were at the pre-COVID level. The prevalence of Flu A decreased dramatically, and circulation activity was low compared to pre-COVID levels, while the incidence of PIV3 increased significantly. There were no significant differences in the detection rates of RSV, ADV, Flu B, and PIV1 between the two periods. Our results showed that respiratory viruses accounted for CAP in hospitalized children at pre-COVID levels as communities and schools reopened within the zero-COVID policy, although the prevalence aetiology spectrum varied.

Objective To investigate the epidemiology and infectious characteristics of Epstein-Barr virus (EBV) infection among children in Shanghai, China from 2017 to 2022. Methods We conducted a retrospective analysis of 10,260 inpatient patients who were subjected EBV nucleic acid testing from July 2017 to December 2022. Demographic information, clinical diagnosis, laboratory findings, etc. were collected and analyzed. EBV nucleic acid testing were performed by real-time PCR. Results A total of 2192 (21.4%) inpatient children were EBV-positive, with the average age of 7.3 ± 0.1 y. EBV detection was stable from 2017 to 2020 (26.9~30.1%), but showed essential decreases in 2021 (16.0%) and 2022 (9.0%). EBV was highest (>30%) detected from three quarters (Q) including 2018-Q4, 2019-Q4 and 2020-Q3. There were 24.5% of EBV coinfection with other pathogens, including bacteria (16.8%), other viruses (7.1%) and fungi (0.7%). EBV viral loads increased when coinfecting with bacteria ((142.2 ± 40.1) ×10 4 /mL) or other viruses ((165.7 ± 37.4) ×10 4 /mL). CRP significantly increased in EBV/fungi coinfection, while procalcitonin (PCT) and IL-6 showed remarkable increases in EBV/bacteria coinfection. Most (58.9%) of EBV-associated diseases belonged to immune disorders. The primary EBV-related diseases were systemic lupus erythematosus (SLE, 16.1%), immunodeficiency (12.4%), infectious mononucleosis (IM, 10.7%), pneumonia (10.4%) and Henoch-schonlein purpura (HSP, 10.2%). EBV viral loads were highest ((233.7 ± 27.4) × 10 4 /mL) in patients with IM. Conclusion EBV was prevalent among children in China, the viral loads increased when coinfecting with bacteria or other viruses. SLE, immunodeficiency and IM were the primary EBV-related diseases.

IntroductionHuman astrovirus (HAstV) is an important pathogen of acute gastroenteritis (AGE) in children. This study was aimed at investigating the diversity and epidemiology of classic and novel HAstV in outpatient children aged 0–16 years old with AGE in Shanghai.MethodsFrom May 2020 to December 2022, a total of 1,482 stool samples were collected from children diagnosed as AGE from the Children’s Hospital of Fudan University. HAstV was identified using pan-astrovirus consensus primers by Reverse transcription PCR.ResultsDuring the study period, 3.3% (49/1,482) of specimens were identified as HAstV, with a detection rate of 2.5% (37/1,482) for classic HAstV and 0.8% (12/1,482) for novel HAstV. Among the 12 novel HAstV strains, 11 (91.7%) belonged to the HAstV-MLB and 1 (8.3%) was HAstV-VA. Genotyping revealed six circulating genotypes. Strain HAstV-1 was predominant in the study population with a detection rate of 1.8% (26/1,482) followed by HAstV-MLB1 (0.7%, 10/1,482) and HAstV-4 (0.6%, 9/1,482). Of note, all the HAstV-4 strains detected in this study were close to one astrovirus strain isolated from Bactrian camels with 99.0-100.0% amino acid sequences identity. In this study, HAstV was detected in all age groups with the highest detection rate of HAstV-positive specimens observed in children older than 73 months (5.7%, 12/209).DiscussionThis study provided useful information and contributed to the molecular epidemiology of both classic and novel HAstV, which were simultaneously characterized and reported for the first time in Shanghai.

BackgroundCytomegalovirus (CMV) is the leading cause of congenital infections worldwide and contributes to long-term sequelae in neonates and children. CMV envelope glycoproteins play a vital role in virus entry and cell fusion. The association between CMV polymorphisms and clinical outcomes remains controversial. The present study aims to demonstrate the distribution of glycoprotein B (gB), H (gH) and N (gN) genotypes in congenitally CMV (cCMV) infected symptomatic infants and attempts to figure out the association between viral glycoprotein genotypes and clinical outcomes.MethodsGenotyping of gB, gH and gN was performed in 42 cCMV symptomatic infants and 149 infants with postnatal CMV (pCMV) infection in Children's hospital of Fudan university. Nested PCR, gene sequencing and phylogenetic analyses were used to identify the genotypes.ResultsOur study demonstrated that: 1. The CMV gB1, gH1 and gN1 were the predominant genotypes among symptomatic cCMV infected infants, while gB1, gH1 and gN3a were more prevalent in pCMV group. gH1 genotype has a significant association with symptomatic cCMV infection (p = 0.006). 2. No significant correlation was found between CMV genotypes and hearing impairment. However, gH1 was more prevalent among cCMV infected infants with moderate/severe hearing loss although without statistical difference (p = 0.130). 3. gB3 was more prevalent among infants with skin petechiae (p = 0.049) and found to be associated with an increased risk of skin petechiae (OR = 6.563). The gN4a subtype was significantly associated with chorioretinitis due to cCMV infection (p = 0.007). 4. Urine viral loads were not significantly associated with different genotypes or hearing impairment among symptomatic cCMV infected infants.ConclusionsOur findings demonstrated the overall distribution of gB, gH and gN genotypes in infants with symptomatic cCMV infection in Shanghai for the first time. The findings in our study may suggest a possible association between gH1 genotype and early infancy hearing loss. gB3 genotype was associated with a 6.5-fold increased risk of petechiae while gN4a strongly correlated with chorioretinitis due to cCMV infection. No significant correlation was found between urine viral loads and CMV genotypes or hearing impairment in cCMV infected infants.

Norovirus (NoV) is a major pathogen that causes acute gastroenteritis (AGE) in people of all ages, especially in children. In this study, we investigated the molecular epidemiological characteristics of NoV in children with AGE in Shanghai from 2018 to 2021. The overall detection rate of NoV was 11.9% (181/1545), with annual detection rates of 9.4% (36/381), 13.6% (29/213), 5.8% (13/226) and 14.2% (103/725), respectively. Of note, the prevalence of NoV in 2020 was significantly lower than that in 2018-2019 (10.9%, 65/594) (P = 0.023) and 2021 (14.2%, 103/725) (P = 0.000). The 181 NoV strains identified in this study were classified into the GI group (1.1%, 2/181), GII group (98.3%, 178/181) and GIX group (0.6%, 1/181) according to the VP1 gene. The most common NoV VP1 genotype was GII.4 Sydney_2012 (63.5%, 115/181), followed by GII.3 (19.9%, 36/181) and GII.2 (9.4%, 17/181). For P genotypes, 174 strains were sequenced successfully according to the RdRp gene, and the predominant genotype was GII.P16 (44.8%, 78/174), followed by GII.P31 (25.9%, 45/174) and GII.P12 (21.3%, 37/174). Among the 174 cases, GII.4 Sydney_2012[P16] (36.8%, 64/174) was the dominant genotype, followed by GII.4 Sydney_2012[P31] (25.3%, 44/174), GII.3[P12] (20.1%, 35/174) and GII.2[P16] (8.0%, 14/ 174). In particular, the dominant genotypes in Shanghai changed from GII.4 Sydney_2012[P31] in 2018-2019 to GII.4 Sydney_2012[P16] in 2020-2021. This is the first report to describe the epidemiological changes in NoV infection before and during the COVID-19 pandemic in Shanghai. These data highlight the importance of continuous surveillance for NoV in children with AGE in Shanghai.

Background Human adenovirus (HAdV) has been recognized as one of the common enteric viruses associated with acute gastroenteritis (AGE) in children. The aim of this study was carried out to illustrate the epidemiological characterization of HAdV Infections among children younger than 15 years in Shanghai during COVID-19. Methods During May 2020 and April 2022, 1048 fecal samples were collected from children ≤ 15 years diagnosed with AGE in the Children’s Hospital of Fudan University. HAdV was identified by PCR and sequenced with specific primers. All the obtained sequences were analyzed by MEGA (version 6.0). Demographic information and clinical features data were also collected and analyzed. Results In total, 97 (9.3%, 97/1048) samples were detected to be HAdV during May 2020 and April 2022. We found an atypical upsurge in HAdV infection in the year 2021 after a major suppression in the year 2020. Approximately 84.5% (82/97) of HAdV-infected children were aged 0–60 months. Among the 97 HAdV-positive samples, only two species and five genotypes were detected. HAdV-F (88.7%, 86/97) was the most prevalent species and HAdV-F41 (87.6%, 85/97) was the most common genotype. Diarrhea, vomiting, and fever were the main clinical manifestations in children infected with HAdV. The children aged from 0 to 12 months showed simpler patterns of clinical presentation than those of children older than 13 months. Conclusions Our findings described the epidemiological changes of HAdV infection in children with AGE during the COVID-19, which further underscored the importance of continuous surveillance of HAdV at both local and global scales.

背景 新型冠状病毒肺炎(COVID-19)疫情发生以来中国政府采取了一系列防控措施,在有效遏制COVID-19疫情蔓延的同时对其他常见呼吸道病原的流行产生了影响.目的 分析COVID-19流行期间儿童急性呼吸道感染(ARTI)肺炎支原体(Mp)和沙眼衣原体(CT)的流行病学特征.设计观察性研究.方法 2019年2月1日至2021年5月31日于复旦大学附属儿科医院(我院)诊断为ARTI并行Mp、CT和9种常见呼吸道病毒检测的数据,分为单一病原体感染(仅检出Mp或CT)和混合感染(Mp+CT,Mp或CT+9种常见呼吸道病毒中任意1种及以上,Mp+CT+9种常见呼吸道病毒中任意1种及以上).呼吸道样本(鼻咽部抽吸物/肺泡灌洗液)采集和检测均在我院完成.①COVID-19疫情前(简称疫情前):2019年2月1日至2020年1月31日,不主动实施COVID-19疫情防控措施;②COVID-19疫情中(简称疫情中):2020年2月1日至2020年5月31日,COVID-19疫情大流行全国范围内严格实施非药物干预措施(NPI),学校停课;③COVID-19疫情后(简称疫情后):2020年6月1日至2021年5月31日,COVID-19疫情防控常态化阶段,NPI措施有所放松,学校重新复课,社会复工复产.对纳入的病原体样本,根据当次诊断ARTI时患儿年龄分为≤28 d、～12月、～3岁、～6岁和≥7岁.主要结局指标COVID-19流行期间Mp、CT流行病学.结果 10358份因ARTI行呼吸道病原体检测的样本纳入本文分析,其中疫情前、中和后分别为6080份、754份和3524份,疫情后较前病原体送检率下降42.04％[(6080-3524)/6080×100％].男6138例,女4220例.Mp总检出率12.39％,疫情前、中、后呈陡然下降趋势,疫情后较前Mp检出率下降96.29％,差异有统计学意义(P<0.001).CT总检出率为1.45％,疫情前、中、后呈上升趋势,疫情后较前阶段检出率上升65.49％,差异有统计学意义(P=0.003).单纯Mp或CT检出率10.84％,疫情后较前Mp检出率下降96.05％、CT检出率上升119.70％,差异均有统计学意义.混合感染检出率2.89％,疫情后较前Mp混合感染检出率下降97.32％,差异有统计学意义,Mp+CT混合感染和CT混合感染检出率差异均无统计学意义.疫情前Mp呈明显的夏季检出率高的特征,疫情后季节检出特征消失.CT检出率全年分布均匀.疫情前、中、后Mp和CT送检率以及CT检出率12月龄后随着年龄的增加均呈下降趋势,而疫情前、中、后Mp检出率随年龄增加分别呈现明显上升、上升和略有上升趋势.疫情前、中、后≤28 d至～12月龄组CT检出率随着年龄的增加呈明显上升趋势.结论 COVID-19疫情期间采取的一系列防控措施,不仅遏制了新型冠状病毒的传播,同时影响了非典型呼吸道病原体的流行病学,Mp检出率明显降低,且消弥了Mp检出高峰季,而CT的检出率出现上升.

BACKGROUND:Enterovirus (EV), parechovirus (HPeV), herpes simplex virus 1 and 2 (HSV1/2) are common viruses leading to viral central nervous system (CNS) infections which are increasingly predominant but exhibit deficiency in definite pathogen diagnosis with gold-standard quantitative PCR method. Previous studies have shown that droplet digital PCR (ddPCR) has great potential in pathogen detection and quantification, especially in low concentration samples.METHODS:Targeting four common viruses of EV, HPeV, HSV1, and HSV2 in cerebrospinal fluid (CSF), we developed a multiplex ddPCR assay using probe ratio-based multiplexing strategy, analyzed the performance, and evaluated it in 97 CSF samples collected from patients with suspected viral CNS infections on a two-channel ddPCR detection system.RESULTS:The four viruses were clearly distinguished by their corresponding fluorescence amplitude. The limits of detection for EV, HPeV, HSV1, and HSV2 were 5, 10, 5, and 10 copies per reaction, respectively. The dynamic range was at least four orders of magnitude spanning from 2000 to 2 copies per reaction. The results of 97 tested clinical CSF specimens were identical to those deduced from qPCR/qRT-PCR assays using commercial kits.CONCLUSION:The multiplex ddPCR assay was demonstrated to be an accurate and robust method which could detect EV, HPeV, HSV1, and HSV2 simultaneously. It provides a useful tool for clinical diagnosis and disease monitoring of viral CNS infections.

Background Human rhinovirus (HRV) is the predominant etiological agent of the common cold in children and adults. A recent study showed that the inhibitory effect of face masks on viral shedding of HRV was less prominent than that on other respiratory viruses. Considering that most Chinese people have worn face masks in public area since the outbreak of coronavirus disease 2019, we aimed to find out whether HRV prevailed among children in 2020 and demonstrate the details of the epidemiological features of HRV under such a special circumstance. Methods We summarized the incidences of various respiratory virus infections in patients who visited the Children's Hospital of Fudan University during 2018-2020, and genotyped HRV positive nasopharyngeal specimens collected from 316 inpatients and 72 outpatients that visited the hospital in 2020. Results There was a major prevalence of HRV among children in the latter half of 2020, with a clear seasonality that HRV-As prevailed in summer while HRV-Cs in autumn. HRV-As were more prone to cause severe lower respiratory tract infections (LRTI), while HRV-Cs were closely associated with childhood wheezing. The predominant genotypes were A11, A28, A47, A82, A101, C40 and C43. Notably, A21, A82 and A101 took up larger proportions in severe cases than in non-severe cases. Conclusions Our findings described a major prevalence of HRVs among children in 2020, which highlight the unique transmitting pattern of HRV and help to narrow the targets for antiviral strategies.

Nonpharmaceutical interventions (NPIs) taken to combat the coronavirus disease 2019 (COVID-19) pandemic have not only decreased the spread of severe acute respiratory syndrome coronavirus 2 but also have had an impact on the prevalence of other common viruses. This study aimed to investigate the long-term impact of NPIs on common respiratory and enteric viruses among children in Shanghai, China, as NPIs were relaxed after June 2020. The laboratory results and clinical data of outpatient children with acute respiratory tract infections (ARTI) and acute gastroenteritis (AGE) were analyzed and compared between the post-COVID-19 period (from June 2020 to January 2022) and pre-COVID-19 period (from June 2018 to January 2020). A total of 107 453 patients were enrolled from June 2018 to January 2022, including 43 190 patients with ARTI and 64 263 patients with AGE. The positive rates of most viruses decreased during the post-COVID-19 period, with the greatest decrease for influenza A (-0.94%), followed by adenoviruses (AdV) (-61.54%), rotaviruses (-48.17%), and influenza B (-40%). However, the positive rates of respiratory syncytial virus (RSV) and enteric AdV increased during the post-COVID-19 period as the NPIs were relaxed. Besides this, in the summer of 2021, an unexpected out-of-season resurgence of RSV activity was observed, and the resurgence was more prominent among children older than 5 years. The effectiveness of the current relaxed NPIs in control of common respiratory and enteric viruses was variable. Relaxation of NPIs might lead to the resurgence of common viruses.

ObjectivesThis study aimed to assess the impact of COVID-19 on the prevalence of respiratory pathogens among hospitalized children with lower respiratory tract infections (LRTIs) in Shanghai.MethodsRespiratory specimens were collected from children with LRTIs in Children’s Hospital of Fudan University from February 2019 to January 2021 and common respiratory pathogens were detected using multiplex PCR. The data of 13 respiratory pathogens were analyzed and compared between the year of 2020 (from February 2020 to January 2021) and 2019 (from February 2019 to January 2020).ResultsA total of 1,049 patients were enrolled, including 417 patients in 2019 and 632 patients in 2020. In 2020, 27.53% of patients were tested positive for at least one pathogen, which was significantly lower than that in 2019 (78.66%). The top three pathogens were Mycoplasma pneumoniae (Mp), human adenovirus (ADV) and human rhinovirus (RV) in 2019, whereas RV, human respiratory syncytial virus (RSV) and human parainfluenza virus (PIV) were the predominant ones in 2020. The positive rates of Mp, ADV, RV, PIV, Influenza virus B (InfB), H3N2, and H1N1 were significantly decreased in 2020. RV was the most detectable respiratory pathogen in 2020, and become the most frequent pathogen in all five age groups. PIV had a high prevalence from October to December 2020 which was even higher than that in 2019. Influenza virus A (InfA) was not detected in 2020. Co-infection was significantly less frequent in 2020.ConclusionThe public health interventions aiming to eliminate COVID-19 have great impact on the prevalence of common respiratory pathogens. The prevalence of RV and PIV reminds us a possible resurgence of some pathogens.

Respiratory syncytial virus (RSV) is the most common pathogen causing acute lower respiratory tract infection (LRTI) in children. RSV usually peaks in winter and declines by early spring in China. The outbreak of coronavirus disease 2019 (COVID-19) was reported to bring changes to the transmission pattern of respiratory pathogens including RSV. Here in this paper, we analyzed RSV-positive nasopharyngeal aspirates from inpatients in the Children’s Hospital of Fudan University from October 2019 to October 2021 and compared the clinical features of the RSV-positive patients before and during COVID-19. We found an atypical upsurge of RSV infection in the late summer of 2021 after a major suppression in 2020. RSV B was the main subtype spreading among children throughout the study. Phylogenetic analysis revealed that all RSV A strains belonged to ON1 genotype and all RSV B strains were BA9 genotype. Deduced amino acid analysis displayed different substitutions in the RSV strains observed before and during COVID-19. Demographic analysis suggested that males and infants aged under 5 months were the main populations infected with RSV by gender and age, respectively. Less severe clinical outcomes were observed in patients during COVID-19 than before the pandemic, especially in RSV B-positive patients. Our findings described the epidemiological changes in RSV infection brought by COVID-19, which further underscored the importance of continuous surveillance of RSV in the shadow of COVID-19 at both local and global scales.

BACKGROUND:Group A rotavirus (RVA) remains the main causative agent of acute diarrhea among children under five years in countries that have not yet introduced the RVA vaccine worldwide. Long-term and continuous monitoring data on RVA infection in outpatient children were lacking in Shanghai. We investigated the prevalence and distribution of RVA genotypes in outpatient children with acute diarrhea in Shanghai from 2012 to 2018.METHODS:Stool specimens of outpatient children under five years were collected from the Children's Hospital of Fudan University in Shanghai, China. All the samples enrolled in this study were detected and characterized for the P and G genotypes of RVA were determined using the semi-multiplex RT-PCR technique.RESULTS:Of 1814 children enrolled with acute diarrhea and having specimens collected, 246 (13.6%) were infected with RVA. The highest frequency of RVA was observed in children younger than two years old (87.0%, 214/246). Year-round RVA transmission was observed and the RVA detection rate peaked every winter and troughed in summer. In this study, 12 different RVA strains were identified in children. G9P[8] (49.2%, 121/246) was detected as the most prevalent genotype, followed by G-P[8] (22.8%, 56/246), G3P[8] (11.4%, 28/246), and G9P- (4.9%, 12/246). Although RVA strains detected in this study varied with the time, G9P[8] has been the most predominant circulating genotype since 2012. Furthermore, 12.2% (30/246) RVA positive samples were co-infected with other diarrhea viruses.CONCLUSION:The present analysis showed that RVA was still a major cause of children with acute diarrhea in Shanghai from 2012 to 2018. A great diversity of RVA strains circulated in children with acute diarrhea with G9P[8] being the predominant genotype since 2012. Long-term and continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy in Shanghai.