BackgroundNeurosyphilis (NS) diagnosis is challenging due to the cerebrospinal fluid-Venereal Disease Research Laboratory (CSF-VDRL) assay has limited sensitivity, whereas CSF abnormalities lack sufficient specificity.MethodsTo identify novel CSF peptide biomarkers for NS, we performed comparative peptidomic analysis of CSF samples from 51 individuals across four groups: NS, syphilis/non-NS (NNS), infectious brain diseases without syphilis (IBD), and non-infectious brain disorders without syphilis (NIBD). Peptides were profiled by high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). Bioinformatic analysis and machine learning identified candidate biomarkers, validated by parallel reaction monitoring (PRM) in an independent cohort (n = 23).ResultsA total of 4,738 peptides were identified. The insulin-like growth factor 2 (IGF2)-derived peptide GHVLAKELE showed strong discriminative performance: area under the curve (AUC) values of 0.914 (NS vs. NNS), 0.964 (NS vs. IBD), and 0.878 (NS vs. NIBD).ConclusionThis first systematic CSF peptidomic characterization of neurosyphilis identifies GHVLAKELE as a promising diagnostic biomarker.

Currently, nucleic acid and antibody tests for infectious diseases are conducted independently, often resulting in fragmented diagnostics and delayed clinical decision-making. Given the diversity of analytes involved in infectious diseases, comprehensive detection is essential in clinical practice. Here, we introduce One-potNASH, a novel DNA and antibody hybrid plasmonic nanoplatform that unifies nucleic acid and antibody detection within a single assay. By integrating extraction-free thermal lysis of 1 μL of serum, One-potNASH achieves single-DNA copy sensitivity while enhancing antibody detection sensitivity by more than 2 orders of magnitude compared to that of an enzyme-linked immunosorbent assay. Clinically, One-potNASH for hepatitis B, monkeypox (MPX), and associated infections can detect DNA and multiplexed antibodies (anti-HBc, anti-HCV, and anti-HIV for hepatitis B and anti-A29L, anti-H3L, and anti-HIV for MPX) with 100% sensitivity and specificity. This integrated approach addresses critical clinical needs by streamlining workflows, reducing diagnosis time, and enabling a comprehensive evaluation of infectious diseases, thereby facilitating rapid therapeutic interventions and improved patient outcomes.

Influenza is an acute respiratory infectious disease caused by influenza viruses, and it poses a serious threat to global public health. High-risk groups include the elderly, infants and young children, pregnant women, and patients with chronic underlying diseases. These groups are prone to developing severe illness after infection, which can lead to serious complications and even death. Early antiviral treatment is key to reducing the rate of severe illness and death. Currently, authoritative guidelines at home and abroad recommend early, single-agent antiviral therapy as the standard regimen. However, anti-influenza virus monotherapy has problems such as drug resistance and poor therapeutic effect. To address these problems, this consensus was developed by organizing experts from the departments of Infectious Diseases, Respiratory Medicine, Critical Care Medicine, and Pharmacy. These experts systematically sorted out domestic and international evidence on combined antiviral therapy for influenza and formulated expert recommendations on combined antiviral therapy for influenza in specific populations.

Dengue virus (DENV) remains a pervasive global health threat, further complicated by the occurrence of neutropenia—a distinct clinical feature indicative of an altered host immune response, closely correlated with progressive disease deterioration and increased severity. Nevertheless, the molecular mechanisms underlying dengue-associated neutropenia remain inadequately elucidated. In this study, the comprehensive plasma proteomic profiling of dengue fever (DF) patients, DF patients with neutropenia (DFN), and healthy controls (HC) was systematically analyzed using a deep data-independent acquisition (DIA) workflow combined with LC-MS/MS analysis, to elucidate key cellular pathways and identify promising biomarkers. DFN patients exhibited significant dual hematological alterations, with notable changes in both platelet and neutrophil counts, reflecting a complex disturbance in hematological homeostasis during dengue progression. DIA analysis quantified 2,475 proteins, revealing widespread proteomic alterations among the DF, DFN, and HC subjects. Differential analysis highlighted significant fluctuations in proteins related to cytoskeletal organization, metabolic regulation, and intracellular signaling. Enrichment analyses implicated pathways such as focal adhesion, platelet activation, and PI3K-Akt signaling. Machine learning methods further identified a panel of four biomarkers—CNST, DSTN, DUSP3, and PDIA5—with high predictive accuracy for dengue diagnosis and subgroup differentiation. In conclusion, this study advances our understanding of dengue’s plasma proteomic landscape and underscores the synergistic potential of DIA-based proteomics and machine learning in unveiling host-response mechanisms, thereby informing early diagnosis and targeted therapeutic strategies.

Accurately diagnosing infectious diseases in a resource-limited setting is a major challenge. Plasmonic materials, via localized surface plasmon resonance (LSPR), have greatly enhanced fluorescence signal and detection sensitivity. However, traditional plasmonic-enhanced fluorescence methods largely rely on near-infrared or visible-light fluorophores with small Stokes shift, limiting naked-eye visibility without filters. In this study, we developed a novel plasmonic silver film (pSilverF) to enhance visible-light fluorescence with large Stokes shift, allowing for improved biomarker detection sensitivity under naked-eye observation. Integrated with bright fluorescent nanoparticles, we designed a multiplexed assay for detecting Hepatitis C Virus (HCV), Hepatitis B Virus (HBV), and Human Immunodeficiency Virus (HIV) antibodies, achieving detection sensitivities down to 0.0032, 0.023, and 0.168 NCU/mL, respectively. In a cohort of 68 clinical samples, our method achieved 100% sensitivity and specificity for HIV and HCV detection and 96% sensitivity and 100% specificity for HBV detection. Notably, the results can be visualized by the naked eye and directly captured by a standard mobile phone camera without any modification for signal analysis using RGB image splitting. This platform demonstrated potential for field detection of multiple infectious diseases with simple settings, providing a useful tool for disease control in communities and areas with limited medical resources.

Dengue, the most prevalent mosquito-borne disease worldwide, poses a significant health burden. This study integrates clinical data and transcriptomic datasets from different phases of dengue to investigate distinctive and shared cellular and molecular features. Clinical data from 29 dengue patients were collected and analyzed alongside a public transcriptomic data set (GSE28405) to perform differential gene expression analysis, functional enrichment, immune landscape assessment, and development of machine learning model. Neutropenia was observed in 54.79% of dengue patients, particularly during the defervescence phase (65.79%) in clinical cohorts. Bioinformatics analyses corroborated a significant reduction in neutrophil immune infiltration in dengue patients. Receiver operating characteristic curve analysis demonstrated that dynamic changes in neutrophil infiltration levels could predict disease progression, especially during the defervescence phase, with the area under the curve of 0.96. Three neutrophil-associated biomarkers-DHRS12, Transforming growth factor alpha, and ZDHHC19-were identified as promising for diagnosing and predicting dengue progression. In addition, the activation of neutrophil extracellular traps was significantly enhanced and linked to Fc gamma R-mediated signaling pathways and Toll-like receptor signaling pathways. Neutrophil activation and depletion play a critical role in dengue's immune response. The identified biomarkers and their associated pathways offer potential for improved diagnosis and understanding of dengue pathogenesis and progression.

Hand, foot, and mouth disease (HFMD) is a common children infectious disease caused by human enteroviruses. Most of the cases have minimal symptoms, however, some patients may develop serious neurological, cardiac complications, or even death. The pathological mechanism leading to severe HFMD is not clearly understood, and the immunological status of the individual patient may play an important role. Transcriptomes of peripheral blood mononuclear cells from EV71-infected patients (n = 45) and healthy controls (n = 36) were examined. Immune pathways were up-regulated in patients with mild disease symptoms (n = 11, M) compared to the healthy controls (n = 36, H), demonstrating an effective anti-viral response upon EV71 infection. However, in patients with severe symptoms (n = 23, S) as well as severe patients following treatment (n = 11, A), their innate and acquired immune pathways were down-regulated, indicating a global immunity suppression. Such immune suppression characteristics could thus provide an opportunity for early EV-71 infection prognosis prediction. Based on our cohort, an SVM model using RNA-seq expression levels of five genes (MCL1, ZBTB37, PLEKHM1P, IFNAR2 and YEATS2) was developed and achieved a high ROC-AUC (91.3%) in predicting severe HFMD. Meanwhile, qPCR fold-changes method was performed based three genes (MCL1, IFNAR2 and YEATS2) on additional cohort. This qPCR method achieved a ROC-AUC of 78.6% in predicting severe HFMD, which the patients could be distinguished in 2-3 h. Therefore, our models demonstrate the possibility of HFMD severity prediction based on the selected biomarkers that predict severe HFMD effectively.

Objective:To analyze the clinical characteristics of Brucella infection in Shenzhen City, and to provide reference for clinical diagnosis and treatment of patients with Brucella infection. Methods:The clinical characteristics of 57 patients with Brucella infection from January 1, 2018 to December 31, 2020 in The Third People′s Hospital of Shenzhen were retrospectively analyzed. The clinical characteristics of patients with brucellosis and latent Brucella infection, patients with or without comorbidities were compared respectively, and magnetic resonance imaging (MRI) and lumbar puncture examination findings of 57 patients were also analyzed. Statistical analysis was performed using Wilcoxon rank sum test and chi-square test. Results:Among the 57 patients with Brucella infection, 10 cases (17.5%) were latent infections and 47 cases (82.5%) were brucellosis patients. Among brucellosis patients, 91.5%(43/47) had fever and 74.4%(32/43) had maximum body temperature ≥38.1 ℃, 40.4%(19/47) had chills orshivering, 25.5%(12/47) had hyperhidrosis, 17.0%(8/47) had fatigue, 21.3%(10/47) had headache, 23.4%(11/47) had neck/back/low back pain, and 31.9%(15/47) had joint pain. A total of 18 cases (38.3%) had comorbidities. Cases with positive blood cultures in latent infection and brucellosis were seven and 39, respectively. The time from symptom onset to diagnosis was 30.0 (15.0, 67.5) days in 18 patients of brucellosis with comorbidity, which was longer than 20.0 (13.0, 30.0) days in 29 patients without comorbidity. Neck/back/low back pain and joint pain occurred in patients with brucellosis with comorbidity were seven and nine, respectively, and those without comorbidity were four and six, respectively, with statistically significant differences ( Z=-2.00, χ2=3.90 and 4.39, respectively, all P<0.050). Of the 11 brucellosis patients with neck/back/low back pain, six had spondylitis. Of the 15 brucellosis patients with joint pain, six had arthritis. Lumbar puncture examination did not indicate meningitis in six cases of latent infection, while revealed six cases of brucellosis meningitis in 32 brucellosis patients. Fifty-four patients had good outcomes, and three patients were cured after an extended course of treatment. Conclusions:Although patients with latent Brucella infection have no comorbidities, they have a high positive blood culture rate. Active standardized anti- Brucella treatment is recommended. MRI examination of relevant sites is recommended in brucellosis patients with joint, neck/back/low back pain, and lumbar puncture is recommended in brucellosis patients regardless of headache.

目的:分析2019新型冠状病毒奥密克戎变异株感染者的临床特征，为奥密克戎变异株的防控提供参考。方法:纳入2021年12月23日至2022年1月31日深圳市第三人民医院收治的38例2019新型冠状病毒奥密克戎变异株感染者，回顾性分析患者的流行病学资料、临床表现、新型冠状病毒疫苗接种和实验室检查情况。采集鼻咽拭子样本进行病毒核酸检测，采用实时荧光聚合酶链反应扩增2019新型冠状病毒的开放阅读框(open reading frame， ORF)1 ab基因和 N基因。采集血液样本检测2019新型冠状病毒IgM和IgG抗体水平。 结果:38例患者中输入性病例35例(92.1%)，其中美国输入20例(57.1%)。36例(94.7%)患者接种过新型冠状病毒疫苗，其中末次接种后≤1个月发病者占5.7%(2/35)，>3个月发病者占65.7%(23/35)。3例为无症状感染者。35例确诊患者中，咳嗽31例(88.6%)，咽痛14例(40.0%)，发热13例(37.1%)，鼻塞10例(28.6%)，流涕8例(22.9%)；入院时白细胞计数正常者33例(94.3%)，降低者1例(2.9%)；淋巴细胞计数减少者19例(54.3%)；C反应蛋白升高者18例(51.4%)；白细胞介素6水平升高者35例(100.0%)；降钙素原升高者10例(28.6%)；D-二聚体升高者6例(17.1%)；ALT升高者1例(2.9%)；血钾降低者10例(28.6%)。 ORF1 ab基因循环阈值(Ct值)为22.15±6.00，最低值为14.22， N基因循环阈值为21.86±5.72，最低值为13.04。2019新型冠状病毒IgM抗体水平为0.46(0.21，1.12) AU/mL；IgG抗体水平为126.55(8.31，289.85) AU/mL，其中20例患者IgG抗体>100 AU/mL，12例IgG抗体>200 AU/mL，最高达414.48 AU/mL。 结论:目前奥密克戎变异株感染者的主要临床表现为咳嗽、咽痛、发热、鼻塞，接种新型冠状病毒疫苗后仍有可能感染奥密克戎变异株，且病毒核酸水平较高，需注意防护。

Due to the concurrent prevalence and increasing risk of coinfection of the clinically important Arboviruses, timely and accurate differential diagnosis is important for clinical management and the epidemiological investigation. A two-tube multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for the simultaneous detection of Zika virus (ZIKV), chikungunya virus (CHIKV), dengue virus (DENV), yellow fever virus (YFV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) was developed and optimized with high specificity and sensitivity. The detection limit for all the six viruses could reach as low as five genome equivalent copies and 2.8 x 10(-)(3) tissue culture infectious doses (TCID50) for ZIKV, YFV, CHIKV and 2.8 x 10(-2) TCID50 for JEV per reaction, with high accuracy and precision (R-2 > 0.99). The coefficient of variation of intra-assay and inter-assay for our quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was low, and the obtained positive rates ad C-t values of this assay were comparable with singleplex commercial kits. Moreover, the multiplex qRT-PCR assay was able to detect possible co-infections without competitive inhibition of target viral genomes. In conclusion, our rapid, sensitive, cost-effective multiplex qRT-PCR will be of great use for differential diagnosis in a clinical setting and epidemiological investigation during surveillance.

Background: The rapid worldwide spread of the Omicron variant of SARS-CoV-2 has unleashed a new wave of COVID-19 outbreaks. The efficacy of molnupiravir, an approved drug, is still unknown in patients infected with the Omicron variant. Objective: Evaluated the antiviral efficacy and safety of molnupiravir in patients infected with SARS-CoV-2 Omicron variant, with symptom duration within 5 days. Methods: We conducted a randomized, controlled trial involving patients with mild or moderate COVID-19. Patients were randomized to orally receive molnupiravir (800 mg) plus basic treatment or only basic treatment for 5 days (BID). The antiviral efficacy of the drug was evaluated using reverse transcriptase polymerase chain reaction. Results: Results showed that the time of viral RNA clearance (primary endpoint) was significantly decreased in the molnupiravir group (median, 9 days) compared to the control group (median, 10 days) (Log-Rank p = 0.0092). Of patients receiving molnupiravir, 18.42% achieved viral RNA clearance on day 5 of treatment, compared to the control group (0%) (p = 0.0092). On day 7, 40.79%, and 6.45% of patients in the molnupiravir and control groups, respectively, achieved viral RNA clearance (p = 0.0004). In addition, molnupiravir has a good safety profile, and no serious adverse events were reported. Conclusion: Molnupiravir significantly accelerated the SARS-CoV-2 Omicron RNA clearance in patients with COVID-19. Clinical Trial Registration: [chictr.org.cn], identifier [ChiCTR2200056817].

COVID-19 patients show heterogeneous and dynamic immune features which determine the clinical outcome. Here, we built a single-cell RNA sequencing (scRNA-seq) dataset for dissecting these complicated immune responses through a longitudinal survey of COVID-19 patients with various categories of outcomes. The data reveals a highly fluctuating peripheral immune landscape in severe COVID-19, whereas the one in asymptomatic/mild COVID-19 is relatively steady. Then, the perturbed immune landscape in peripheral blood returned to normal state in those recovered from severe COVID-19. Importantly, the imbalance of the excessively strong innate immune response and delayed adaptive immunity in the early stage of viral infection accelerates the progression of the disease, indicated by a transient strong IFN response and weak T/B-cell specific response. The proportion of abnormal monocytes appeared early and rose further throughout the severe disease. Our data indicate that a dynamic immune landscape is associated with the progression and recovery of severe COVID-19, and have provided multiple immune biomarkers for early warning of severe COVID-19.

Introduction The novel coronavirus (COVID-19) has become a global pandemic with sharp rises in the number of confirmed cases and rapid spread across the world. Here, we looked at the effects of geographic differences on clinical manifestations of SARS-CoV-2 infected patients. Methods A total of 114 confirmed COVID-19 patients were included in this study. The epidemiological, demographic, clinical, as well as laboratory findings were extracted from the electronic medical records of these patients. Results We report the observation that patients from overseas residents diagnosed with COVID-19 were mildly symptomatic with cough and presented with lower inflammatory response and attenuated virus clearance rate, as well as correspondingly prolonged days of hospital stay than local Chinese patients. Moreover, the receiver-operating characteristic (ROC) analysis, performed to provide a measure of the difference between two groups, showed that serum albumin had the highest area under the curve value (0.81, p < 0.001). Discussion Our results suggested that blood albumin level acted as a predictive value in distinguishing clinical features between local and overseas Chinese. This work underscores the need to identify distinguishably prognostic factors of geographical dissimilarity in COVID-19 patients.

噬血细胞综合征是一种少见的由免疫介导的可危及生命的疾病。本例患者经骨髓病理与免疫组织化学检查结果明确诊断为弥漫大B细胞淋巴瘤，检测2019新型冠状病毒核酸阳性，故先采取了抗病毒治疗，但病程中反复出现高热，且白细胞计数、血红蛋白、血小板计数明显降低，血脂升高，血清铁蛋白明显升高，病原学检查均阴性，结合脾大和骨髓活组织检查发现噬血细胞，最终诊断为新型冠状病毒肺炎合并弥漫大B细胞淋巴瘤及噬血细胞综合征。经过小剂量多柔比星脂质体+小剂量依托泊苷+甲泼尼龙组成的方案进行化学治疗后，患者症状缓解，脾脏的淋巴瘤病变缩小，且未影响2019新型冠状病毒核酸转阴。本例患者发生噬血细胞综合征的主要原因考虑与弥漫大B细胞淋巴瘤有关，但新型冠状病毒肺炎引起的可能性也不能除外。目前，新型冠状病毒肺炎在全球暴发流行，所以对于淋巴瘤合并新型冠状病毒肺炎患者，需警惕可能发生噬血细胞综合征。

Background The incidence of hand foot and mouth disease (HFMD) has increased in recent years, making it a very common childhood illness worldwide. The relationship between different enterovirus genotypes and disease severity is not clearly understood. Given that enteroviruses are transmitted through the gastrointestinal tract, we hypothesized that variation in intestinal microorganisms of the host might play a role in the prognosis of HFMD. Methods We carried out a meta-transcriptomic-wide association study of fecal samples obtained from a cohort of children (254 patients, 227 tested positive for enterovirus, including 16 patients co-infectied with 2 kinds of enterovirus) with mild and severe HFMD and healthy controls. Results We found there was no significant difference in the amount of each virus type between the mild and severe cases. Genes of enterovirus 71 (EV71) and coxsackievirus A (CV-A) from the severe and mild cases did not show significant clustering. Clostridium sp. L2-50 and Bacteroides stercoris ATCC 43183 were enriched in the guts of children with severe HFMD and KEGG enrichment was found between mild and severe cases. Conclusions Intestinal microorganisms appear to interact with enterovirus to determine the progression of HFMD. Genes of Bacteroides and Clostridium may be used as predictive markers for a more efficient prognosis and intervention. The enrichment of intestinal bacteria genes with functions may facilitate the development of severe symptoms for HFMD patients.

The outbreak of Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, December 2019, and continuously poses a serious threat to public health. Our previous study has shown that cytokine storm occurred during SARS-CoV-2 infection, while the detailed role of cytokines in the disease severity and progression remained unclear due to the limited case number. In this study, we examined 48 cytokines in the plasma samples from 53 COVID-19 cases, among whom 34 were severe cases, and the others moderate. Results showed that 14 cytokines were significantly elevated upon admission in COVID-19 cases. Moreover, IP-10, MCP-3, and IL-1ra were significantly higher in severe cases, and highly associated with the PaO 2 /FaO 2 and Murray score. Furthermore, the three cytokines were independent predictors for the progression of COVID-19, and the combination of IP-10, MCP-3 and IL-1ra showed the biggest area under the curve (AUC) of the receiver-operating characteristics (ROC) calculations. Serial detection of IP-10, MCP-3 and IL-1ra in 14 severe cases showed that the continuous high levels of these cytokines were associated with disease deterioration and fatal outcome. In conclusion, we report biomarkers that closely associated with disease severity and outcome of COVID-19. These findings add to our understanding of the immunopathologic mechanisms of SARS-CoV-2 infection, providing novel therapeutic targets and strategy.

In December, 2019, an outbreak of the coronavirus disease 2019 (COVID-19), which was caused by a novel coronavirus, started in Wuhan, China. So far, there is limited clinical evidence on the effect of corticosteroid therapy for this disease. This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Patients with mild COVID-19 were enrolled from two medical centers in China between January 13, 2020 and February 29, 2020. Baseline characteristics and durations of RNA clearance were compared between the corticosteroid and non-corticosteroid therapy groups. The independent effects of corticosteroid therapy on the duration of RNA clearance were estimated by generalized linear models. Of 82 patients with a mild infection, 40 patients were male (48.8%), with a median age of 49 years (interquartile range, IQR 36–61). Among those patients, 36 patients (43.9%) received corticosteroid therapy. The adjusted multivariate models showed that the effects of corticosteroids were non-significant on the durations of onset to first RNA clearance [β 2.48, 95% CI (95% confidence interval) − 0.42 to 5.38, P = 0.0926] and to persistent RNA clearance (β 1.54, 95% CI − 1.41 to 4.48, P = 0.3016), and durations of therapy to first RNA clearance (β 2.16, 95% CI − 0.56 to 4.89, P = 0.1184) and to persistent RNA clearance (β 1.22, 95% CI − 1.52 to 3.95, P = 0.3787). Corticosteroid therapy in patients with mild COVID-19 was not associated with the duration of SARS-CoV-2 clearance, suggesting that the use of corticosteroids may not be beneficial for patients with mild COVID-19 and should be prudently recommended in clinical practice. However, further studies are needed to verify the findings.

Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed "genetic tuning," actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection.

Background: The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 was first reported in Wuhan, December 2019, and continuously poses a serious threat to public health, highlighting the urgent need of identifying biomarkers for disease severity and progression. Objective: We sought to identify biomarkers for disease severity and progression of COVID-19. Methods: Forty-eight cytokines in the plasma samples from 50 COVID-19 cases including 11 critically ill, 25 severe, and 14 moderate patients were measured and analyzed in combination with clinical data. Results: Levels of 14 cytokines were found to be significantly elevated in COVID-19 cases and showed different expression profiles in patients with different disease severity. Moreover, expression levels of IFN-gamma-induced protein 10, monocyte chemotactic protein-3, hepatocyte growth factor, monokine-induced gamma IFN, and macrophage inflammatory protein 1 alpha, which were shown to be highly associated with disease severity during disease progression, were remarkably higher in critically ill patients, followed by severe and then the moderate patients. Serial detection of the 5 cytokines in 16 cases showed that continuously high levels were associated with deteriorated progression of disease and fatal outcome. Furthermore, IFN-gamma-induced protein 10 and monocyte chemotactic protein-3 were excellent predictors for the progression of COVID-19, and the combination of the 2 cytokines showed the biggest area under the curve of the receiver-operating characteristics calculations with a value of 0.99. Conclusions: In this study, we report biomarkers that are highly associated with disease severity and progression of COVID-19. These findings add to our understanding of the immunopathologic mechanisms of severe acute respiratory syndrome coronavirus 2 infection, and provide potential therapeutic targets and strategies.

The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N12,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed thein vivoH7N9 mutations at the level of whole genomes and have compared with the genomes derived byin vitrocultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.