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.

Development of Equine Polyclonal Antibodies as a Broad-Spectrum Therapy Against SARS-CoV-2 Variants (preprint)

The Coronavirus disease 19 (COVID-19) pandemic has accumulated over 550 million confirmed cases and more than 6.34 million deaths worldwide. Although vaccinations has largely protected the population through the last two years, the effect of vaccination has been increasingly challenged by the emerging SARS-CoV-2 variants. Although several therapeutics including both monoclonal antibodies and small molecule drugs have been used clinically, high cost, viral escape mutations, and potential side effects have reduced their efficacy. There is an urgent need to develop a low cost treatment with wide-spectrum effect against the novel variants of SARS-CoV-2. Here we report a product of equine polyclonal antibodies that showed potential broad spectrum neutralization effect against the major variants of SARS-CoV-2. The equine polyclonal antibodies were generated by horse immunization with the receptor binding domain (RBD) of SARS-CoV-2 spike protein and purified from equine serum. A high binding affinity between the generated equine antibodies and the RBD was observed. Although designed against the RBD of the early wild type strain sequenced in 2020, the equine antibodies also showed a highly efficient neutralization capacity against the major variants of SARS-CoV-2, including the recent BA.2 Omicron variant (IC50 =1.867g/ml) in viral neutralization assay in Vero E6 cells using live virus cultured. The broad-spectrum neutralization capacity of the equine antibodies was further confirmed using pseudovirus neutralization assay covering the major SARS-CoV-2 variants including wild type, alpha, beta, delta, and omicron, showing effective neutralization against all the tested strains. Ex vivo reconstructed human respiratory organoids representing nasal, bronchial, and lung epitheliums were employed to test the treatment efficacy of the equine antibodies. Antibody treatment protected the human nasal, bronchial, and lung epithelial organoids against infection of the novel SARS-CoV-2 variants challenging public health, the Delta and Omicron BA.2 isolates, by reducing >95% of the viral load. The equine antibodies were further tested for potential side effects in a mouse model by inhalation and no significant pathological feature was observed. Equine antibodies, as a mature medical product, have been widely applied in the treatment of infectious diseases for more than a century, which limits the potential side effects and are capable of large scale production at a low cost. A cost-effective, wide-spectrum equine antibody therapy effective against the major SARS-CoV-2 variants can contribute as an affordable therapy to cover a large portion of the world population, and thus potentially reduce the transmission and mutation of SARS-CoV-2.

Insights into the practical effectiveness of RT-PCR testing for SARS-CoV-2 from serologic data, a cohort study (preprint)

Background: Virologic detection of SARS-CoV-2 through Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) has limitations for surveillance. Serologic tests can be an important complementary approach. Objective: Assess the practical performance of RT-PCR based surveillance protocols, and the extent of undetected SARS-CoV-2 transmission in Shenzhen, China. Design: Cohort study nested in a public health response. Setting: Shenzhen, China; January-May 2020. Participants: 880 PCR-negative close-contacts of confirmed COVID-19 cases and 400 residents without known exposure (main analysis). Fifty-seven PCR-positive case contacts (timing analysis). Measurements: Virological testing by RT-PCR. Measurement of anti-SARS-CoV-2 antibodies in PCR-negative contacts 2-15 weeks after initial testing using total Ab ELISA. Rates of undetected infection, performance of RT-PCR over the course of infection, and characteristics of seropositive but PCR-negative individuals were assessed. Results: The adjusted seropositivity rate for total Ab among 880 PCR-negative close-contacts was 4.1% (95%CI, 2.9% to 5.7%), significantly higher than among residents without known exposure to cases (0.0%, 95%CI, 0.0% to 1.0%). PCR-positive cases were 8.0 times (RR; 95% CI, 5.3 to 12.7) more likely to report symptoms than the PCR-negative individuals who were seropositive, but otherwise similar. RT-PCR missed 36% (95%CI, 28% to 44%) of infected close-contacts, and false negative rates appear to be highly dependent on stage of infection. Limitations: No serological data were available on PCR-positive cases. Sample size was limited, and only 20% of PCR-negative contacts met inclusion criteria. Conclusion: Even rigorous RT-PCR testing protocols may miss a significant proportion of infections, perhaps in part due to difficulties timing testing of asymptomatics for optimal sensitivity. Surveillance and control protocols relying on RT-PCR were, nevertheless, able to contain community spread in Shenzhen.

Study on the COVID-19 infection status, prevention and control strategies among entry people in Shenzhen (preprint)

Background The overseas COVID-19 confirmed cases continue to rise for months, while people overseas prefer to return China at present. It is risky to have a large number of imported cases which may cause a relapse of COVID-19 outbreak. In order to prevent imported infection, Shenzhen government has implemented the closed-loop management strategy by taking nucleic acid testing (NAT) for severe acute respiratory syndromes coronavirus 2 (SARS-CoV-2) and requiring14-days medical observation for individuals with overseas tour history (Hong Kong, Macao, Taiwan province and other countries) within 14 days. Our study aim to describe the status of COVID-19 infection among entry people in Shenzhen, and evaluate the effect of closed-loop management strategy.Methods We made a descriptive study and risk analyze by the entry time, reported time, local confirmed cases in origin countries. The NAT were completed in Shenzhen center for disease control and prevention (CDC), ten district-level CDCs, as well as fever clinics.Results A total of 86,844 people overseas entered Shenzhen from January 1 to April 18, 2020, there were 39 imported cases and 293 closed contacts. The infection rate of entry people was 4.49‰ (95% CI: 3.26‰ − 6.05‰). 14 imported cases (35.9%) came from the UK, 9 (23.08%) came from the US. Entry people from the US since Mar 9 or from the UK since Mar 13 are the high-risk population. As of July 17, there have been no new confirmed cases in Shenzhen for 153 days, and the number of confirmed case, close contact, and asymptomatic case are 0. So the closed-loop management is effective to prevent imported infection and control domestic relapse. The distribution of entry time and report time for imported cases overseas was similar. So it is important to take closed-loop management at the port.Conclusions The risk of imported infection from the US and UK were higher that other countries and regions in Shenzhen. The closed-loop management is effective to prevent imported infection and control domestic relapse. Every country is closely connected under the background of globalization. In order to control COVID-19 outbreak, we need the collaboration and cooperation at the global, national, and subnational levels to prevent, detect, and respond effectively.

Study on the COVID-19 infection status, prevention and control strategies among entry people in Shenzhen (preprint)

Background The COVID-19 confirmed cases overseas continue to rise for months, while people overseas prefer to return at present. It is risky to have a large number of infected imported cases which may cause COVID-19 spread to China and even lead to outbreak again. In order to prevent imported infection, Shenzhen implemented the losed-loop management strategy by taking nucleic acid testing (NAT) for severe acute respiratory syndromes coronavirus 2 (SARS-CoV-2) and medical observation for 14 days among individuals who have epidemic history (Hong Kong, Macao, Taiwan province and other countries) within 14 days. Our study described the status of COVID-19 infection among entry people in Shenzhen, and also evaluated the effect of closed-loop management strategy.Methods A total of 86,844 people overseas entered Shenzhen from January 1 to April 18, 2020, and there were 39 imported cases. We made a descriptive study by analyzing the entry time, reported time, local confirmed cases in origin countries, and the number of entry people from abroad. The NAT were completed in Shenzhen center for disease control and prevention (CDC), ten district-level CDCs, as well as fever clinics.Results The infection rate of entry people was 4.49‰ (95% CI: 3.26‰ − 6.05‰). Most of the entry people or imported cases have Chinese nationality. The number of entry people and imported cases in Nanshan and Futian districts were larger than others. 15.73% of the entry people came from the US, and 12.67% came from the UK. 14 imported cases (35.9%) came from the UK, 9 (23.08%) came from the US. The imported risks from the US and UK in Shenzhen were higher than other countries or regions. According to the 14-days’ incubation period and the number of entry people, individuals from the US since Mar 9 were the high-risk population. Accordingly, entry people from the UK since Mar 13 were the high-risk population. It is important to evaluate the imported risk by analyzing local confirmed cases status in origin countries or regions and the number of entry people from these countries or regions to Shenzhen. The distribution of entry time and report time for imported cases in Shenzhen were similar. So it is important to prevent and control COVID-19 imported infection by taking NAT and medical observation at port.Conclusions It is effective to implement closed-loop management strategy for individuals who have epidemic history (Hong Kong, Macao, Taiwan province and other countries) within 14 days. In order to control COVID-19 outbreak, we need the collaboration and cooperation at the global, national, and subnational levels to prevent, detect, and respond effectively.

Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study (preprint)

SummaryO_ST_ABSBackgroundC_ST_ABSManaging discharged COVID-19 (DC) patients with recurrent positive (RP) SARS-CoV-2 RNA test results is challenging. We aimed to comprehensively characterize the viral RNA level and serum antibody responses in RP-DC patients and evaluate their viral transmission risk. MethodsA population-based observational cohort study was performed on 479 DC patients discharged from February 1 to May 5, 2020 in Shenzhen, China. We conducted RT-qPCR, antibody assays, neutralisation assays, virus isolation, whole genome sequencing (WGS), and epidemiological investigation of close contacts. FindingsOf 479 DC patients, the 93 (19%) RP individuals, including 36 with multiple RP results, were characterised by young age (median age: 34 years, 95% confidence interval [CI]: 29-38 years). The median discharge-to-RP length was 8 days (95% CI: 7-14 days; maximum: 90 days). After readmission, RP-DC patients exhibited mild (28%) or absent (72%) symptoms, with no disease progression. The viral RNA level in RP-DC patients ranged from 1{middle dot}9-5{middle dot}7 log10 copies/mL (median: 3{middle dot}2, 95% CI: 3{middle dot}1-3{middle dot}5). At RP detection, the IgM, IgG, IgA, total antibody, and neutralising antibody (NAb) seropositivity rates in RP-DC patients were 38% (18/48), 98% (47/48), 63% (30/48), 100% (48/48), and 91% (39/43), respectively. Regarding antibody levels, there was no significant difference between RP-DC and non-RP-DC patients. The antibody level remained constant in RP-DC patients pre- and post-RP detection. Virus isolation of nine representative specimens returned negative results. WGS of six specimens yielded only genomic fragments. No clinical symptoms were exhibited by 96 close contacts of 23 RP-DC patients; their viral RNA (96/96) and antibody (20/20) test results were negative. After full recovery, 60% of patients (n=162, 78 no longer RP RP-DC and 84 non-RP-DC) had NAb titres of [≥]1:32. InterpretationRP may occur in DC patients following intermittent and non-stable excretion of low viral RNA levels. RP-DC patients pose a low risk of transmitting SARS-CoV-2. An NAb titre of [≥] 1:32 may provide a reference indicator for evaluating humoral responses in COVID-19 vaccine clinical trials. FundingSanming Project of Medicine in Shenzhen, China National Science and Technology Major Projects Foundation, Special Foundation of Science and Technology Innovation Strategy of Guangdong Province of China, and Shenzhen Committee of Scientific and Technical Innovation grants.

Effects of home quarantine for COVID-19 community control in Shenzhen, China, 2020 (preprint)

Background: Shenzhen implement classification management to prevent and control coronavirus disease 2019 (COVID-19) outbreak. Individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms were instructed to take home quarantine for 14 days and nucleic acid testing (NAT) for SARS-CoV-2. We described the infection status of the home-quarantined individuals, and effects of community control strategies in the three incubations after Wuhan closure in Shenzhen.Methods: This was a descriptive research, the sample size was 2,004 individuals based on multistage sampling during the pre-investigation. And the formal investigation expanded the sample size to 57,012 individuals based on pre-investigation. A single throat swab was collected from each individual for nucleic acid testing (NAT) by reverse transcription-polymerase chain reaction (RT-PCR). NAT was performed by a third-party institution. We collected information related to demographics, disease history, travel history, and personal protective measures before home quarantine, and monitored close-contact histories using the We Chat questionnaire.Results: The total infection rate of home-quarantined individuals was 0.12‰ (95% CI: 0.05‰–0.24‰) out of the total sample size of 59,016. The detection period for seven confirmed cases was primarily concentrated between February 8 and 18, 2020, which was during the second incubation period after Wuhan's closure. The home quarantined individuals with epidemic histories (came from Hubei and any other affected regions) were considered the high risk population during the first two incubations after Wuhan’s closure. No positive cases were detected from February 25 to March 5(the third incubation after Wuhan’s closure). The number of newly-confirmed cases per day was 0 for eight consecutive days from February 22 to 29 in Shenzhen.Conclusions: The community control strategies for home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms to take the NAT in the first two incubations is effective to control COVID-19. But it is not advocating for home-quarantined person to take the NAT since the third incubation.

Household transmission of COVID-19, Shenzhen, January-February 2020 (preprint)

Coronavirus disease 2019 has led to more than three million cases globally. Since the first family cluster of COVID-19 cases identified in Shenzhen in early January, most of the local transmission occurred within household contacts. Identifying the factors associated with household transmission is of great importance to guide preventive measures.

Evolving Epidemiology and Effect of Non-pharmaceutical Interventions on the Epidemic of Coronavirus Disease 2019 in Shenzhen, China (preprint)

Previous studies have demonstrated the characteristics of patients with 2019 novel coronavirus disease (COVID-19). However, the effect of non-pharmaceutical interventions on the epidemic in Shenzhen, China remains unknown. Individual data of 417 cases were extracted from the epidemiological investigations and the National Infectious Disease Information System between January 1, 2020 and February 29, 2020. On the basis of important interventions, the epidemic was divided into four periods (January 1-15, January 16-22, January 23-February 5 and after February 6). We used a susceptible-exposed-infectious-asymptomatic-recovered model to evaluate the effect of interventions. Results suggested that about 53.7% were imported from Wuhan. The median age was 47 years and 52.8% were women. Severity risk increased with age and associated with male and co-existing disorders. The attack rate peaked in the third period and drastically decreased afterwards across sex, age groups and geographic regions. Children younger than 5 years showed a higher attack rate than those aged of 6~19. The effective reproductive number decreased from 1.44 to 0.05 after the highest level emergency response since January 23. Overall, the non-pharmaceutical interventions have effectively mitigated the COVID-19 outbreak in Shenzhen, China. These findings may facilitate the introduction of public health policies in other countries and regions.

Research on COVID-19 prevention and control strategies, and the effect of home quarantine in Shenzhen, China, 2020 (preprint)

AbstractBackground: To study the prevention and control strategies of coronavirus disease 2019 (COVID-19), and to analyze the infection of the home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms in the three incubations after Wuhan closure in Shenzhen.Methods: The sample size was 2,004 individuals based on multistage sampling during the pre-investigation. Based on the results of the pre-investigation, the formal investigation expanded the sample size to 57,012 individuals. A single throat swab was collected from each individual for nucleic acid testing (NAT) by reverse transcription-polymerase chain reaction (RT-PCR). NAT was performed by a third-party institution, BGI. We collected information related to demographics, disease history, travel history, and personal protective measures before home quarantine, and monitored close-contact histories using the We Chat questionnaire.Results: The total infection rate of home-quarantined individuals was 0.11% (95% CI: 0.05%–0.24%) out of the total sample size of 59,016. The detection period for seven confirmed cases was primarily concentrated between February 8 and 18, 2020, which was during the second incubation period after Wuhan's closure. The home quarantined individuals with epidemic histories (came from Hubei and any other affected regions) were considered the high risk population during the first two incubations after Wuhan’s closure. No positive cases were detected from February 25 to present (the third incubation after Wuhan’s closure). The number of newly-confirmed cases per day was 0 for 8 days from February 22 to 29 in Shenzhen. Thus, the strategies of prevention and control were effective.Conclusions: The strategies and policies were effective for the prevention and control of COVID-19. Additionally, the strategy of implementing NAT during the first two incubations for home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms, facilitated early detection, early reporting, early diagnosis, early quarantining, and early treatment. However, our findings do not support NAT for home quarantined persons during the third incubation after Wuhan’s closure to present.

Epidemiological and clinical characteristics of COVID-19 in Shenzhen, the largest migrant city of China (preprint)

We conducted a retrospective study among 417 confirmed COVID-19 cases from Jan 1 to Feb 28, 2020 in Shenzhen, the largest migrant city of China, to identify the epidemiological and clinical features in settings of high population mobility. We estimated the median incubation time to be 5.0 days. 342 (82.0%) cases were imported, 161 (38.6%) cases were identified by surveillance, and 247 (59.2%) cases were reported from cluster events. The main symptoms on admission were fever and dry cough. Most patients (91.4%) had mild or moderate illnesses. Age of 50 years or older, breathing problems, diarrhea, and longer time between the first medical visit and admission were associated with higher level of clinical severity. Surveillance-identified cases were much less likely to progress to severe illness. Although the COVID-19 epidemic has been contained in Shenzhen, close monitoring and risk assessments are imperative for prevention and control of COVID-19 in future.

Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts (preprint)

Background Rapid spread of SARS-CoV-2 in Wuhan prompted heightened surveillance in Shenzhen and elsewhere in China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control. Methods The Shenzhen CDC identified 391 SARS-CoV-2 cases from January 14 to February 12, 2020 and 1286 close contacts. We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We estimate metrics of disease transmission and analyze factors influencing transmission risk. Findings Cases were older than the general population (mean age 45) and balanced between males (187) and females (204). Ninety-one percent had mild or moderate clinical severity at initial assessment. Three have died, 225 have recovered (median time to recovery is 21 days). Cases were isolated on average 4.6 days after developing symptoms; contact tracing reduced this by 1.9 days. Household contacts and those travelling with a case where at higher risk of infection (ORs 6 and 7) than other close contacts. The household secondary attack rate was 15%, and children were as likely to be infected as adults. The observed reproductive number was 0.4, with a mean serial interval of 6.3 days. Interpretation Our data on cases as well as their infected and uninfected close contacts provide key insights into SARS-CoV-2 epidemiology. This work shows that heightened surveillance and isolation, particularly contact tracing, reduces the time cases are infectious in the community, thereby reducing R. Its overall impact, however, is uncertain and highly dependent on the number of asymptomatic cases. We further show that children are at similar risk of infection as the general population, though less likely to have severe symptoms; hence should be considered in analyses of transmission and control.