Using signal-to-cutoff ratios of HIV screening assay to predict HIV infection.

BACKGROUND: The sensitivity of HIV screening assays often leads to a high rate of false-positive results, requiring retests and confirmatory tests. This study aimed to analyze the capability of signal-to-cutoff (S/CO) ratios of HIV screening assay to predict HIV infection. METHODS: A retrospective study on the HIV screening-positive population was performed at Zhongshan Hospital, Xiamen University, the correlation between HIV screening assay S/CO ratios and HIV infection was assessed, and plotted Receiver Operating Characteristic (ROC) curves were generated to establish the optimal cutoff value for predicting HIV infection. RESULTS: Out of 396,679 patients, 836 were confirmed to be HIV-infected, with an HIV prevalence of 0.21%. The median S/CO ratios in HIV infection were significantly higher than that in non-HIV infection (296.9 vs. 2.41, P < 0.001). The rate of confirmed HIV infection was increased with higher S/CO ratios in the screening assay. The ROC curve based on the HIV screening assay S/CO ratio achieved a sensitivity of 93.78% and a specificity of 93.12% with an optimal cutoff value of 14.09. The area under the ROC curve was 0.9612. Further analysis of the ROC curve indicated that the S/CO ratio thresholds yielding positive predictive values of 99%, 99.5%, and 100% for HIV infection were 26.25, 285.7, and 354.5, respectively. CONCLUSION: Using HIV screening assay S/CO ratio to predict HIV infection can largely reduce necessitating retests and confirmatory tests. Incorporating the S/CO ratio into HIV testing algorithms can have significant implications for medical and public health practices.

Performance of the nontreponemal tests and treponemal tests on cerebrospinal fluid for the diagnosis of neurosyphilis: A meta-analysis.

Background: Nontreponemal and treponemal tests for analyzing cerebrospinal fluid to confirm the existence of neurosyphilis have been widely used, so we aim to evaluate and compare their performance on the cerebrospinal fluid in the diagnosis of neurosyphilis. Methods: We conducted a systematic literature search on five databases and utilized a bivariate random-effects model to perform the quantitative synthesis. Results: Nontreponemal tests demonstrated a pooled sensitivity of 0.77 (95% CI: 0.68-0.83), a pooled specificity of 0.99 (95% CI: 0.97-1.00), and a summary AUC of 0.97 (95% CI: 0.95-0.98). The pooled sensitivity, pooled specificity, and summary AUC of treponemal tests were 0.95 (95% CI: 0.90-0.98), 0.85 (95% CI: 0.67-0.94), and 0.97 (95% CI: 0.95-0.98), respectively. The pooled specificity of all nontreponemal tests varied minimally (ranging from 0.97 to 0.99), with TRUST (0.83) having a higher pooled sensitivity than VDRL (0.77) and RPR (0.73). Among all treponemal tests, EIA has outstanding diagnostic performance with a pooled sensitivity of 0.99 and a pooled specificity of 0.98. Conclusion: Nontreponemal tests exhibited a higher pooled specificity, and treponemal tests exhibited a higher pooled sensitivity in diagnosing neurosyphilis on cerebrospinal fluid. TRUST may be a satisfactory substitute for VDRL. EIA is a prospective diagnostic tool that deserves further study in the future. Our study may be useful to clinical laboratories in selecting appropriate serological tests on the cerebrospinal fluid for the diagnosis of neurosyphilis.

Nasal swab is a good alternative sample for detecting SARS-CoV-2 with rapid antigen test: A meta-analysis.

BACKGROUND: We aim to determine if nasal samples have equivalent detection sensitivity to nasopharyngeal swabs for RAT and evaluate the diagnostic accuracy of nasal swabs with RAT. METHODS: PubMed and Web of Science were searched for eligible studies published before August 23, 2022. A bivariate random effects model was used to perform the quantitative synthesis. RESULTS: The pooled sensitivity, pooled specificity, positive likelihood ratio, negative likelihood ratio, and summary AUC on nasal swabs with RAT were 0.81 (95% CI, 0.77-0.85), 1.00 (95% CI: 0.99-1.00), 0.97 (95% CI, 0.95-0.98), 298.91 (95% CI, 144.71-617.42) and 0.19 (95% CI, 0.15-0.23), respectively. WHO required RAT kits to perform with a sensitivity of 0.80 and a specificity of 0.97, nasal swabs (0.81) achieved the required sensitivity while nasopharyngeal swabs (0.75) did not. The symptomatic population yielded higher pooled sensitivity than the asymptomatic population (0.86 versus 0.71), with a pooled sensitivity of 0.90 for five days of symptom onset. CONCLUSION: Nasal sampling had a great performance and yielded a high sensitivity in detecting SARS-CoV-2 using RAT, we believe that RAT performed with nasal swabs is a good alternative for detecting SARS-CoV-2, especially early in the onset of symptoms.

Evaluating the Value of Anti-SARS-CoV-2 Antibody-Based Tests for COVID-19 Diagnosis.

BACKGROUND: The early detection of COVID-19 patients is fundamental for containing the pandemic. A reverse-transcriptase quantitative polymerase chain reaction (RT-PCR), which detects SARS-CoV-2 RNA, is the gold standard diagnostic test, although it can contribute to false-negative results. Consequently, supplementary diagnostic tests are urgently needed. METHODS: To assess the value of anti-SARS-CoV-2 antibody-based tests for confirming COVID-19, a retrospective study was conducted on 3120 inbound overseas travelers who underwent a 14-day government quarantine in Xiamen from August 2020 to October 2020. The diagnostic accuracy of the total antibody that detected the anti-SARS-CoV-2 antibody and the RT-PCR that detected SARS-CoV-2 RNA was determined in comparison to the clinical diagnosis. RESULTS: The COVID-19 positive rate was 3.14% (98/3120). The sensitivity and specificity of the RT-PCR test on the first day of quarantine were 14.29% and 100%, respectively, and the sensitivity and specificity of the total antibody were 93.88% and 99.40%, respectively. The kappa value between an RT-PCR on the first day of quarantine and a clinical diagnosis was 0.24 (95% CI, 0.14-0.35), indicating poor consistency. The kappa value between total antibodies and a clinical diagnosis was 0.88 (95% CI, 0.83-0.93), indicating perfect consistency. There were no differences in the positive rates of an RT-PCR in symptomatic COVID-19 (7.41% (2/27)) and asymptomatic COVID-19 (16.90 (12/71) (p = 0.338). Similarly, the positive rate of the total antibody tests showed no difference in symptomatic COVID-19 (96.30% (26/27)) and asymptomatic COVID-19 (92.96% (66/71)) (p = 0.676). CONCLUSION: SARS-CoV-2 antibodies are developed by the body in response to an infection or after vaccination; this can easily lead to a missed diagnosis. In the context of low sensitivity for an RT-PCR, SARS-CoV-2 antibody detection is an effective adjunct to RT-PCR detection, which can improve the diagnostic accuracy of COVID-19 and provide an effective complement to the false-negative results of an RT-PCR.

Evaluation of the cycle threshold values of RT-PCR for SARS-CoV-2 in COVID-19 patients in predicting epidemic dynamics and monitoring surface contamination.

To evaluate the application of cycle threshold (Ct) values of coronavirus disease 2019 (COVID-19) patients in predicting epidemic dynamics and monitoring surface contamination. The Ct value of reverse transcriptase-polymerase chain reaction for SARS­CoV-2 from COVID-19 patients inbound overseas in Xiamen, China was collected from October 2020 to December 2021, and the correlation of patients' Ct values with epidemic dynamics and surface contamination was evaluated. The results showed that there was an extreme inverse correlation of positivity rate in the current calendar month (ORF1ab, r = -0.692, P = 0.004; N,r = -0.629, P = 0.012) and the following calendar month (ORF1ab,r = -0.801, P = 0.001; N,r = -0.620, P = 0.018) with the median Ct values. Ct value showed better performance for monitoring surface contamination, with the area under the curve value 0.808(95 %CI: 0.748-0.869) for ORF1ab and 0.807(95 %CI:0.746-0.868) for the N gene. The patients' ORF1ab Ct value< 29.09 or N Ct value< 28.03 were 11.25 times and 10.48 times more likely to result in surface contamination than those with ORF1ab Ct value ≥ 29.09 or N Ct value≥ 28.03 (OR:11.25,95 % CI: 5.52-22.35; OR:10.48,95 % CI:5.29-20.70). Ct values were associated with the positivity rate in the current or following calendar month and predicted the epidemic dynamics. The Ct values can be used as a predictor for monitoring surface contamination to develop public health responses to COVID-19.

Global airborne bacterial community-interactions with Earth's microbiomes and anthropogenic activities.

Airborne bacteria are an influential component of the Earth's microbiomes, but their community structure and biogeographic distribution patterns have yet to be understood. We analyzed the bacterial communities of 370 air particulate samples collected from 63 sites around the world and constructed an airborne bacterial reference catalog with more than 27 million nonredundant 16S ribosomal RNA (rRNA) gene sequences. We present their biogeographic pattern and decipher the interlacing of the microbiome co-occurrence network with surface environments of the Earth. While the total abundance of global airborne bacteria in the troposphere (1.72 × 1024 cells) is 1 to 3 orders of magnitude lower than that of other habitats, the number of bacterial taxa (i.e., richness) in the atmosphere (4.71 × 108 to 3.08 × 109) is comparable to that in the hydrosphere, and its maximum occurs in midlatitude regions, as is also observed in other ecosystems. The airborne bacterial community harbors a unique set of dominant taxa (24 species); however, its structure appears to be more easily perturbed, due to the more prominent role of stochastic processes in shaping community assembly. This is corroborated by the major contribution of surface microbiomes to airborne bacteria (averaging 46.3%), while atmospheric conditions such as meteorological factors and air quality also play a role. Particularly in urban areas, human impacts weaken the relative importance of plant sources of airborne bacteria and elevate the occurrence of potential pathogens from anthropogenic sources. These findings serve as a key reference for predicting planetary microbiome responses and the health impacts of inhalable microbiomes with future changes in the environment.

Diagnostic accuracy of rapid antigen test for SARS-CoV-2: A systematic review and meta-analysis of 166,943 suspected COVID-19 patients.

To assess the diagnostic accuracy of the rapid antigen test (RAT) compared with RT-PCR (reference standard) for SARS-CoV-2, we searched MEDLINE/PubMed and Web of Science for relevant records. The QUADAS-2 tool was used to assess study quality, and quantitative synthesis was conducted using a bivariate random-effects model. The meta-analysis included 135 studies (166,943 samples). The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 0.76 (95%CI: 0.73-0.79), 1.00 (95%CI: 1.00-1.00), 276.1 (95% CI, 184.1-414.1), 0.24 (95% CI, 0.21-0.27), and 1171 (95% CI, 782-1755), respectively. Compared to other sample types, nasal samples had the best RAT sensitivity [0.79 (95%CI: 0.71-0.85)]. The sensitivities of the different RAT kits ranged from 0.41 (95%CI: 0.23-0.61) to 0.90 (95%CI: 0.70-0.97). Sensitivity was markedly better in samples with lower Ct, and RAT achieved excellent pooled sensitivity at 1.00 (95%CI: 0.70-1.00) among samples with Ct < 20. Testing within 10 days of symptom onset resulted in a high sensitivity. For ≤ 3, ≤ 7, and ≤ 10 days, the sensitivities were 0.91 (95%CI: 0.83-0.96), 0.89 (95%CI: 0.84-0.93), and 0.88 (95%CI: 0.83-0.92), respectively. RAT kits show high sensitivity and specificity in early infection, especially when the viral load is high. Moreover, using nasal samples for antigen testing, which are moderately sensitive and patient-friendly, is a reliable alternative to nasopharyngeal sampling. RAT might be effective for fighting the COVID-19 pandemic; however, it must be complemented by the careful handling of negative test results.

A 14+7 day quarantine period and a dual nucleic acid testing reagent strategy detect potentially indiscoverable Coronavirus disease 2019 infections in Xiamen, China.

BACKGROUND: Determining what quarantine period and detection strategy are more effective and sustainable remains a challenge for further prevention and social stability. METHODS: From October 2020 to December 2021, 290,547 inbound overseas travelers were subject to government quarantine in Xiamen, China. The detection rate of COVID-19 during different quarantine periods using dual or single nucleic acid testing reagents. RESULTS: The COVID-19 positive rate was 1.79% (519/290,547). The detection rates during the 7-day, 14-day and 14+7-day quarantine periods using the dual reagents were 78.4%, 91.7%, and 100%, respectively. The detection rate of the 7-day, 14-day and 14+7-day quarantine periods were 73.99%, 86.51%, and 94.22%, respectively, using the Liferiver reagent and 72.25%, 84.59%, and 91.91%, respectively, using the Daan reagent. Based on the 14+7 day strategy, dual nucleic acid testing reagent strategy detected all imported cases, but 30 cases (5.78%) were not detected via Liferiver reagent and 42 (8.09%) cases not detected via Daan reagent. CONCLUSION: A 14+7-day quarantine period and dual nucleic acid testing reagent strategy are effective screening methods for COVID-19 among inbound overseas travelers. The superior detection rate of these strategies reduce the risk of secondary transmission of the SARS-CoV-2 virus.