Wastewater surveillance and an automated robot: effectively tracking SARS-CoV-2 transmission in the post-epidemic era.

Wastewater-based epidemiology (WBE) has exhibited great utility in the early and rapid identification of SARS-CoV-2. However, the efficacy of wastewater surveillance under China's previous strict epidemic prevention policy remains to be described. We collected the WBE data of wastewater treatment plants (WWTPs) in the Third People's Hospital of Shenzhen and several communities to determine the significant effectiveness of routine wastewater surveillance in monitoring the local spread of SARS-CoV-2 under tight containment of the epidemic. The results of 1 month of continuous wastewater surveillance showed that positive signals for SARS-CoV-2 RNA were detected in the wastewater samples, and a significant positive correlation was observed between the virus concentration and the number of daily cases. In addition, the community's domestic wastewater surveillance results were confirmed even 3 days before, or simultaneously with, the infected patient being confirmed as having the virus. Meanwhile, an automated sewage virus detection robot, ShenNong No.1 robot, was developed, showing a high degree of agreement with experimental data, offering the possibility of large-scale multi-point surveillance. Overall, our results illustrated the clear indicative role of wastewater surveillance in combating COVID-19 and provided a practical basis for rapidly expanding the feasibility and value of routine wastewater surveillance for future emerging infectious diseases.

Acquisition of T6SS Effector TseL Contributes to the Emerging of Novel Epidemic Strains of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an opportunistic pathogen with multiple strategies to interact with other microbes and host cells, gaining fitness in complicated infection sites. The contact-dependent type VI secretion system (T6SS) is one critical secretion apparatus involved in both interbacterial competition and pathogenesis. To date, only limited numbers of T6SS-effectors have been clearly characterized in P. aeruginosa laboratory strains, and the importance of T6SS diversity in the evolution of clinical P. aeruginosa remains unclear. Recently, we characterized a P. aeruginosa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. Bioinformatic analysis has revealed a putative type VI secretion system (T6SS) dependent lipase effector in LYSZa7, which is a homologue of TseL in Vibrio cholerae and is widely distributed in pathogens. We experimentally validated that this TseL homologue belongs to the Tle2, a subfamily of T6SS-lipase effectors; thereby, we name this effector TseL (TseLPA in this work). Further, we showed the lipase-dependent bacterial toxicity of TseLPA, which primarily targets bacterial periplasm. The toxicity of TseLPA can be neutralized by two immunity proteins, TsiP1 and TsiP2, which are encoded upstream of tseL. In addition, we proved this TseLPA contributes to bacterial pathogenesis by promoting bacterial internalization into host cells. Our study suggests that clinical bacterial strains employ a diversified group of T6SS effectors for interbacterial competition and might contribute to emerging of new epidemic clonal lineages. IMPORTANCE Pseudomonas aeruginosa is one predominant pathogen that causes hospital-acquired infections and is one of the commonest coinfecting bacteria in immunocompromised patients and chronic wounds. This bacterium harbors a diverse accessory genome with a high frequency of gene recombination, rendering its population highly heterogeneous. Numerous Pa lineages coexist in the biofilm, where successful epidemic clonal lineage or strain-specific type commonly acquires genes to increase its fitness over the other organisms. Current studies of Pa genomic diversity commonly focused on antibiotic resistant genes and novel phages, overlooking the contribution of type VI secretion system (T6SS). We characterized a Pa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. We report, in this study, a novel T6SS-lipase effector that is broadly distributed in Pa clinical isolates and other predominant pathogens. The study suggests that hospital transmission may raise the emergence of new epidemic clonal lineages with specified T6SS effectors.

Modeling the effect of age on quantiles of the incubation period distribution of COVID-19.

BACKGROUND: The novel coronavirus SARS-CoV-2 (coronavirus disease 2019, COVID-19) has caused serious consequences on many aspects of social life throughout the world since the first case of pneumonia with unknown etiology was identified in Wuhan, Hubei province in China in December 2019. Note that the incubation period distribution is key to the prevention and control efforts of COVID-19. This study aimed to investigate the conditional distribution of the incubation period of COVID-19 given the age of infected cases and estimate its corresponding quantiles from the information of 2172 confirmed cases from 29 provinces outside Hubei in China. METHODS: We collected data on the infection dates, onset dates, and ages of the confirmed cases through February 16th, 2020. All the data were downloaded from the official websites of the health commission. As the epidemic was still ongoing at the time we collected data, the observations subject to biased sampling. To address this issue, we developed a new maximum likelihood method, which enables us to comprehensively study the effect of age on the incubation period. RESULTS: Based on the collected data, we found that the conditional quantiles of the incubation period distribution of COVID-19 vary by age. In detail, the high conditional quantiles of people in the middle age group are shorter than those of others while the low quantiles did not show the same differences. We estimated that the 0.95-th quantile related to people in the age group 23 ∼55 is less than 15 days. CONCLUSIONS: Observing that the conditional quantiles vary across age, we may take more precise measures for people of different ages. For example, we may consider carrying out an age-dependent quarantine duration in practice, rather than a uniform 14-days quarantine period. Remarkably, we may need to extend the current quarantine duration for people aged 0 ∼22 and over 55 because the related 0.95-th quantiles are much greater than 14 days.

The Recommendations for the Management of Chinese Children With Epilepsy During the COVID-19 Outbreak.

The coronavirus disease (COVID-19) is the most severe public health problem facing the world currently. Social distancing and avoidance of unnecessary movements are preventive strategies that are being advocated to prevent the spread of the causative virus [severe acute respiratory syndrome (SARS)-CoV2]. It is known that epileptic children need long term treatments (antiepileptic drugs and/or immunosuppressive agents) as well as close follow up due to the nature of the disease. In addition, it is clear that epilepsy can concur with other chronic illnesses which can lower body immunity. As a result, epileptic children have high risk of acquiring this novel disease due to weak/immature immune system. Of concern, the management of children with epilepsy has become more challenging during this outbreak due to the prevention measures that are being taken. Although children with controlled seizures can be managed at home, it is challenging for pediatricians when it comes to cases with uncontrolled seizures/severe cases. To this end, we provide recommendations for the management of epileptic children at home, outpatient and inpatient settings.