Journal of clinical virology plus最新文献

Background

Human respiratory syncytial virus (HRSV) is an important pathogen causing severe acute respiratory infection (SARI), particularly in children under 5 years old. We investigated the HRSV infection status and genogroups in pediatric patients with SARI between January 2019 and December 2022 in Huzhou, China.

Methods

Nasopharyngeal swabs (NPSs) were collected from pediatric patients in the First People's Hospital of Huzhou. Real-time quantitative RT-PCR for respiratory syncytial virus (A/B)was performed with an QuantStudio 7 Flex Real-Time PCR System. For genotyping, the primer sets A-F/A-R and B-F/B-R were used to amplify the G protein sequences of HRSV-A and HRSV-B, respectively. Phylogenetic analysis was performed using MEGA software.

Results

In total, 973 NPSs were collected between January 2019 and December 2022, and 63 samples were positive for HRSV nucleic acid, representing a detection rate of 6.47%. Of the positive specimens, 28 were classified as HRSV-A and 35 were classified as HRSV-B. Infection with HRSV was found in all age groups tested, with children < 5 years old accounting for 88.89% of the positive cases. The detection rate was high from November to the following March. Phylogenetic analysis clustered HRSV-A strains into the ON1 genogroup and HRSV-B strains belonged to the BA9 genogroup.

Conclusions

HRSV is an important respiratory pathogen among children in Huzhou, China, with a high incidence in children under 5 years old between winter and spring. HRSV subgroups A and B were co-circulating, and ON1 and BA9 were the two main genogroups identified in this study.

Nucleocapsid gene-positive, envelope gene-negative (N2+/E-) SARS-CoV-2 PCR results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are an infrequent phenomenon. We assessed the validity of the N2+/E- cases with an indirect approach by analyzing their occurrence in relation to overall positive PCR rates and absolute number of PCR tests (24,909 samples, collected June 2021 to July 2022). Additionally, 3022 samples were analyzed with the Xpert Xpress CoV-2-plus assay in August/September 2022. The incidence of monthly N2+/E- cases closely followed the overall frequency of positive tests (p < 0.001), while there was no correlation with the monthly number of PCR test. The observed distribution of N2+/E- cases implicates, that they are not merely artefacts, but rather represent samples with a very low viral load. This phenomenon will persist with the Xpert Xpress SARS-CoV-2 plus assay, which also produced more than 10% results where only one target gene replicated with a very high Ct value.

Background

Dengue, ranked as one of the most critical viral diseases, requires rapid, accurate, and early diagnosis for better patient care.

Objectives

This study pertains to the development and clinical validation of an in house easy to do, affordable kit for the detection of dengue NS1 antigen based on lateral flow immunoassay in serum samples of patients.

Study Design

Clinically uncharacterized serum specimens were obtained and analyzed using the developed NS1 detection kit and compared against the ELISA results.

Results

The performance of the kit was evaluated with both positive and negative patients’ serum samples for NS1 antigen and found to be highly specific and sensitive. An overall sensitivity of 92.16 % and specificity of 97.25 % were recorded. Kit stability tests were also carried out and the performance of the kit was found to be similar to real time tests.

Conclusion

The results indicate that the developed NS1 detection kit has good reliability with comparable performance to ELISA results.

Background & Aims The use of direct acting antiviral agents (DAAs) in patients with chronic HCV genotype (GT) 3a infection results in sustained virologic response (SVR) rates of 93–98%, but 5–8% of patients experience virologic failure. Methods. We observed 48 patients infected with HCV subtype 3a who failed previous treatment with DAAs, including 43 subjects (89.6%) with liver cirrhosis. Thirty-seven (77%) subjects previously received NS5A inhibitors of the first generation (daclatasvir) and 11 subjects (23%) – of the second generation (velpatasvir). All patients received retreatment with sofosbuvir (SOF)/ velpatasvir (VEL) and ribavirin (RBV) for 24 weeks. We compared SVR₁₂ rates depending on fibrosis stage, presence of NS5A mutation (L31M or A30K and Y93H), and on the generation of previously used NS5A inhibitors. Results. Observed SVR₁₂ rate were: 83,3% (40/48 patients) overall; 100% in patients without cirrhosis (n=5) vs 81,4% (n=35) in those with cirrhosis (n=43) (P=0,01); 86,7% (n=13) with single L31M or A30K(n=15) vs 77,8% (n=21) with Y93H mutation (n=27) (P=0,46), 86,5% (n=32) in patients who previously failed first generation (n=37) vs 72,7% (n=8) in those who failed second generation NS5A inhibitors (n=11) (P=0,35). Conclusions. Retreatment with SOF/VEL+RBV was highly effective and safe in patients with chronic HCV GT3a infection, including those with liver cirrhosis, who previously failed DAA containing NS5A inhibitors. Presence of NS5A RASs L31M, A30K, and Y93H at the baseline, as well as the generation of previously used NS5A inhibitors did not impact SVR₁₂ rates.

Objectives

Shotgun proteomics is a generic method enabling detection of multiple viral species in one assay. The reliable and accurate identification of these viral species by analyzing peptides from MS-spectra is a challenging task. The aim of this study was to develop an easy accessible proteome analysis approach for the identification of viruses that cause respiratory and gastrointestinal infections.

Methods

For this purpose, a shotgun proteomics based method and a web application, ‘proteome2virus’, were developed. Identified peptides were searched in a database comprising proteomic data of 46 viruses known to be infectious to humans.

Results

The method was successfully tested for cultured viruses and eight fecal samples consisting of ten different viral species from seven different virus families, including SARS-CoV-2. The samples were prepared with two different sample preparation methods and were measured with two different mass spectrometers.

Conclusions

The results demonstrate that the developed web application is applicable to different MS data sets, generated from two different instruments, and that with this approach a high variety of clinically relevant viral species can be identified. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.

Headache is a common neurological symptom of Coronavirus disease 2019 (COVID-19) patients. However, the prevalence, comorbidities, and ethnic susceptibilities of COVID-19-induced headaches are not well-defined.

We performed a retrospective chart review of patients who tested positive for SARS-CoV2 by reverse transcriptase-polymerase chain reaction (RT-PCR) in March and April 2020 at Massachusetts General Hospital, Boston, Massachusetts, USA.

In the study, we identified 450 patients, 202 (44.9%) male, and 248 (55.1%) female, who tested positive for COVID-19. Headache is a significant painful symptom affecting 26% of patients. Female predominance is determined in sore throat, nasal congestion, hypogeusia, headache, and ear pain. In contrast, pneumonia and inpatient hospitalization were more prevalent in males. Younger patients (< 50) were more likely to develop sore throat, fatigue, anosmia, hypogeusia, ear pain, myalgia /arthralgia, and headache. In contrast, older (> 50) patients were prone to develop pneumonia and required hospitalization.

Ethnic subgroup analysis suggests Hispanic patients were prone to headaches, nausea/vomiting, nasal congestion, fever, fatigue, anosmia, and myalgia/arthralgia compared to non-Hispanics. Headache risk factors include nausea/vomiting, sore throat, nasal congestion, fever, cough, fatigue, anosmia, hypogeusia, dizziness, ear pain, eye pain, and myalgia/arthralgia.

Our study demonstrates regional gender, age, and ethnic variabilities in COVID symptomatology in Boston and the vicinity. It identifies mild viral, painful, and neurological symptoms are positive predictors of headache development in COVID-19.

Introduction

High cycle threshold values (Ct) value) results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be true infections or false-positive results. Misinterpretation of results has negative consequences. Goal of this study was to evaluate quantitative real-time polymerase chain reaction (qPCR) results with high Ct-values, to reach a point where a correct interpretation can be given.

Methods

High Ct-value results of SARS-CoV-2 in respiratory samples taken between April 2020 and January 2021 were analysed. Three different SARS-CoV-2 qPCR assays (in-house, Alinity M and Xpert Xpress) were used for screening patients and healthcare workers (HCW). High Ct-value results were defined as “inconclusive”. The Ct-value cut-off for the interpretation of the test as “positive” and “inconclusive” were based on quality assurance panel results and manufacturers’ instructions.

Results

Out of totally 50.295 samples tested for SARS-CoV-2, the in-house and Alinity M qPCR together yielded 379 inconclusive results. A second sample existed for 217 samples, allowing dynamics of the PCR in time. Of these, 187 were negative (86%), 11 again inconclusive (5%) and 19 positive (9%). Sixteen out of 19 persons with a positive result were HCW, 14 (74%) had a link to a SARS-CoV-2 infected person. The majority of inconclusive results detected with the Xpert Xpress (n=45 of 3603), were related to individuals with a known history of SARS-CoV-2 infection (n=28, 62%).

Conclusion

This study shows the importance of re-testing inconclusive SARS-CoV-2 qPCR results. Only then, the correct (true or false) interpretation can be given, leading to the right measures.

Background

Detection of mpox virus during investigation of viral vesicular rash illness is required to identify mpox infection.

Objectives

This study evaluated the performance of a research-use-only (RUO) AusDiagnostics MT-PCR syndromic assay containing an mpox virus target.

Methods

The analytical specificity and limit of detection (LoD) of the AusDiagnostics MT-PCR mpox assay was verified using control material. Clinical performance was evaluated using anonymised residual nucleic acids extracted from swab specimens previously tested for mpox virus using a laboratory developed test (LDT). Residual nucleic acids were derived from consecutive sample panels collected during two periods in the 2022 mpox outbreak.

Results

The AusDiagnostics MT-PCR assay demonstrated an LoD of 35 input copies of mpox virus and correctly detected all relevant members of a specificity panel (n = 34). 175 residual nucleic acids were included in the study with a prevalence of mpox of 40.0% (95%CI 32.7–47.6). The AusDiagnostics MT-PCR mpox assay demonstrated an accuracy of 98.9% (95%CI 93.8–99.9), sensitivity of 94.2% (95%CI 85.2 – 98.1) and specificity of 100% (95%CI 95.6 -100), when compared to the LDT qPCR assay. The AusDiagnostics MT-PCR mpox assay detected additional vesicular rash pathogens in 26.8% samples. Co-detection with other vesicular rash pathogens was described in 12.8% of mpox virus detected samples

Conclusions

Performance of the RUO AusDiagnostics MT-PCR mpox assay was comparable to an LDT qPCR for the detection of mpox virus in nucleic acids extracted from swab specimens. The RUO AusDiagnostics MT-PCR mpox assay facilitated the simultaneous detection of additional infective etiologies of vesicular rash syndromes.