Longitudinal wastewater surveillance addressed public health priorities during the transition from "dynamic COVID-zero" to "opening up" in China: a population-based study (preprint)

Background Wastewater surveillance provides real-time, cost-effective monitoring of SARS-CoV-2 transmission. We developed the first city-level wastewater warning system in mainland China, located in Shenzhen. Our study aimed to reveal cryptic transmissions under the "dynamic COVID-zero" policy and characterize the dynamics of the infected population and variant prevalence, and then guide the allocation of medical resources during the transition to "opening up" in China. Methods In this population-based study, a total of 1,204 COVID-19 cases were enrolled to evaluate the contribution of Omicron variant-specific faecal shedding rates in wastewater. After that, wastewater samples from up to 334 sites distributed in communities and port areas in two districts of Shenzhen covering 1.74 million people were tested daily to evaluate the sensitivity and specificity of this approach and were validated against daily SARS-CoV-2 screening. After the public health policy was switched to "opening up" in December 7, 2022, we conducted wastewater surveillance at wastewater treatment plants and pump stations covering 3.55 million people to estimate infected populations using model prediction and detect the relative abundance of SARS-CoV-2 lineages using wastewater sequencing. Findings In total, 82.4% of SARS-CoV-2 Omicron cases tested positive for faecal viral RNA within the first four days after the diagnosis, which was far more than the proportion of the ancestral variant. A total of 27,759 wastewater samples were detected from July 26 to November 30 in 2022, showing a sensitivity of 73.8% and a specificity of 99.8%. We further found that wastewater surveillance played roles in providing early warnings and revealing cryptic transmissions in two communities. Based on the above results, we employed a prediction model to monitor the daily number of infected individuals in Shenzhen during the transition to "opening up" in China, with over 80% of the population infected in both Futian District and Nanshan District. Notably, the prediction of the daily number of hospital admission was consistent with the actual number. Further sequencing revealed that the Omicron subvariant BA.5.2.48 accounted for the most abundant SARS-CoV-2 RNA in wastewater, and BF.7.14 and BA.5.2.49 ranked second and third, respectively, which was consistent with the clinical sequencing. Interpretation This study provides a scalable solution for wastewater surveillance of SARS-CoV-2 to provide real-time monitoring of the new variants, infected populations and facilitate the precise prediction of hospital admission. This novel framework could be a One Health system for the surveillance of other infectious and emerging pathogens with faecal shedding and antibiotic resistance genes in the future. Funding Sanming Project of Medicine in Shenzhen, Shenzhen Key Medical Discipline Construction Fund.

AdaGT: An Adaptive Group Testing Method for Improving Efficiency and Sensitivity of Large-Scale Screening Against COVID-19

The ongoing coronavirus disease 2019 (COVID-19) is a pandemic causing millions of deaths, devastating social and economic disruptions. Testing individuals for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen of COVID-19, is critical for mitigating and containing COVID-19. Many countries are implementing group testing strategies against COVID-19 to improve testing capacity and efficiency while saving required workloads and consumables. A group of individuals’ nasopharyngeal/oropharyngeal (NP/OP) swab samples is mixed to conduct one test. However, existing group testing methods neglect the fact that mixing samples usually leads to substantial dilution of viral ribonucleic acid (RNA) of SARS-CoV-2, which seriously impacts the sensitivity of tests. In this paper, we aim to screen individuals infected with COVID-19 with as few tests as possible, under the premise that the sensitivity of tests is high enough. To achieve this goal, we propose an Adaptive Group Testing (AdaGT) method. By collecting information on the number of positive and negative samples that have been identified during the screening process, the AdaGT method can estimate the ratio of positive samples in real-time. Based on this ratio, the AdaGT algorithm adjusts its testing strategy adaptively between an individual testing strategy and a group testing strategy. The group size of the group testing strategy is carefully selected to guarantee that the sensitivity of each test is higher than a predetermined threshold and that this group contains at most one positive sample on average. Theoretical performance analysis on the AdaGT algorithm is provided and then validated in experiments. Experimental results also show that the AdaGT algorithm outperforms existing methods in terms of efficiency and sensitivity. Note to Practitioners—Real-time reverse transcription-polymerase chain reaction (rRT-PCR) tests provide scope for automation and are one of the most widely used laboratory methods for detecting the SARS-CoV-2 virus. This paper is motivated by the following challenges: (1) Many countries are experiencing an acute shortage of professionals and consumables for conducting rRT-PCR tests;(2) Group sizes of existing group testing methods against COVID-19 may not be optimal, which adversely impacts the efficiency of the screening of the SARS-CoV-2 virus;(3) Existing group testing methods do not consider the fact that the sensitivity of rRT-PCR tests usually decreases with the group size. The objective of this paper is to improve the efficiency and sensitivity of large-scale screening against COVID-19. For achieving this goal, we propose an Adaptive Group Testing (AdaGT) algorithm, which has the following advantages: (1) It can improve the efficiency for screening the SARS-CoV-2 virus, mainly by adaptively adjusting its testing strategy between an individual testing strategy and a group testing strategy based upon an estimated ratio of positive samples during the screening process;(2) It can guarantee a high sensitivity of the rRT-PCR tests by determining the group sizes of the group testing strategy based upon some constraints;(3) We derive an appropriate threshold for the estimated ratio of positive samples such that the AdaGT algorithm can achieve a minimum average number of rRT-PCR tests and can be directly employed in practical applications. [ FROM AUTHOR] Copyright of IEEE Transactions on Automation Science & Engineering is the property of IEEE and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Ludangshen Oral Liquid for Treatment of Convalescent COVID-19 Patients: A Randomized, Double-Blind, Placebo-Controlled Multicenter Trial (preprint)

Objective To explore the effect of Ludangshen Oral Liquid for treatment of convalescent patients with coronavirus disease 2019 (COVID-19) with randomized, double-blind, placebo-controlled multicenter method.Methods200 convalescent COVID-19 patients who had symptoms related to decreased digestive and respiratory function were randomly divided to either receive Ludangshen Oral Liquid or placebo for 2 weeks. The severity of clinical symptoms including fatigue, anorexia, abdominal distension, loose stools, and shortness of breath were assessed by visual analogue scale and observed at before and after treatment. The improvement and resolution rates of clinical symptoms were evaluated. Full analysis set (FAS) and per-protocol set (PPS) were used for statistical analyses. Adverse events were recorded during the study. Results8 patients did not complete the study. After 2 weeks of treatment, both FAS and PPS results showed that patients in Ludangshen group had significantly lower score of fatigue, anorexia, loose stools, and shortness of breath than placebo group (P < 0.05), while there was no significant difference in distention (P > 0.05). The improvement rate of fatigue, anorexia, distension, loose stools and shortness of breath were significantly higher in Ludangshen group (P < 0.05), as well as the resolution rates (P < 0.05) except for shortness of breath (P > 0.05). There were two cases of adverse events, with one nose bleeding in Ludangshen group and one headache in placebo group. ConclusionThe study suggested that two weeks of Ludangshen Oral Liquid treatment may have certain effects for convalescent COVID-19 patients on improving digestive and respiratory symptoms including fatigue, anorexia, loose stools and shortness of breath, which may be one of the choices for management of convalescent COVID-19 patients with digestive and respiratory symptoms.

Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2 (preprint)

IntroductionSince March of 2020, over 210 million SARS-CoV-2 cases have been reported and roughly five billion doses of a SARS-CoV-2 vaccine have been delivered. The rise of the more infectious delta variant has recently indicated the value of reinstating previously relaxed non-pharmacological and test-driven preventative measures. These efforts have been met with resistance, due, in part, to a lack of site-specific quantitative evidence which can justify their value. As vaccination rates continue to increase, a gap in knowledge exists regarding appropriate thresholds for escalation and de-escalation of COVID-19 preventative measures. MethodsWe conducted a series of simulation experiments, trialing the spread of SARS-CoV-2 virus in a hypothesized working environment that is subject to COVID-19 infections from the surrounding community. We established cohorts of individuals who would, in simulation, work together for a set period of time. With these cohorts, we tested the rates of workplace and community acquired infections based on applied isolation strategies, community infection rates (CIR), scales of testing, non-pharmaceutical interventions, variant predominances and testing strategies, vaccination coverages, and vaccination efficacies of the members included. Permuting through each combination of these variables, we estimated expected case counts for 33,462 unique workplace scenarios. ResultsWhen the CIR is 5 new confirmed cases per 100,000 or fewer, and at 50% of the workforce is vaccinated with a 95% efficacious vaccine, then testing daily with an antigen-based or PCR based test in only unvaccinated workers will result in less than one infection through 4,800 person weeks. When the community infection rate per 100,000 persons is less than or equal to 60, and the vaccination coverage of the workforce is 100% with 95% vaccine efficacy then no masking or routine testing + isolation strategies are needed to prevent workplace acquired infections regardless of variant predominance. Identifying and isolating workers with antigen-based SARS-CoV-2 testing methods results in the same or fewer workplace acquired infections than testing with polymerase chain reaction (PCR) methods. ConclusionsSpecific scenarios exist in which preventative measures taken to prevent SARS-CoV-2 spread, including masking, and testing plus isolation strategies can safely be relaxed. Further, efficacious testing with quarantine strategies exist for implementation in only unvaccinated cohorts in a workplace. Due to shorter turnaround time, antigen-based testing with lower sensitivity is more effective than PCR testing with higher sensitivities in comparable testing strategies. The general reference interactive heatmap we provide can be used for site specific, immediate, parameter-based case count predictions to inform appropriate institutional policy making.

Optimal test-assisted quarantine strategies for COVID-19 (preprint)

Background: Until herd immunity occurs for COVID-19, quarantine will remain a pillar for disease mitigation. A 14-day quarantine, although widely recommended for self-quarantine after potential infections and mandated by many government agencies can be physically and mentally stressful for those under quarantine and leads to lost productivity. Testing during quarantine is currently implemented by businesses and governments as a promising method to shorten the duration of quarantine. However, to our knowledge, no study has been performed to evaluate the performance of test-assisted quarantines and to identify the most effective choices of testing schedule. Methods: Based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and sensitivity of various SARS-CoV-2 tests, we performed extensive simulations to evaluate the performance of quarantine strategies with one or more tests administered during quarantine. Sensitivity analyses were performed to evaluate the impact of model assumptions on the selection of optimal strategies. Findings: We found that SARS-CoV-2 testing can effectively reduce the length of quarantine without compromising safety. Whereas a single RT-PCR test performed before the end of quarantine can reduce the duration of quarantine to 10 days, two tests can further reduce the duration to 8-days and three tests with a highly sensitive RT-PCR test can justify a 6-day quarantine. More strategic testing schedules and one more day of quarantine are needed if tests are administrated with a less sensitive but more cost-effective antigen test. Interpretation: Testing during quarantine could substantially reduce the length of quarantine, reducing the physical and mental stress caused by long quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, testing-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.

Viral shedding and immunological features of children COVID-19 patients (preprint)

Abstract Background SARS-CoV-2 could infect people at all ages, and the viral shedding and immunological features of children COVID-19 patients were analyzed. Methods Epidemiological information and clinical data were collected from 35 children patients. Viral RNAs in respiratory and fecal samples were detected. Plasma of 11 patients were collected and measured for 48 cytokines. Results 40% (14/35) of the children COVID-19 patients showed asymptomatic infections, while pneumonia shown by CT scan occurred in most of the cases (32/35, 91.43%). Elevated LDH, AST, CRP, neutropenia, leukopenia, lymphopenia and thrombocytopenia occurred in some cases, and CD4 and CD8 counts were normal. A total of 22 cytokines were significantly higher than the healthy control, and IP-10, IFN-2 of them in children were significantly lower than the adult patients. Meanwhile, MCP-3, HGF, MIP-1, and IL-1ra were similar or lower than healthy control, while significantly lower than adult patients. Viral RNAs were detected as early as the first day after illness onset (d.a.o) in both the respiratory and fecal samples. Viral RNAs decreased as the disease progression and mostly became negative in respiratory samples within 18 d.a.o, while maintained relatively stable during the disease progression and still detectable in some cases during 36~42 d.a.o. Conclusion COVID-19 in children was mild, and asymptomatic infection was common. Immune responses were relatively normal in children COVID-19 patients. Cytokine storm also occurred in children patients, while much weaker than adult patients. Positive rate of viral RNAs in fecal samples was high, and profile of viral shedding were different between respiratory and gastrointestinal tract.

The Asymptomatic Infection of COVID-19 Risen in Imported Population in Shenzhen, China (preprint)

Background As of July 24 2020, the global reported number of COVID-19 cases was > 15.4 millions, with over 640,000 deaths. The present study aimed to carry out an epidemiological analysis of confirmed cases and asymptomatic infections in Shenzhen City to provide scientific reference for the prevention and control of COVID-19.Methods The epidemiological information of the 462 confirmed cases and 45 asymptomatic infections from January 19th to June 30th was collected in Shenzhen City, Southern China, and a descriptive analysis was performed.Results A total of 462 confirmed COVID-19 cases from January 19 to April 30, 2020 were reported in Shenzhen City, including 423 domestic cases (91.56%) and 39 imported cases (8.44%) who came back from other countries. Among domestic cases, the majority were cases imported from Hubei Province (n = 312, 67.53%), followed by local ones (n = 69, 14.94%). During the same period, a total of 45 asymptomatic infections were reported in Shenzhen City, including 31 local ones (68.89%) and 14 imported from abroad (31.11%). The proportion of asymptomatic infections in Shenzhen City was increasing over time (Z = 13.1888, P < 0.0001). The total number of local asymptomatic infections in Shenzhen City exceeded as the same pattern as that in other provinces (χ2 = 118.830, P < 0.0001). The proportion of asymptomatic infections among cases imported from abroad was higher than that of the same in domestic cases (χ2 = 22.5121, P < 0.0001, OR = 4.8983, 95%: 2.4052, 9.9756). No statistical significance was noted in the proportions of asymptomatic infections among imported cases from different countries (χ2 = 7.7202, P = 0.6561).Conclusions The majority of COVID-19 cases in Shenzhen City were imported cases who came back from Hubei Province in the early stage (before 1st March, 2020) and from abroad in the later stage (after 1st April, 2020). Scientific and effective prevention and control measures have resulted in only a few local infections in Shenzhen City. Asymptomatic infections accounted for an increasing proportion among cases imported from abroad, indicating that the prevention measures carried out in Shenzhen City did avoid the import of infected cases. Improving the detection capability to identify asymptomatic infections as early as possible will be of significance for the control outbreak of COVID-19.

Viral shedding and immunological features of children COVID-19 patients (preprint)

Background SARS-CoV-2 could infect people at all ages, and the viral shedding and immunological features of children COVID-19 patients were analyzed.Methods Epidemiological information and clinical data were collected from 35 children patients. Viral RNAs in respiratory and fecal samples were detected. Plasma of 11 patients were collected and measured for 48 cytokines.Results 40% (14/35) of the children COVID-19 patients showed asymptomatic infections, while pneumonia shown by CT scan occurred in most of the cases (32/35, 91.43%). Elevated LDH, AST, CRP, neutropenia, leukopenia, lymphopenia and thrombocytopenia occurred in some cases, and CD4 and CD8 counts were normal. A total of 22 cytokines were significantly higher than the healthy control, and IP-10, IFN-α2 of them in children were significantly lower than the adult patients. Meanwhile, MCP-3, HGF, MIP-1α, and IL-1ra were similar or lower than healthy control, while significantly lower than adult patients. Viral RNAs were detected as early as the first day after illness onset (d.a.o) in both the respiratory and fecal samples. Viral RNAs decreased as the disease progression and mostly became negative in respiratory samples within 18 d.a.o, while maintained relatively stable during the disease progression and still detectable in some cases during 36~42 d.a.o. Conclusion COVID-19 in children was mild, and asymptomatic infection was common. Immune responses were relatively normal in children COVID-19 patients. Cytokine storm also occurred in children patients, while much weaker than adult patients. Positive rate of viral RNAs in fecal samples was high, and profile of viral shedding were different between respiratory and gastrointestinal tract.

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

High Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection. One Sentence SummaryCRISPR-Cas12a-based COVID-19 diagnosis.

Comparative Evaluation of Six Molecular Assays based on RT-PCR and Cross Primer Isothermal Amplification for SARS-CoV-2 RNA Detection (preprint)

Background: SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B–F) to evaluate their sensitivity, specificity, predictive values and accuracy. Methods: Fifty-two clinical samples were used including throat swabs (n=30), nasal swabs (n=7), nasopharyngeal swabs (n=7) and sputum specimens (n=8), comprising confirmed (n=26) and negative cases (n=26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits’ evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. Results: For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa≥0.75); Kits D and E were less congruent (0.4≤Kappa<0.75). Differences between all kits were statistically significant (P<0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. Conclusions: This is the first comparative study to evaluate CPA and RT-qPCR kits’ specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic. Keywords: SARS-CoV-2; COVID-19; nucleic acid detection; real-time reverse transcriptase PCR (RT-qPCR); cross-priming isothermal amplification (CPA)

Population simulations of COVID-19 outbreaks provide tools for risk assessment and continuity planning (preprint)

Essential industrial sectors, healthcare systems, and government agencies must continue operations despite the risk of COVID-19 infection. They need tools to assess risks associated with operations, so they can devise emergency plans. We developed a population-based simulator to study COVID-19 outbreaks in enclosed environments and evaluate the effectiveness of preventative measures and action plans, such as pre-dispatch quarantine and removal of symptomatic cases. AvailabilityThe simulation tool is publicly available at http://github.com/ictr/covid19-outbreak-simulator and is free for non-commercial use.

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China (preprint)

Highlights: 1) 1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020; 2) Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples. 3) Genomic analyses reveal multiple virus importations into Guangdong Province, resulting in genetically distinct clusters that require careful interpretation. 4) Large-scale epidemiological surveillance and intervention measures were effective in interrupting community transmission in Guangdong Summary: COVID-19 is caused by the SARS-CoV-2 coronavirus and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain due to low virus genetic variation early in the pandemic. Our results illustrate how the timing, size and duration of putative local transmission chains were constrained by national travel restrictions and by the province's large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required as the number of cases imported from other countries is increasing.

Clinical characteristics of a group of deaths with COVID-19 pneumonia in Wuhan, China: retrospective case series (preprint)

Background: With the widespread outbreak of novel coronavirus diseases 2019(COVID-19), more and more death cases were reported, however, limited data are available for the patients who died. We aimed to explore the clinial characteristics of deaths with COVID-19 pneumonia Methods: We abstracted and analyzed epidemiological, demographic, clinical, and laboratory data from 83 death cases with COVID-19 pneumonia in East hospital of Wuhan university Renmin hospital,between January 26, 2020, and February 28, 2020.Results: Of the 83 deaths, none was the medical staff. The mean age was 71.8 years (SD 13.2; range, 34-97 years) and 53(63.9%) were male. The median from onset to admission was 10 days (IQR 7-14: range, 2-43 days), to death was 17days (IQR 14-21: range, 6-54 days). Most deaths (66[80%]) had underlying comorbid diseases, the most of which was hypertension [47(57%)]. The main initial symptoms of these 83 deaths were shortness of breath(98.8%), fever(94%) and myalgia or fatigue(90.4%). Laboratory analyses showed the lymphocytopenia in 69(83%) deaths, hypoalbuminemia in 77(93%) deaths, the elevation of lactate dehydrogenase in 79(95%) deaths, procalcitonin in 69(83%) deaths and C-reactive protein in 79(95%) deaths. All 83 patients received antiviral treatment, 81(97.6%) deaths received antibiotic therapy, and 54(65.1%) deaths received glucocorticoid therapy and 20(24.1%) patients received invasive mechanical ventilation.Conclusion: Most of the deaths with COVID-19 pneumonia were elderly patients with underlying comorbid diseases, especially those over 70 years of age. The time of death was mostly 15-21 days after the onset of the disease. More care should be given to the elderly in the further prevention and control strategies of COVID-19.