The Positive Rate of Nucleic Acid Testing and the Epidemiological Characteristics of COVID-19 in Chongqing

ObjectiveThe purpose of this study is to analyze the positive rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid testing (NAT), cases of and deaths due to SARS-CoV-2, and the epidemiological characteristics of SARS-CoV-2 to identify high-risk populations.MethodsA retrospective study in Jiulongpo district of Chongqing was conducted by performing continuous observations of the frequency of SARS-CoV-2 NAT, analyzing the data of close contacts of patients and asymptomatic carriers, and collecting epidemiological data. Data were collected from January 20, 2020, when the first case of SARS-CoV-2 infection was reported, to March 26, 2020. Descriptive statistical analysis and Cochrane–Mantel–Haenszel analysis were used to compare the positive detection rates and positive diagnostic rates of different exposure groups.ResultsA total of 7,118 people received 10,377 SARS-CoV-2 nucleic acid tests in one district, and the SARS-CoV-2 positive rates were 0.40% (18/4446) and 0.15% (4/2672) in people receiving one and ≥ two nucleic acid tests (p = 0.06), respectively. Those with suspected cases (12.35%) and close contacts (8%) had higher positive rates than people tested at fever clinics (0.39%) (p < 0.001). The median latency (range) of cases was 5 (2, 9) days, and the median time from diagnosis to recovery was 22 (14, 25) days. One recovered patient received a positive test result at 28 days after recovery when she attempted to donate blood. Six clustered cases, including one patient who died, indicated persistent human-to-human transmission. One patient who was diagnosed after death was found to have infected 13 close contacts. People working in catering and other public service departments (36.36%) and people who are unemployed and retirees (45.45%) have an increased risk of infection compared with technical staff (9.09%) and farmers (9.09%).ConclusionThe total positive rate was low in the tested population, and more effective detection ranges should be defined to improve precise and differentiated epidemic control strategies. Moreover, in asymptomatic carriers, SARS-CoV-2 tests were positive after recovery, and patients with suspected SARS-CoV-2 infection who die may pose serious potential transmission threats.

Effects of prolonged incubation period and centralized quarantine on the COVID-19 outbreak in Shijiazhuang, China: a modeling study

Background From 2 January to 14 February 2021, a local outbreak of COVID-19 occurred in Shijiazhuang, the capital city of Hebei Province, with a population of 10 million. We analyzed the characteristics of the local outbreak of COVID-19 in Shijiazhuang and evaluated the effects of serial interventions. Methods Publicly available data, which included age, sex, date of diagnosis, and other patient information, were used to analyze the epidemiological characteristics of the COVID-19 outbreak in Shijiazhuang. The maximum likelihood method and Hamiltonian Monte Carlo method were used to estimate the serial interval and incubation period, respectively. The impact of incubation period and different interventions were simulated using a well-fitted SEIR+q model. Results From 2 January to 14 February 2021, there were 869 patients with symptomatic COVID-19 in Shijiazhuang, and most cases (89.6%) were confirmed before 20 January. Overall, 40.2% of the cases were male, 16.3% were aged 0 to 19 years, and 21.9% were initially diagnosed as asymptomatic but then became symptomatic. The estimated incubation period was 11.6 days (95% CI 10.6, 12.7 days) and the estimated serial interval was 6.6 days (0.025th, 0.975th: 0.6, 20.0 days). The results of the SEIR+q model indicated that a longer incubation period led to a longer epidemic period. If the comprehensive quarantine measures were reduced by 10%, then the nucleic acid testing would need to increase by 20% or more to minimize the cumulative number of cases. Conclusions Incubation period was longer than serial interval suggested that more secondary transmission may occur before symptoms onset. The long incubation period made it necessary to extend the isolation period to control the outbreak. Timely contact tracing and implementation of a centralized quarantine quickly contained this epidemic in Shijiazhuang. Large-scale nucleic acid testing also helped to identify cases and reduce virus transmission.

Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13

The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.

The Nasopharynx Swab Test for Coronavirus Disease-2019 Is Mild and Will Not Cause Significant Pain and Anxiety: A Cross-Sectional Study Based on Psychiatrists

BackgroundLaboratory viral nucleic acid testing (NAT), such as the nasopharyngeal swab test, is now recommended as the gold standard for the diagnosis of Coronavirus disease-2019 (COVID-19). However, the nasopharyngeal swab testing process may cause some discomfort.ObjectiveTo investigate the influence of nasopharyngeal swab tests on the anxiety and pain felt by psychiatric medical staff.MethodsA total of 174 psychiatric medical staff (namely 97 doctors, 68 nurses, and nine administrators) and 27 controls were included in the current study. A self-designed questionnaire was used to collect their general demographic information (age, gender, marriage, occupation, profession, smoking history, alcohol consumption history, tea drinking history, previous history of anxiety and depression) as well as their subjective experience, such as nausea, vomiting, coughing, worry, fear, etc, during nasopharyngeal swab collection. The Numerical Rating Scale (NRS) and the State-Trait Anxiety Inventory (STAI) were used to assess the subjects’ pain and state anxiety, respectively.ResultsThere were no statistical differences (p>0.05) in age, marriage, smoking history, a history of anxiety and depression, pain scores, and anxiety scores between different professions and genders. The results of partial correlation analysis (controlled for gender and history of depression or anxiety) indicated that the male gender was negatively correlated with being anxious (r=-0.148, p=0.037) and nervous (r=-0.171 p=0.016), although there was no significant difference in pain and anxiety between men and women. In addition, marriage might help women resist negative emotions.Conclusions1) There will be mild discomfort during nucleic acid testing, but not enough to cause pain and anxiety; 2) women are more likely to be anxious and nervous during the nucleic acid testing.

Wide-scale Pooled Sample Testing for COVID-19: Application, Optimisation and Probabilistic Analysis

Background Currently, coronavirus disease 2019 (COVID-19) has become the most severe infectious disease affecting the world, which has spread around the world to more than 200 countries in 2020. Until COVID-19 vaccine technology completely matures, nucleic acid testing is considered as an effective way to screen virus carriers and control the spread of the virus. Considering that the medical resources and infection rates are different across various countries and regions, if all infected areas adopt the traditional individual nucleic acid testing method, the workload will be heavy and time-consuming. Therefore, this will not lead to the control of the pandemic. Methods After Wuhan completed a citywide nucleic acid testing in May 2020, China basically controlled the spread of COVID-19 and entered the post-epidemic period. Since then, although some cities in China, such as Qingdao, Xinjiang, Beijing, Dalian, have experienced a local epidemic resurgence, the pandemic was quickly suppressed through wide-scale pooled nucleic acid testing methods. Combined with the successful experience of mass nucleic acid testing in China, this study introduces two main pooled testing methods used in two cities with a population of more than ten million people, Wuhan’s “five-in-one” and Qingdao's “ten-in-one” rapid pooled testing methods. This study proposes an improved method for optimising the second round of “ten-in-one” pooled testing, known as “the pentagram mini-pooled testing method”, which speeds up the testing process (as a result of reducing the numbers of testing by 40%) and significantly reduces the cost. Findings Qingdao's optimised “ten-in-one” pooled testing method quickly screens out the infections by running fewer testing. This study also mathematically examines the probabilistic principles and applicability conditions for pooled testing of COVID-19. Herein, the study theoretically determines the optimal number of samples that could successfully be combined into a pool under different infection rates. Then, it quantitatively discusses the applicability and principles for choosing the pooled testing instead of individual testing.Interpretation Overall, this research offers a reference for other countries with different infection rates to help them in implementing the mass testing for COVID-19 to reduce the spread of coronavirus.