Respiratory viral infections pose persistent global health threats, yet traditionalin vitroand animal models inadequately recapitulate human tissue microenvironments. Organ-on-a-chip technology integrates microfluidic engineering with cell biology to recreate three-dimensional architectures, mechanical forces, and multicellular interactions of the human respiratory system. This review systematically summarizes recent advances in organ-on-a-chip platforms for modeling respiratory viral infections and host immune responses. We highlight their unique capabilities in simulating alveolar-capillary barriers, lymphoid follicle formation, and multi-organ axes including lung-brain and gut-lung communication. Furthermore, we discuss applications in antiviral drug screening, vaccine evaluation, and personalized medicine, while addressing current challenges and future directions toward standardized, multi-organ integrated, and intelligently monitored systems.

Seasonal influenza A virus subtype H3N2 (A/H3N2) circulates globally and has been linked to higher hospitalization rates and summer outbreaks in temperate regions. Here, A/H3N2 circulation in Shanghai, China was systematically studied using data and materials generated by the Shanghai influenza surveillance network from 2005 to 2023. Time-series analysis of incidence and subtyping data showed that A/H3N2 co-circulated with other (sub)types and dominated in multiple seasonal influenza peaks, preferentially in summer. Whole genomes of 528 representative strains were sequenced, and spatiotemporal phylodynamic analysis using these and GISAID-archived sequences demonstrated that in the years before the COVID-19 pandemic, phylogenetically similar strains were circulating locally and elsewhere. However, clade 1a.1 (within 3C.2a.1b.2a), circulated in and only in Shanghai and domestically in 2022, while the sibling clade 2 predominated in other regions. Interestingly, clade 1a.1 was swiftly and completely replaced by clade 2, mostly 2a.3a.1, at the start of 2023. In hemagglutination inhibition and neutralization assays, sera from healthy donors collected in 2022 displayed higher or similar reactivity against 2a.3a.1 compared to 1a.1. By contrast, transcription and replication competence of 2a.3a.1 in MDCK cells was higher than 1a.1. These results indicated that instead of antigenicity differences enabling evasion of pre-existing immunity, higher replicative capability more likely contributed to 2a.3a.1 viruses achieving dominance in China. In addition to summarizing patterns of A/H3N2 local circulation in Shanghai, this work revealed an unusual episode in A/H3N2 global circulation and evolution dynamics in connection to the COVID-19 pandemic and explored possible mechanistic explanations.

Abstract Influenza A virus (H1N1) poses a significant threat to global human health that imperative demands the development of sensitive and accurate point‐of‐care testing (POCT) methods. Here, for the first time, Fe‐MoS2 nanosheets were employed as a multifunctional nanotag in the development of catalytic colorimetric‐photothermal dual‐mode lateral flow immunoassay (dLFIA) strips for the sensitive detection of H1N1 inactivated virus. The Fe‐MoS2 nanosheets featuring large size, high specific surface area, and ultrathin structure could flow smoothly on the strips and thus quickly produce an ideal colorimetric signal for qualitative analysis. Both the limit of detection (LOD) of catalytic colorimetric and photothermal signals reached 1000 copies/mL and the corresponding calculated LOD was 550 and 691 copies/mL, respectively, which were about 50–90‐fold more sensitive than traditional gold nanoparticles based‐LFIA (5 × 104 copies/mL). The developed assay could correctly identify eight positive clinical samples with Ct values less than 35 and 10 negative actual samples, proving significant promise for rapid, sensitive, and accurate detection of H1N1, especially in resource‐limited areas.

The coronavirus disease 2019 (COVID-19) pandemic highlighted the need for rapid and accurate viral detection at the point-of-care testing (POCT). Compared with nucleic acid detection, lateral flow immunoassay (LFIA) is a rapid and flexible method for POCT detection. However, the sensitivity of LFIA limits its use for early identification of patients with COVID-19. Here, an innovative surface-enhanced Raman scattering (SERS)-LFIA platform based on two-dimensional black phosphorus decorated with Ag nanoparticles as important antigen-capturing and Raman-signal-amplification unit was developed for detection of SARS-CoV-2 variants within 5-20 min. The novel SERS-LFIA platform realized a limit of detection of 0.5 pg/mL and 100 copies/mL for N protein and SARS-CoV-2, demonstrating 1000 times more sensitivity than the commercial LFIA strips. It could reliably detect seven different SARS-CoV-2 variants with cycle threshold (Ct) < 38, with sensitivity and specificity of 97 and 100%, respectively, exhibiting the same sensitivity with q-PCR. Furthermore, the detection results for 48 SARS-CoV-2-positive nasopharyngeal swabs (Ct = 19.8-38.95) and 96 negative nasopharyngeal swabs proved the reliability of the strips in clinical application. The method also had good specificity in double-blind experiments involving several other coronaviruses, respiratory viruses, and respiratory medications. The results showed that the innovative SERS-LFIA platform is expected to be the next-generation antigen detection technology. The inexpensive amplification-free assay combines the advantages of rapid low-cost POCT and highly sensitive nucleic acid detection, and it is suitable for rapid detection of SARS-CoV-2 variants and other pathogens. Thus, it could replace existing antigens and nucleic acids to some extent.

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.

Respiratory syncytial virus A (RSV-A) is one of the commonest pathogens causing acute respiratory tract infections in infants and children globally. The currently dominant circulating genotype of RSV-A, ON1, was first detected in Shanghai, China in 2011, but little data are available regarding its subsequent circulation and clinical impact here. In this work, we analyzed RSV-A infection in a cohort of patients hospitalized for acute respiratory infections in Shanghai Children's Hospital, and RSV-A was detected in ~10% of these cases. RSV-A G gene sequencing revealed that all successfully sequenced strains belonged to ON1 genotype, but in phylogenetic analysis, the majority of these sequences formed a clade separate from the four previously established lineages within ON1. The new lineage, denoted ON1-5, was supported by phylogenetic analyses using additional G gene sequences from RSV-A strains isolated in Shanghai and elsewhere. ON1-5 first appeared in 2015 in China and the Netherlands, and has since spread to multiple continents and gained dominance in Asia. In our cohort, ON1-5 was not associated with markedly different clinical presentations compared to other ON1 lineages. ON1-5 strains are characterized by four amino acid variations in the two mucin-like regions of G protein, and one variation (N178G) within the highly conserved CCD domain that is involved in receptor binding. These data highlight the continuous evolution of RSV-A, and suggest the possibility of the virus acquiring variations in domains traditionally considered to be conserved for fitness gain.

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 collectedResultsEight 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.

目的 研究2018-2020年上海市本地感染及输入性来源登革1型病毒(Dengue Serotype 1 virus,DENV-1)分离株全基因组序列特征.方法 收集登革热疑似病例血清样本,对DENV-1阳性样本进行病毒分离、全基因组扩增与测序,进一步通过构建进化树对全基因组序列进行同源性分析、核苷酸序列及氨基酸序列相似性分析、编码蛋白氨基酸位点差异分析.结果 从88份DENV-1阳性样本中获得31株分离株的全基因组核苷酸序列,其中3株为本地感染病例来源,28株为输入病例来源.进化分析显示,28株分离株的基因型为G-Ⅰ型,与G-Ⅰ型参考序列的核苷酸(氨基酸)相似性均值为96.47％～97.37％(98.78％～99.16％);3株分离株的基因型为G-Ⅳ型,与G-Ⅳ型参考序列的核苷酸(氨基酸)相似性均值为96.66％～96.86％(99.01％～99.26％);3株本地感染病例来源分离株均为G-Ⅰ型,根据同源性分析,存在输入性病例引起本地感染可能.分离株与对照株比较各结构蛋白与非结构蛋白氨基酸位点均存在差异,其中E蛋白的495个氨基酸位点中,有31个位点存在差异.结论 2018-2020年上海市DENV-1包含G-Ⅰ与G-Ⅳ两种基因型,以G-Ⅰ型为主;首次分离得到3株上海市本地感染病例来源DENV-1,为G-Ⅰ型,存在输入性病例引起本地感染可能.

Coxsackievirus A10 (CVA10) is one of the major causative agents of hand, foot and mouth disease (HFMD). To investigate the epidemiological characteristics as well as genetic features of CVA10 currently circulating in Shanghai, China, we collected a total of 9,952 sporadic HFMD cases from January 2016 to December 2020. In the past five years, CVA10 was the fourth prevalent causatives associated with HFMD in Shanghai and the overall positive rate was 2.78%. The annual distribution experienced significant fluctuations over the past five years. In addition to entire VP1 sequencing, complete genome sequencing and recombination analysis of CVA10 isolates in Shanghai were further performed. A total of 64 near complete genomes and 11 entire VP1 sequences in this study combined with reference sequences publicly available were integrated into phylogenetic analysis. The CVA10 sequences in this study mainly belonged to genogroup C and presented 91%–100% nucleotide identity with other Chinese isolates based on VP1 region. For the first time, our study reported the appearance of CVA10 genogroup D in Chinese mainland, which had led to large-scale outbreaks in Europe previously. The recombination analysis showed the recombination break point located between 5,100 nt and 6,700 nt, which suggesting intertypic recombination with CVA16 genogroup D. To conclusion, CVA10 genogroup C was the predominant genogroup in Shanghai during 2016–2020. CVA10 recombinant genogroup D was firstly reported in circulating in Chinese mainland. Continuous surveillance is needed to better understand the evolution relationships and transmission pathways of CVA10 to help to guide disease control and prevention.

On April 27, 2022, an international flight KL857 from Amsterdam, the Netherlands arrived at Pudong International Airport, Shanghai Municipality. Passengers were transferred to the quarantine hotel for a routine 14-day medical observation in Songjiang District and regularly tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One of the passengers (a 37-year-old Chinese male) was reported positive and diagnosed as a mild case on April 29. The case set out from Uganda (flight KL535) on April 25 and transferred at Amsterdam, the Netherlands on April 26 and Seoul, the Republic of Korea (KL857) on April 27. The patient has been vaccinated in four doses against coronavirus disease 2019 (COVID-19) (Beijing Institute of Biological Products Co., Ltd) in China and Uganda. After diagnosis, he was transferred to Shanghai Public Health Clinical Center for treatment. He recovered after treatment and was discharged on May 12. A nasopharyngeal swab from the patient was sampled on April 29 and sequenced using MGISEQ-200 (MGI TECH CO., LTD, Wuhan City, Hubei Province, China) on May 13. Genotyping analysis revealed that the patient was infected by SARS-CoV-2 variant of concern (VOC)/Omicron subvariant BA.5. The genome is most closely related to a sequence (GISAID ID: EPI_ISL_12713186) uploaded in South Africa (Figure 1) and 34 nonsynonymous mutations (T19I, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, and L24del, P25del, P26del, H69del, V70del) occurred in the spike gene matching the signature of the sublineage BA.5. The sequence of BA.5 was first uploaded to GISAID on March 15, 2022 from a patient’s nasopharyngeal and oropharyngeal swab collected on February 25 in South Africa. Together with BA.4, BA.5 has increased in prevalence in South Africa in recent weeks and has already spread to additional 19 countries in 3 months (total of 2,614 sequences submitted to GISAID);BA.5 caused a rise in the number of cases in some countries, such as Portugal, and South Africa has also reported a moderate increase in hospital admissions since late April (1). The L452R, F486V, and 69–70del mutations may impact the characteristics of BA.5 and make it appear to have a growth advantage over BA.1 and BA.2, which may mainly be driven by immune evasion (2-4). The 69–70del mutation is also responsible for S-gene target failure in polymerase chain reaction (PCR) tests, but PCR assays that include multiple gene targets will maintain accuracy for detecting this lineage (5-6). Due to the short duration of the epidemic, studies showed that the extent of vaccination and the high level of BA.2 waves in each country likely influence the emergence of BA.5 (7), but ongoing monitoring and assessment are needed to further elucidate the characteristics and impact of this lineage.

The global spread of SARS-CoV-2 is currently continuing, and the World Health Organization has announced the risk assessment of the viruses as high. In this study, we analyzed virology features of SARS-CoV-2 causing a family cluster outbreak. Among the six family members, five have been laboratory-confirmed infection of SARS-CoV-2 viruses. A total of five SARS-CoV-2 viruses have been isolated from the nasopharyngeal swabs. The complete genome of the viruses exhibited 100% nucleotide identity with each other. Only two nucleotide differences have been observed between genomes of the isolated viruses and the HCoV/Wuhan/ IVDC-HB-01/2019 strain. Therefore, SARS-CoV-2 has been confirmed as the causation of the family cluster infections.

[目的]观察不同温度保存条件下细胞培养物中新型冠状病毒(简称"新冠病毒")存活情况,判断温度对病毒稳定性的影响,为新冠病毒肺炎疫情趋势研判及防控提供基础数据.[方法]将病毒接种于Vero E6细胞适应培养后,收获病毒液,根据所测得病毒半数组织培养感染剂量(TCID50)将不同稀释度(10-1、10-3、10-5、10-6)的病毒在不同温度下(4℃、22.5℃、37℃)保存1～7 d,并分别感染细胞,通过观察细胞病变效应(CPE)、实时荧光定量检测病毒核酸确定病毒感染性,以评价病毒在不同温度条件下的稳定性.[结果]不同浓度的新冠病毒在4℃条件下保存较为稳定,均具有感染性;22.5℃条件下,高浓度(10-1稀释度)病毒放置7d感染性逐渐下降,其他较低浓度病毒放置1d则完全失去感染性;37℃保存超过1d病毒即失去感染性.[结论]在细胞培养环境中,新冠病毒在4℃条件下高度稳定,对热敏感,且与病毒浓度相关,高浓度病毒室温22.5℃条件下仍可存活7d,37℃条件下放置1d病毒完全失活.

目的 了解上海市急性呼吸道感染病例中人冠状病毒(HCoV)的分布特征,深入了解HCoV的流行规律,为其防控提供科学依据.方法 收集2015-2019年上海市急性呼吸道感染监测标本3531份,利用多重PCR技术进行常见呼吸道病原体的检测.结果 在3531份标本中,病毒总检出率为39.73％(1403/3531).其中,HCoV检出率为3.14％(111/3531).HCoV在急性呼吸道感染病例中的总检出率仅次于流感病毒和人鼻病毒/肠道病毒,流行亚型以HCoV-OC43、HCoV-NL63为主,不同HCoV亚型在人群中呈隔年交替流行的趋势.混合感染发生率高达36.93％(41/111),混合感染病例中的重症比例较高.结论 HCoV是上海市急性呼吸道感染的重要病原,应加强急性呼吸道感染病例病原学监测,重点关注HCoV与其他病原的混合感染.

新型冠状病毒肺炎（coronavirus disease 2019,COVID-19）疫情对人类生命健康构成极大威胁。病毒的分离是构建新型冠状病毒（2019 novel coronavirus, 2019-nCoV）细胞感染模型和动物感染模型的基础。本研究利用冠状病毒易感的Vero E6细胞,从1例上海感染者的咽拭子中分离到一株2019-nCoV,命名为nCoV-SH01。对该毒株全基因组采用一代Sanger和二代Illumina法测序,发现该毒株与GenBank MN908947的同源性＞99.99%。免疫荧光检测显示,该毒株与COVID-19康复者的血清呈阳性反应。当nCoV-SH01感染Vero E6细胞后,导致典型的合胞体病变,细胞病变效应明显且进展迅速,提示nCoV-SH01可用于进一步建立2019-nCoV的细胞感染和动物感染模型,为开展致病性研究以及抗病毒药物和疫苗研发奠定了基础。

[目的]通过监测2018—2019年度上海市优势流行株A/H1N1(pdm09)亚型流感病毒对神经氨酸酶抑制剂(NAIs)的耐药情况,为上海市流感临床用药提供参考.[方法]随机选取60株A/H1N1(pdm09)亚型流行株,采用神经氨酸酶抑制实验及神经氨酸酶(NA)基因测序的方法,开展流行株对奥司他韦及扎那米韦敏感性和耐药性的监测和分析.[结果]60株流行株均对奥司他韦和扎那米韦敏感,未发现敏感性降低或者显著降低的情况;基因序列分析也未发现NA在催化活性关键位点及辅助位点出现氨基酸变异,佐证了神经氨酸酶抑制实验的表型检测结果.[结论]上海市2018—2019年度流行的A/H1N1(pdm09)亚型流感病毒对神经氨酸酶抑制剂依然敏感,为临床用药提供了科学参考.随着药物的广泛使用,应持续加强流感病毒耐药性监测,以有效指导临床用药.

The A(H7N9) virus strain that emerged in 2013 was associated with a high fatality rate and may become a long-term threat to public health. A(H7N9) disease incidence is disproportionate to viral exposure, suggesting that host genetic factors may significantly influence susceptibility to A(H7N9) infection. Human genome variation in conferring risk for A(H7N9) infection in Chinese populations was identified by a two-stage investigation involving 121 A(H7N9) patients and 187 healthy controls using next generation sequencing followed by functional analysis. As a result, a low frequency variant (rs189256251; P = 0.0303, OR = 3.45, 95% CI 1.05–11.35, chi-square test) and three HLA alleles (DQB1*06:01, DQA1*05:05 and C*12:02) were identified in A(H7N9) infected volunteers. In an A549 cell line carrying the rs189256251 variant CT genotype, A(H7N9) infection incidence was elevated 6.665-fold over control cells carrying the CC genotype. Serum levels of interferon alpha were significantly lower in patients with the CT genotype compared to the CC genotype (P = 0.01). The study findings of genetic predisposition to A(H7N9) in the Chinese population may be valuable in systematic investigations of A(H7N9) disease etiology.

Objective To analyze the antigenicity,genetic characteristics and variation of the hemagglutinin(HA) protein of influenza A(H1N1)pdm09 virus circulating in Shanghai during 2018-2019 influenza surveillance year.Methods Hemagglutinin inhibition test was performed to analyze the antigenicity of eighty-four influenza A(H1N1)pdm09 virus strains isolated in Shanghai from April 2018 to March 2019.Sixty-five influenza virus strains isolated from different districts of Shanghai were sequenced and analyzed.Results Clade 6B.1 H1N1 virus was the predominant strains circulating in Shanghai.A few epidemic strains belong to the 6B.2 branch.The similarities of clade 6B.1 nucleotide sequences compared with the vaccine strain A/Michigan/45/2015 were 97.1％-98.8％.The homology with the newly recommended vaccine strain A/Brisbane/02/2018 were 97.5％-99.4％.Mainly fifteen amino acids had mutated in the HA protein sequence,and three mutations,S91R,S181T and T202I were involved in three different epitopes which indicated that the antigenic drift had occurred in the influenza virus.Conclusions The majority of influenza A(H1 N 1)pdm09 subtype virus strains circulating in Shanghai were well matched with the vaccine strain A/Michigan/45/2015 recommended by WHO.It is necessary to continue strengthening the surveillance on influenza virus variation to improve the efficacy of influenza vaccines.

目的分析2018—2020年上海市分离的B/Victoria系流感毒株与疫苗株的匹配性及基因变异情况。方法利用血凝抑制实验,对142株B/Victoria系流感毒株进行了抗原性分析,并选取了63株开展了血凝素（HA）及神经氨酸酶（NA）基因序列分析。结果 2018—2020年上海市流行的B/Victoria系流感毒株主要属于V1A.3分支,少数属于V1A.1分支及未缺失的V1A分支;抗原性分析显示,26.76%的流行株是疫苗株B/Colorado/06/2017鸡胚株的低反应株,与疫苗株相比,V1A.3分支流行株在HA蛋白的120环、150环、160环及190螺旋等关键的抗原决定簇及受体结合关键部位发生了5个氨基酸位点改变。结论 2018—2020监测年度B/Victoria系流行株与世界卫生组织推荐的疫苗株组分B/Colorado/06/2017匹配性不佳,仍需密切监测流行株的谱系及变异情况,为疫苗株的筛选提供可靠的数据。

Previous studies have reported that rearing infant rat pups in continuous moderate-level noise delayed the formation of topographic representational order and the refinement of response selectivity in the primary auditory (A1) cortex. The present study further verified that exposure to long-term moderate-intensity white noise (70 dB sound pressure level) from postnatal day (P) 12 to P30 elevated the hearing thresholds of infant rats. Compared with age-matched control rats, noise exposure (NE) rats had elevated hearing thresholds ranging from low to high frequencies, accompanied by decreased amplitudes and increased latencies of the two initial auditory brainstem response waves. The power of raw local field potential oscillations and high-frequency β oscillation in the A1 cortex of NE rats were larger, whereas the power of high-frequency γ oscillation was smaller than that of control rats. In addition, the expression levels of five glutamate receptor (GluR) subunits in the A1 cortex of NE rats were decreased with laminar specificity. These results suggest that the altered neural excitability and decreased GluR expression may underlie the delay of functional maturation in the A1 cortex, and may have implications for the treatment of hearing impairment induced by environmental noise.