Effect of sampling positions in nucleic acid test on the test result: a report from 47 confirmed COVID-19 cases in Jinan City

Objective: To investigate the effect of sampling positions in nucleic acid test for COVID-19 on test results.

A comprehensive analysis of 47 COVID-19 cases in Jinan city

Objective: To comprehensively analyze the epidemic characteristics of COVID-19 cases in Jinan in order to provide a basis for establishing and implementing effective prevent and control measures.

Consideration about cluster epidemic of 37 COVID-19 cases

Objective: To summarize the cluster epidemic characteristics of coronavirus disease 2019(COVID-19) in Jinan City in order to provide reference for further preventive measures.

Reflection and epidemiological characteristics of Coronavirus disease 2019 in Jinan City

Objective There were 47 confirmed cases of coronavirus disease 2019 (COVID-2019) reported in Jinan City from January 23 to February 11, 2020. Since February 25, 2020, there were no confirmed cases reported in Jinan City for 14 consecutive days. In order to provide reference for future epidemic prevention and control, we analyzed the current epidemic situation and epidemiological characteristics. Methods The demographic, clinical and epidemiological characteristics of confirmed cases in Jinan City were evaluated with descriptive analysis and family clusters were traced. Results 74.5% of 47 confirmed cases were clinical common type, and 24 (51.1%) were cured and discharged. No death occurred. Fever (66.0%) was the first dominant symptom. CT showed 82.1% of the cases were bilateral pneumonia. The distribution of cases was similar between male and female. Most patients (70.2%) aged 20 to 59 years, 83.0% lived in the central urban area, and 40.4% had a history of Wuhan exposure before onset. Five of 10 family cluster outbreaks were sourced from Wuhan exposure. 70.2% (33 cases) of 47 cases were related to the family cluster outbreaks. Conclusion The epidemic prevention and control work in Jinan City has achieved phased results. Preventing importation from surrounding areas and high incidence risk areas is still the focus of future efforts.

Variability in transmission risk of SARS-CoV-2 in close contact settings: A contact tracing study in Shandong Province, China.

BACKGROUND: Understanding the relative transmissibility of SARS-CoV-2 virus across different contact settings and the possibility of superspreading events is important for prioritizing disease control. Such assessment requires proper consideration of individual level exposure history, which is made possible by contact tracing. METHODS: The case-ascertained study in Shandong, China including 97 laboratory-confirmed index cases and 3158 close contacts. All close contacts were quarantined after their last exposure of index cases. Contacts were tested for COVID-19 regularly by PCR to identify both symptomatic and asymptomatic infections. We developed a Bayesian transmission model to the contact tracing data to account for different duration of exposure among individuals to transmission risk in different settings, and the heterogeneity of infectivity of cases. RESULTS: We estimate secondary attack rates (SAR) to be 39% (95% credible interval (CrI): 20-64%) in households, 30% (95% CrI: 11-67%) in healthcare facilities, 23% (95% CrI: 7-51%) at workplaces, and 4% (95% CrI: 1-17%) during air travel. Models allowing heterogeneity of infectivity of cases provided a better goodness-of-fit. We estimated that 64% (95% CrI: 55-72%) of cases did not generate secondary transmissions, and 20% (95% CrI: 15-26%) cases explained 80% of secondary transmissions. CONCLUSIONS: Household, healthcare facilities and workplaces are efficient setting for transmission. Timely identification of potential superspreaders in most transmissible settings remains crucial for containing the pandemic.

A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection.

BACKGROUND: Real-time reverse transcription-PCR (rRT-PCR) has been the most effective and widely implemented diagnostic technology since the beginning of the COVID-19 pandemic. However, fuzzy rRT-PCR readouts with high Ct values are frequently encountered, resulting in uncertainty in diagnosis. METHODS: A Specific Enhancer for PCR-amplified Nucleic Acid (SENA) was developed based on the Cas12a trans-cleavage activity, which is specifically triggered by the rRT-PCR amplicons of the SARS-CoV-2 Orf1ab (O) and N fragments. SENA was first characterized to determine its sensitivity and specificity, using a systematic titration experiment with pure SARS-CoV-2 RNA standards, and was then verified in several hospitals, employing a couple of commercial rRT-PCR kits and testing various clinical specimens under different scenarios. FINDINGS: The ratio (10 min/5 min) of fluorescence change (FC) with mixed SENA reaction (mix-FCratio) was defined for quantitative analysis of target O and N genes, and the Limit of Detection (LoD) of mix-FCratio with 95% confidence interval was 1.2≤1.6≤2.1. Totally, 295 clinical specimens were analyzed, among which 21 uncertain rRT-PCR cases as well as 4 false negative and 2 false positive samples were characterized by SENA and further verified by next-generation sequencing (NGS). The cut-off values for mix-FCratio were determined as 1.145 for positive and 1.068 for negative. INTERPRETATION: SENA increases both the sensitivity and the specificity of rRT-PCR, solving the uncertainty problem in COVID-19 diagnosis and thus providing a simple and low-cost companion diagnosis for combating the pandemic. FUNDING: Detailed funding information is available at the end of the manuscript.