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.

High-Specificity Targets in SARS-CoV-2 N Protein for Serological Antibody Detection (preprint)

Background The current coronavirus disease (COVID-19) pandemic has created a pressing need to diagnose and screen a large number of close contacts of confirmed and suspected cases. Numerous nucleic acid detection kits are being rapidly developed and approved for viral etiological diagnosis; however, these are limited by the number of false negatives produced in clinical practice. Therefore, there is an urgent need to establish serological detection methods to serve as supplementary diagnostics.Methods We (1) performed a conservation and specificity analysis of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein, which is the main target of serological diagnosis; (2) integrated various B-cell epitope prediction methods to obtain possible dominant epitope regions for the N protein; (3) applied ELISA to analyze differences in the serological antibody levels for different epitopes; and (4) identified N protein epitopes for IgG and IgM with high specificity.Results SARS-CoV-2 strains showed low mutation rates for the N protein, and the construction of a phylogeny was a good characterization of its molecular evolutionary lineage in relation to other coronaviruses. SARS-CoV-2 showed the closest genetic relationship with SARS-CoV, which showed multiple consecutive long conserved regions at the amino acid level, but differed substantially from other coronaviruses. Tests targeting the SARS-CoV-2 N protein produced strong positive results in SARS-CoV patients in recovery. Of the five epitope dominant regions, using N18-39 and N183-197 for IgG and IgM detection, respectively, can effectively overcome the limitations of cross-reactivity.Conclusions The patients infected with both SARS viruses may exhibit cross-reactivity when using the N protein for antibody detection. However, there are regions of the N protein that can be used for antibody detection and some of these regions showed good specificity even between SARS-CoV-2 and SARS-CoV, and the antibody levels detected were consistent with those detected by the complete N protein. These findings provide a basis for serological diagnosis of SARS-CoV-2 patients, and research ideas for developing vaccines.