Objective:To retrospectively analyze the molecular epidemiological features and genetic recombination of coxsackievirus A4 (CVA4) strains isolated in Jiangsu from 2015 to 2022.Methods:Throat or anal swab samples were collected from patients with herpangina or hand, foot and mouth disease (HFMD). Real-time PCR was used to detect CVA4. A comprehensive and systematic phylogenetic analysis was conducted based on 72 whole genomes and 99 VP1 sequences of CVA4 strains. Several bioinformatics software including DNAStar, MEGA7.0 and Similarity plots3.5.1 was used for analysis of homology, genetic recombination and amino acid variation sites.Results:Four genotypes (A, B, C and D) and five sub-genotypes (C1-C5) of CVA4 were identified based on the VP1 nucleotide sequences. C2 was the predominant sub-genotype causing HFMD. The Jiangsu strains showed high homology with the CVA4 prototype in the P1 region, and higher identity with other strains of enterovirus group A (EV-A) in the P2 and P3 regions. Genetic recombination analysis revealed that the Jiangsu strains had three genetic recombination patterns with other EV-A epidemic strains in the P2, P3 and 3′-UTR regions. These recombination patterns took place during the sustained and widespread circulation of CVA4 in people and increased the transmissibility of CVA4.Conclusions:This study analyzes the phylogenetic and molecular features of 28 whole genomes of Jiangsu CVA4 strains, which helps to better understand the genomic diversity of CVA4. By analyzing the genetic recombination and amino acid mutations in the VP1 region, this study elucidates the evolution and transmission of CVA4, which is conducive to the control and prevention of CVA4 infection.

In recent years, global outbreaks of infectious diseases, such as COVID-19, have triggered great concern about emerging infectious diseases. With the rapid development of next-generation sequencing technology and bioinformatic tools for viral metagenomics, there is now a widespread capability to detect and identify various known and unknown pathogenic microorganisms within both environmental and biological contexts. Furthermore, the continuous evolution of machine learning methods has led to the development and application of multiple rapid and highly accurate approaches for virus identification. Concurrently, owing to the continual progress in machine learning methods, several rapid and accurate virus identification techniques have been widely developed and applied. Therefore, this review aims to systematically summarize the key methodologies, frameworks, and the scope of applicability within the field of viral metagenomics, with a specific focus on virus identification and prediction. It could facilitate a deeper understanding of viral characteristics, identify potential novel pathogens, and provide technical support for the early prevention and control of infectious diseases.

Objective:To explore the application of COVID-19-specific IgG antibody in identifying epidemic Omicron BA.5 strain infection.Method:Omicron BF.7/BA.5 naturally infected population, healthy population vaccinated with the COVID-19 vaccine, and Omicron BF.7/BA.5 breakthrough cases were enrolled into this study. The serum WT-S-IgG and BA.5-S-IgG were detected by indirect ELISA, and the serum-specific IgG antibody levels of different populations were compared. The application value of the two antibody titers and the ratio of the two antibodies in identifying Omicron BA.5 epidemic strain infection were explored by the ROC curve, aiming to provide technical support for pathogen diagnosis.Results:The antibody titers of WT-S-IgG and BA.5-S-IgG in the breakthrough cases were higher than those in the naturally infected population and the healthy population ( P<0.05). The area under the curve (AUC) of WT-S-IgG and BA.5-S-IgG in identifying epidemic Omicron BA.5 strain infection was 0.947 and 0.961, respectively. The AUC of BA.5-S-IgG and WT-S-IgG antibody titer ratio was 0.873. When the antibody titer ratio was 0.855, the sensitivity and specificity were 80.00% and 90.00%, respectively. According to the interval since the last infection, the AUC of the ratio of BA.5-S-IgG to WT-S-IgG antibody titer to identify the infection of epidemic strains less than 30 days and more than 30 days was 0.887 and 0.863, respectively, and the sensitivity and specificity were both above 80%. Conclusion:Both BA.5-S-IgG and WT-S-IgG, as well as the combination of these two antibodies, are of high value in the identification of epidemic strains.

In recent years, global outbreaks of infectious diseases, such as COVID-19, have triggered great concern about emerging infectious diseases. With the rapid development of next-generation sequencing technology and bioinformatic tools for viral metagenomics, there is now a widespread capability to detect and identify various known and unknown pathogenic microorganisms within both environmental and biological contexts. Furthermore, the continuous evolution of machine learning methods has led to the development and application of multiple rapid and highly accurate approaches for virus identification. Concurrently, owing to the continual progress in machine learning methods, several rapid and accurate virus identification techniques have been widely developed and applied. Therefore, this review aims to systematically summarize the key methodologies, frameworks, and the scope of applicability within the field of viral metagenomics, with a specific focus on virus identification and prediction. It could facilitate a deeper understanding of viral characteristics, identify potential novel pathogens, and provide technical support for the early prevention and control of infectious diseases.

Objective:To explore the application of COVID-19-specific IgG antibody in identifying epidemic Omicron BA.5 strain infection.Method:Omicron BF.7/BA.5 naturally infected population, healthy population vaccinated with the COVID-19 vaccine, and Omicron BF.7/BA.5 breakthrough cases were enrolled into this study. The serum WT-S-IgG and BA.5-S-IgG were detected by indirect ELISA, and the serum-specific IgG antibody levels of different populations were compared. The application value of the two antibody titers and the ratio of the two antibodies in identifying Omicron BA.5 epidemic strain infection were explored by the ROC curve, aiming to provide technical support for pathogen diagnosis.Results:The antibody titers of WT-S-IgG and BA.5-S-IgG in the breakthrough cases were higher than those in the naturally infected population and the healthy population ( P<0.05). The area under the curve (AUC) of WT-S-IgG and BA.5-S-IgG in identifying epidemic Omicron BA.5 strain infection was 0.947 and 0.961, respectively. The AUC of BA.5-S-IgG and WT-S-IgG antibody titer ratio was 0.873. When the antibody titer ratio was 0.855, the sensitivity and specificity were 80.00% and 90.00%, respectively. According to the interval since the last infection, the AUC of the ratio of BA.5-S-IgG to WT-S-IgG antibody titer to identify the infection of epidemic strains less than 30 days and more than 30 days was 0.887 and 0.863, respectively, and the sensitivity and specificity were both above 80%. Conclusion:Both BA.5-S-IgG and WT-S-IgG, as well as the combination of these two antibodies, are of high value in the identification of epidemic strains.

Objective:To sum up the experience and improve the capability of clinical diagnosis and treatment of thyroid tuberculosis (TTB) .Methods:In Apr. 2020, the Second Department of General Surgery, Friendship Hospital of Yili Kazakh Autonomous Prefecture, Xinjiang, treated a patient with a huge thyroid cancer (TC), who had no history of tuberculosis. Thyroid cancer was considered for surgical treatment after the assessment by ultrasound and enhanced CT scan, yet the postoperative pathological diagnosis was thyroid tuberculosis. The clinical and pathological data of 357 cases of TTB reported in domestic literature were retrospectively analyzed by searching the relevant databases.Results:This reported case was diagnosed eventually with TTB by postoperative pathology, cured by operation, local and systemic anti-tuberculosis treatment. Among the 357 cases of TTB, there were 95 males and 262 females and the ratio of male to female was 1.0:2.8. Most patients had neck mass as the first symptom (95.5%, 256/268), and 53 patients (19.8%, 53/268) merged with tuberculosis poisoning symptoms. There were 59 cases (21%, 59/281) complicated with extra-thyroid tuberculosis. Among 51 cases, 37 cases (73%, 37/51) were diagnosed with TTB. Eighty cases (30%, 80/265) were suspected of TC before the operation.25 patients (8.5%, 25/294) received antituberculosis treatment, and 269 patients (91.5%, 269/294) received surgical treatment, among which 100 patients (37%, 100/269) underwent unilateral lobectomy. The caseation type was the most common pathology with 154 cases (57.9%, 154/266). Two patients died of TTB after an operation, and the remaining patients were followed up for 6 months to 33 years without recurrence.Conclusions:TTB often lacks typical clinical manifestations and is easily confused with TC. The diagnosis mainly relies on puncture pathological examination. Good results can be achieved with appropriate treatment based on a definite diagnosis.

Enterotoxigenic Escherichia coli（ETEC）infection can induce watery diarrhea，leading to dehydration，electrolyte disturbance，and even death in severe cases. Recombinant B subunit/inactivated whole-cell cholera（rBS/WC）vaccine is effective in preventing ETEC infectious diarrhea. On the basis of the latest evidence on etiology and epidemiology of ETEC，as well as the effectiveness，safety，and health economics of rBS/WC vaccine，National Clinical Research Center for Child Health（The Children’s Hospital，Zhejiang University School of Medicine）and Zhejiang Provincial Center for Disease Control and Prevention invited experts to develop expert consensus on rBS/WC vaccine in prevention of ETEC infectious diarrhea. It aims to provide the clinicians and vaccination professionals with guidelines on using rBS/WC vaccine to reduce the incidence of ETEC infectious diarrhea.

Objective:To analyze the whole-genome sequences of coxsackievirus A10 (CVA10) strains isolated in Jiangsu Province from 2015 to 2022 and their molecular epidemiological characteristics.Methods:Forty-five CVA10 isolates circulating in Jiangsu Province during 2015 to 2022 were selected for whole-genome sequencing. Phylogenetic trees were constructed based on the whole genome, VP1, P1, P2 and P3 sequences of CVA10 strains. Bioinformatics software, including DNAStar, MEGA7.0 and Similarity plots3.5.1, was used for analysis of homology, genetic recombination and major amino acid variation sites.Results:The nucleotide and amino acid sequence homology of the whole-genome sequences of 45 CVA10 strains was 90.3%-99.1% and 97.9%-99.8%, respectively. The nucleotide sequence homology of P1 region was the highest (92.1%-100.0%), while the nucleotide sequence homology of P3 region ranged from 84.7% to 100.0%. In contrast to the diversity of nucleotide sequences, the amino acid sequences of each region were conserved. A phylogenetic analysis based on the complete VP1 sequences of CVA10 strains revealed eight genotypes: A-H. The CVA10 isolates in Jiangsu Province and other prevalent strains in China mainly belonged to genogroup C. Results of the phylogenetic analysis based on the whole-genome sequences and complete VP1 sequences were consistent. Phylogenetic analysis bases on different gene segments and Simplot recombination analysis revealed that Jiangsu isolates GD07/Lianyungang/2017 and N180/Suqian/2016 showed high homology with the CVA10 prototype in the P1 region, but had recombination sites with other strains of enterovirus group A in the P2, P3, 5′-UTR and 3′-UTR regions. Compared with the prototype strain AY421767/Kowalik/2004, the Jiangsu isolates showed frequent variations in the VP1 region and many other major amino acid sites, which might result in some imperceptible changes in capsid structure and potential receptor-binding sites.Conclusions:By analyzing the evolution and genetic recombination features of CVA10 strains at the genome level in Jiangsu Province, this study elucidated the influence of genetic recombination and amino acid site mutation on CVA10 infection, providing basic data for the prevention and control of hand-foot-mouth disease in Jiangsu Province.

Objective:To understand the relationship between the RNA shedding time of SARS-CoV-2 infected persons and the single nucleotide mutation of the virus, the population of infected persons, underlying diseases and other factors, so as to provide more clues for the study of SARS-CoV-2 infection dynamics.Methods:The data of epidemiology, clinical manifestations, and underlying diseases of infected persons in a cluster epidemic of COVID-19 in Jiangsu province from July to September 2021 were collected. Nasopharyngeal swab samples of cases were collected, and the whole genome of the virus was sequenced by second-generation sequencing technology. The online analysis platform was used to judge the virus type and analyze the mutation site, and Cox proportional risk model was used to analyze the relationship between the RNA shedding time of SARS-CoV-2 and various research factors.Results:There were 350 persons who finally obtained the whole genome sequence of the virus in this COVID-19 outbreak, of which 60.3% were female, the median age was 49 years old (interquartile range, IQR: 37-65 years old)), and the median time of virus shedding was 33 days ( IQR, 26-44 days). The whole-genome sequencing analysis showed that compared with the Wuhan reference strain sequence, the infected persons’ sequence had 34~41 nucleotide mutation sites, belonging to VOC/Delta variant (B.1.617.2 evolutionary branch), and C346T, C1060T, T2803C, T7513C, A29681C were the main single nucleotide polymorphisms (SNPs) of this epidemic. Cox regression analysis showed that age, underlying disease, clinical classification, vaccination, SNP T2803C and T7513C had an impact on the RNA shedding time of SARS-CoV-2. The adjusted multivariate Cox regression result showed that age [ HR=0.73, 95% CI (0.55, 0.95)] and T7513C [ HR=0.37, 95% CI (0.18, 0.77)] were still the risk factors for the extension of SARS-CoV-2 RNA shedding time. Conclusions:This study analyzed the effects of the individual factors and viral single nucleotide variations on the time of viral RNA shedding. Those who were older, suffered from hypertension, had more severe clinical symptoms, were not vaccinated or incompletely vaccinated, and had T7513C mutation in the infected virus, had a risk of a long RNA shedding time of SARS-CoV-2, which should be given special attention and follow-up after rehabilitation.

Covalent organic frameworks(COFs)are a novel type of crystalline porous organic polymer materials recently developed.It has several advantages in chromatographic separation field,such as high thermal stability,porosity,structural regularity,and large specific surface area.Here,a novel spherical COF 1,3,5-tris(4-aminophenyl)benzene(TAPB)and 2,5-bis(2-propyn-1-yloxy)-1,4-benzenedicarboxaldehyde(BPTA)was developed as an electrochromatographic stationary phase for capillary electro-chromatography separation.The COFTTAPB-BPTA modified capillary column was fabricated via a facile in situ growth method at room temperature.The characterization results of scanning electron microscopy(SEM),Fourier transform infrared(FT-IR)spectroscopy,and X-ray diffraction(XRD)confirmed that COF TAPB-BPTA were successfully modified onto the capillary inner surface.The electrochromatography separation performance of the COF TAPB-BPTA modified capillary was investigated.The prepared column demonstrated outstanding separation performance toward alkylbenzenes,phenols,and chlorobenzenes compounds.Furthermore,the baseline separations of non-steroidal anti-inflammatory drugs(NSAIDs)and parabens with good efficiency and high resolution were achieved.Also,the prepared column possessed satisfactory precision of the intra-day runs(n=5),inter-day runs(n=3),and parallel columns(n=3),and the relative standard deviations(RSDs)of the retention times of tested alkylbenzenes were all less than 2.58％.Thus,this new COF-based stationary phase shows tremendous application potential in chromatographic separation field.