Our group studies the genetic variation, evolution and molecular epidemiology of viruses, in particular HIV, enteroviruses and coronaviruses. We also work on pandemic preparedness in close collaboration with the Department of Clinical Microbiology at the Karolinska University Hospital, where I have a position as senior consultant (överläkare).
HIV
For many persons living with HIV the time of infection is not known. This is a major limitation for HIV prevention, epidemiology and research. In our group we develop novel, improved methods for estimation of time of HIV infection based on next-generation sequencing (NGS) and other biomarkers. Our prospective TIME-study of new patients diagnosed with HIV infection forms the basis for the project. The project organization consists of clinical partners at the HIV clinics in Stockholm and Gothenburg, theoretical experts at Los Alamos National Laboratory and Stockholm University and lab engineers and bioinformaticians in my group. The project has support from NIH, VR and ALF.
Based on biomarker analyses on samples from the study subjects we gain detailed new knowledge HIV incidence and the number of infected, but undiagnosed, patients in Sweden as well as the molecular epidemiology of HIV spread into and within Sweden. The project is clinically and scientifically relevant because undiagnosed HIV infected persons are a significant source of onward transmission and a crucial part of the HIV care continuum (i.e. the UNAIDS 95-95-95 target), but methods to accurately the proportion undiagnosed have been lacking.
Enteroviruses and coronaviruses
We also study the genetic evolution, spread and immunity of enteroviruses and coronaviruses. In particular, we study enterovirus D68 (EV-D68), which is an emerging pathogen that has caused large outbreaks where some cases have shown severe respiratory and neurological disease, including polio-like acute flaccid myelitis. We use NGS to sequence the entire genome of EV-D68 cases in Sweden and Europe.
Similarly, we study the genetic evolution, spread and immunity of SARS-CoV-2 and seasonal coronaviruses (229E, NL63, OC43, and HKU1) using data and samples from Clinical Microbiology and results from NGS.
Pandemic preparedness
Emerging SARS-CoV-2 variants of concern (VOCs) illustrate the urgent need for continuous large-scale molecular surveillance of pandemic threats. Our project is supported by the SciLifeLab Pandemic Laboratory Preparedness program. We build on established collaborations between KI, Clinical Microbiology and SciLifeLab, which provides access to samples, data and expertise at Sweden’s largest clinical microbiology laboratory, serving 20% of the Swedish population. In this context we are responsible for surveillance of SARS-CoV-2 variants in the Stockholm Region. We have established large-scale capacity sequencing of SARS-CoV-2 using NGS and have generated more than 30,000 whole genome sequences. As an example of outputs from the project, we have written a report to the Swedish Corona Commission on the early introduction and spread of SARS-CoV-2 in Sweden.
In a separate project we are establishing capacity for metagenomic discovery and characterization of new pandemic threats. We aim to focus on molecular surveillance of respiratory viruses.
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