Journal of clinical virology plus最新文献

Background

Methods

Results

Conclusion

Objective

Methods

Results

Conclusion

Advancements in next-generation sequencing (NGS) technologies and innovative bioinformatics tools have significantly accelerated virus discovery by analyzing of NGS data. This approach provides a cost-effective and efficient method for processing large datasets, allowing for rapid virus detection and identification. Researchers can comprehensively understand virus-host interactions by integrating data mining with other omics data, such as proteomics (the study of proteins) and metabolomics (the study of metabolic processes). Recent progress has significantly enhanced the efficiency and accuracy of virus identification by using a sophisticated NGS data mining approach. This study provides an in-depth discussion of these techniques, offering a detailed overview of workflows and applicable computational methods. Despite these advantages, the virus discovery process through data mining encounters obstacles such as ethical issues, the absence of standardized protocols for virus discovery procedures, and challenges in validation and interpretation. Addressing these obstacles is crucial for fully realizing the potential of NGS data mining in virus research. This review discusses current methodologies, recent advancements, and future directions to overcome these challenges, ultimately contributing to our understanding of viral diversity and virus-host dynamics.

To evaluate four novel SARS-CoV-2 neutralizing antibody assay kits' application in neutralizing antibodies of population. Questionnaires from the voluntary participating researchers and selected the qualified questionnaires to analyse. For negative and positive coincidence rate, four novel SARS-Cov-2 neutralization antibody assay kits were tested. For within-run and between-run Precision verification study, four serum samples with two high and two low titer neutralizing antibodies were used to analyse. Based on the questionnaires, 175 qualified samples were divided into two groups. (1) negative neutralizing antibodies group: 31 samples had not been infected with the novel SARS-Cov-2 nor received the vaccine within the past one year; (2) positive neutralizing antibodies group: 144 samples were infected by COVID-19. There was 28 negative and 3 positive neutralizing antibodies of the individuals among the 31 negative samples which based on the questionnaires. The negative rates of 28 negative individules tested by GenScript, Vazyme and Hygeianey were 82.14 %, 60.71 % and 17.85 %, while the positive rates of the 147 positive samples were 93.87 %, 95.23 % and 100 %. The within-run coefficient of variations (C·V) of PBNAs, GenScript, Vazyme and Hygeianey were 11.49 %, 9.12 %, 7.97 % and 7.48 %, while the between-run coefficient of variations (C·V) were 21.37 %, 14.21 %, 12.29 % and 11.78 %. Due to the large within-run and between-run coefficient of variations, PBNAs was not suitable for large-scale promotion, while ELISAs could be leveraged for routine monitoring the titer of neutralizing antibodies against SARS-CoV-2.

Hepatitis E virus (HEV) is a pathogen that causes hepatitis. There are few reports of HEV seroprevalence among people with human immunodeficiency virus (PWH) in Japan. This study aimed to determine the HEV seroprevalence among PWH at our hospital. Anti-HEV IgG was tested for using enzyme immunoassays and immunoblot assays. Clinical information was obtained from medical records and additional patient questionnaires. Sixty-eight PWH were included in this study. Four patients (5.9 %) showed HEV IgG seropositivity with both methods, while one patient (1.5 %) was seropositive using only the immunoblot assay, and three patients (4.4 %) were seropositive using only the enzyme immunoassay. There was a significant difference in age between anti-HEV IgG-seropositive and -negative individuals (median, 57.5 and 48.0 years, respectively; p = 0.012). There were no significant differences in the other clinical characteristics. Our results revealed that age is a risk factor for HEV infection among PWH.

The novel bunyavirus (SFTSV) causes severe fever with thrombocytopenia syndrome (SFTS), which has a high mortality rate and poses a serious threat to public health. To investigate the genomic characteristics of SFTSV strains isolated in Huzhou, China, in 2023, we sequenced SFTSV isolates and constructed a phylogenetic tree, and analyzed their homologies, average genetic distances, and amino acid (aa) mutations using DNAstar and MEGA software. The two SFTSV strains belonged to genotypes A and D. The nucleotide (nt) and aa sequence similarities of the two strains were 96.61% and 98.64%, respectively. The nt and aa sequence homologies with human reference strains of the same genotypes were 94.44% and 97.28%, respectively. The nt and aa sequence homologies with syngeneic tick host reference strains were 94.56% and 97.96%, respectively. The two SFTSV isolates had different mutation rates in the L, M, and S proteins; the M protein exhibited the highest mutation rate. Further investigations of SFTSV are warranted to explore the distributions of its genotypes, as well as its nt and aa mutations.

Background

T cells and regulatory T cells (Tregs) play a critical role in viral infectious immunity. Exhaustion of T cells during infection and decreased Tregs both contribute to the exacerbation of the disease. In the present study, we assessed T cells and regulatory T cells of COVID-19 patients and a control group according to the expression of the PD-1 molecule.

Methods

Forty-two COVID-19 patients and 40 controls were enrolled in the study. In COVID-19 patients, blood samples were collected on the first day of their hospitalization. Regulatory T cells (CD4+, CD25+, FOXP3+), CD4+PD-1+, and PD-1+ regulatory T cells were assessed by flow cytometry.

Results

The percentage of CD4+PD-1 + T cells in COVID-19 patients was significantly higher compared to the control group (P < 0.0001). The percentage of PD-1+ regulatory T cells was significantly increased in the patient group compared to the control group (P < 0.0001). However, the Treg percentage was significantly decreased in the patient group compared to the control group (P < 0.0001). The frequency of CD4+PD-1 + T cells, Tregs, and PD-1+ Tregs had acceptable sensitivity and specificity for assisting in the diagnosis of severe/critical COVID-19. The declined Tregs and enhanced CD4+CD25+, CD4+PD-1+, and PD-1 + T cells were associated with disease severity.

Conclusion

The decrease in Tregs and the increase in exhaustion of these cells and T cells play an important role in COVID-19 pathogenesis. These immune parameters could be used as meaningful indicators for assisting in the diagnosis of severe/critical COVID-19.

Despite recent efforts to control and eradicate the hepatitis C virus (HCV), Iran still faces significant gaps and challenges in HCV epidemiological data. Accurate prevalence estimates based on comprehensive and up-to-date evidence compilations are critical in eliminating the virus. We used a qualitative approach in summarizing the findings of the included studies. The prevalence of HCV is within the range of 1.26 % (1.02 - 1.56). The introduction of strict screening protocols for blood transfusions has significantly reduced the incidence of transfusion-related HCV transmission in recent years though unsafe injection practices, men who have sex with men (MSM), and injecting drug use are still the primary risk factors for transmission. Studies indicate that the predominant HCV genotype in the country is genotype 1a, closely followed by genotypes 3a and 1b. Population-based studies and comprehensive national HCV surveillance systems are lacking. More efforts are needed to ensure the sustainability of HCV screening and infection control programs in Iran.

Background

The swift global spread of coronavirus disease 2019 (COVID-19), a respiratory ailment primarily marked by pulmonary symptoms, has been linked to the involvement of various organs, including the intestines, kidneys, throat, and ears. Otitis media with effusion (OME), often succeeding an upper respiratory tract infection, mirrors its incidence. As a respiratory infectious disease, it prompts the query of whether the COVID-19 pandemic has spurred an uptick in OME and whether the COVID-19 virus persists in middle ear effusion (MEE) for an extended period.

Methods

To gauge the incidence of OME in the population during the COVID-19 pandemic, a tailored questionnaire was disseminated and subsequently analyzed. Assessing the rise in OME incidence during the pandemic, we compared the proportion of OME cases in the otology outpatient department between pandemic and non-pandemic periods. Statistical analysis involved a t-test. Simultaneously, MEE was collected from patients with COVID-19-associated OME during the pandemic to ascertain the presence of SARS-CoV-2 in MEE via polymerase chain reaction.

Results

Based on the questionnaire data, the estimated OME incidence in the population is approximately 31.4 %. In contrast to the non-pandemic period, the percentage variation in the OME outpatient proportion was 71.4 % (P < 0.05). Among the 61 MEE samples, 13 polymerase chain reaction results were positive, constituting 21.31 %. Nasopharyngeal swabs yielded negative results. Notably, only one patient experienced OME recurrence after 1 month of auripuncture.

Conclusions

COVID-19 can trigger an escalation in OME cases. Even when nasopharyngeal swabs show negative results, SARS-CoV-2 can endure in MEE for an extended duration, suggesting the potential for asymptomatic COVID-19 transmission and recurrence within the population.

Background/purpose

HPV infection is the primary cause of cervical cancer, and genotype distribution varies according to geographical location and carcinogenicity. Therefore, identifying HPV genotype and its association with cervical cancer features is critical for screening, diagnosis, and therapy.

Methods

Data from Vietnamese women with HPV-positive cervical cancer were collected from the northern region. The HPV genotype was identified using the Cobas^®®4800 HPV system, whereas the nucleotide sequences of the E6, E7, and L1 genes were used to identify lineages and sublineages using DNASTAR, Bioedit, ATGC 7.2, and MEGA 11.0.10 softwares.

Results

Of the 180 patients infected with HPV, 82.8 % revealed single infections, and 17.2 % showed multiple infections. HPV16 (64.4 %), HPV18 (28.9 %), and other HPVs (6.7 %) were the most prevalent HPV genotypes. HPV16 lineages included European (sublineage A1 (11.2 %), A2 (1.72 %), and A3 (25.86 %); Asian (sublineage A4 (53.85 %); African-American (sublineage D1 (5.17 %); and Asian-American (sublineage D3 (2.59 %). The HPV18 lineage includes Asian-Ameridian (sublineages A1 (100 %)). HPV18 revealed a higher rate of cervical cancer, cervicitis, warts, and ulcers than HPV16 and other high-risk genotypes in the 35–54–year–old group, but did not show a difference in cancer stages.

Conclusions

HPV16 and HPV18 genotypes are common in cervical cancer in northern Vietnam, with European, Asian, and Asian–Amerindian lineages predominating. HPV18 causes cervical cancer at a higher rate than other genotypes in the 35–54–year–old age group; thus, early identification of the genotype is critical for more successful therapy.