Results of nanopore sequencing of SARS-CoV-2 isolates of over a year

Background: Starting in January 2021 we established fast genetic sequencing of the SARS-CoV2 virus genome using the Nanopore sequencing technology. Up to now we analyzed more than 400 virus samples including all of the so called different Variants of Concern (VOC) emerging in Germany. Method(s): We established a method to sequence the whole SARS-CoV-2 genome by Nanopore sequencing using previously taken nasopharyngeal swabs (already used for SARS-CoV-2 PCR testing) as viral RNA source. The whole analysis pipeline from RNA-isolation to virus variant classification and result report can be conducted within 2-3 working days. The method is highly scalable. Result(s): We analyzed more than 400 SARS-CoV2 viral isolates from 2021 to the present day. We observed, that most Variants of Concern (VOC) (Alpha, Delta, or Omicron) locally take over all infection events within only one week. While 50-70% of the Alpha and Delta variant isolates show besides the variant defining mutations additional mutations in the S gene, additional mutations in the S gene in Omicron were seen rarely. Also we could see that the Omicron variants nearly had no mutations in the ORF3, and ORF6-8 genes, while mutations in Alpha and Delta were frequent. Conclusion(s): We are able to accurately identify different SARS-CoV-2 variants and detect potential new ones in a cost-efficient and fast way even for low sample numbers. Mutational analysis of the different virus isolates show differences in mutation frequency and localization maybe indicating correlations between mutation localization and disease process.

Using country of origin data to improve hepatitis b infection screening at regional family health centers

Background: Hepatitis B viral (HBV) infection is associated with significant morbidity and mortality. In endemic regions, HBV transmission is most commonly vertical (mother-to-child) with affected persons frequently asymptomatic. Screening is an important method for detection of HBV infection, which is essential for disease monitoring and treatment to prevent cirrhosis, liver failure, and hepatocellular carcinoma. Unfortunately, HBV screening is suboptimal and hindered by lack of provider awareness regarding patient country of origin. To improve HBV detection rates, we embarked on a quality improvement (QI) project at regional family health centers serving high-risk refugee populations. Baseline data demonstrated that 270 patients/week were being screened for Hepatitis B. Our smart aim was to improve the weekly number of patients undergoing HBV screening by 20% over the 2-year project. Methods: Using process mapping and failure mode and effects analysis, we constructed a key driver diagram. Identified interventions included: improving provider awareness regarding the risk factors for HBV infection (particularly country of origin) and how to perform HBV screening via didactic sessions and flyers in the clinic work rooms, and electronic health record (EHR)-enabled clinical pathways to capture country of origin data and identify persons from HBV-endemic regions for screening. Our primary outcome was number of patients undergoing HBV screenings per week. We used Microsoft Excel and QI Macros to develop statistical process control charts to examine changes in measures over time and used established rules for interpretation of control charts. Results: Over the project, 4 statistical process control chart shifts occurred. We met our goal to increase HBV screening by 20% within 7 months of starting the project (Figure 1). One notable setback occurred with the COVID-19 pandemic and significant but temporary reduction in healthcare services, but we were nevertheless able to re-achieve our aim by the end of the project period. Conclusion: Using QI methodology, we increased HBV screening by 20% at regional family health centers serving high-risk populations. Substantial improvements occurred after provider education sessions and implementation of EHR country of origin screening. This project shows that, with provider education and EHR-supported functionalities, improved HBV screening can be a feasible goal for health centers serving high-risk populations.

Quantification of exhaled particles for the identification of airborne infection risks in SARS-CoV2 and assessment of protective measures

Research is being conducted to assess and reduce the risk of infection by viruses transmitted via aerosols in enclosed spaces. This includes the development of simulation-based methods requiring the input of exhaled droplet characteristics. Though a number of studies are available for different respiratory activities, there is a lack in data regarding the assessment of the complete size spectrum relevant for aerosol transmission as well as on aerosol release data during realistic use of masks. Therefore a new set-up has been established allowing for the quantitative collection and analysis of respiratory aerosols over a wide size range from 0.1 - ∼ 80 μm under realistic conditions as well as under use of masks. Exhaled particle flux, size distribution and breathing patterns are determined for normal tidal breathing, speaking, coughing and singing in healthy volunteers (n=30) by means of two laser particle spectrometers (PMT Lasair III-110, Lighthouse Boulder Counter). This allows for a quantitative assessment of the particles relevant of the airborne transmission and the determination of the efficacy of medicinal and community masks regarding particle retention under realistic conditions. Based on these data and in combination with exposure simulations, the relevance and efficacy of active protective measures (masks, mouth-nose cover) and passive protective measures (ventilation, air disinfection) can be derived and classified, especially for sensitive areas such as healthcare.