Center for Pathogen Genomics and Microbial Evolution

SARS-CoV-2 Surveillance and Variant Tracking

Northwestern PIs: Egon A Ozer, MD, PhD; Judd F Hultquist, PhD

Early funding through the Dixon Family Foundation and the Northwestern University Clinical and Translational Sciences Institute supported the rapid establishment of SARS-CoV-2 sequencing within weeks of the first cases of COVID-19 diagnosed at Northwestern Memorial Hospital. This has led to ongoing genomic surveillance at Northwestern to perform tracking of emerging viral variants and study clinical impacts.

Surveillance and Transmission of SARS-CoV-2 Among Children in Chicago

Northwestern PIs: Larry K Kociolek, MD, MSCI

This project, led by researchers at Lurie Children’s Hospital and funded by the Walder Foundation, seeks to characterize and map potential SARS-CoV-2 transmissions among students, teachers, and school workers in classrooms where in-person instruction is occurring. It also tracks SARS-CoV-2 dynamics among pediatric infections in Chicago to study viral transmission and dynamics in children and adolescents.

The Global Threat of Antibiotic Resistance

Northwestern PIs: Mehreen Arshad, MBBS; Erica Hartmann PhD.

Infections caused by antibiotic-resistant bacteria are a growing threat around the world. This pilot study funded by the Northwestern Buffett Institute for Global Affairs seeks to develop an infrastructure to share clinical and pathogen genomic data as well as specimens from infections caused by antibiotic-resistant infections between institutions in the US and Pakistan. It also seeks to understand local and global factors influencing decision-making around antibiotic prescribing by healthcare providers.

Group A Streptococcus Molecular Epidemiology

Northwestern PIs: Ami Patel, MD, MPH; Judy Guzman-Cotrill, Robert Tanz, MD, Stan Shulman, MD

Infections with group A streptococci commonly cause can cause strep throat, but also severe invasive infections and post-infectious complications such as rheumatic fever. This CDC-supported project seeks to identify relationships between group A streptococci from across the United States and establish an active clinical and genomic surveillance network.

Role of HIV-1 Recombination in the Tissue Reservoir

Northwestern PIs: Richard T D'Aquila, MD; Ramon Lorenzo Redondo, PhD

This project through the Third Coast Center for AIDS Research (TC-CFAR) aims to develop a multidisciplinary experimental approach to study HIV-1 recombination levels in gastrointestinal tissue explant infection experiments. We plan to optimize this methodology to systematically and directly examine the mechanisms behind diversity preservation in infected tissues.

Phylodynamics and molecular epidemiology of SARS-CoV-2 in Nigeria

Northwestern PIs: Ramon Lorenzo Redondo, PhD

Supported by a Global Health Research Catalyzer Award, this study aims to study SARS-CoV-2 population dynamics in Nigeria in the framework of the current global pandemic to inform public-health responses. Additionally, it examines the population evolution and viral genes under selective pressure as potential therapeutic or immune targets.

Advanced molecular and network data combination to understand the HIV-1 epidemic among youth in Nigeria

Northwestern PIs: Babafemi O Taiwo, MBBS; Ramon Lorenzo Redondo, PhD

This project through the NICHD combines the use of social network and viral phylogenetic data to obtain the most complete picture of the HIV-1 epidemic in the young men who have sex with men (YMSM) population that Intensive Combination Approach to Rollback the Epidemic (iCARE) in Nigerian Adolescents is engaging in Nigeria.

Evolution of SARS-CoV-2 and Other Respiratory Viruses in Hospitalized Adults

Northwestern PIs: Michael G Ison, MD MS

This study aims to define the evolution of respiratory viruses including SARS-CoV-2, influenza, and RSV over time in isolates derived from hospital adults. Information about viral evolution over the course of respiratory infection combined with clinical data can provide insight into global evolutionary trends and host and viral responses and adaptations to infection.

Surveillance of antimicrobial-resistant Gram negative bacteria and fungi in a Pakistan health care system

Surveillance of antimicrobial-resistant Gram negative bacteria and fungi in a Pakistan health care system - CDC

Northwestern Faculty: PI Egon Ozer, MD, PhD

This project is focused on improving surveillance of infections with the antifungal-resistant yeast Candida auris in Pakistan through capacity-building for whole-genome sequencing and bioinformatic analysis.

SARS-CoV-2 surveillance and capacity building in Peru and Bolivia

Northwestern PIs: Egon A. Ozer, MD, PhD

Most countries in South America are underrepresented in global SARS-CoV-2 genomic surveillance efforts. In this project, we are establishing and enriching partnerships in Peru and Bolivia to fill critical gaps in global SARS-CoV-2 genomic surveillance infrastructure and build local capacity for pathogen genomics.

Antiviral resistance of HIV in Nigeria

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

In collaboration with researchers from the University of Ibadan, we are studying the emergence and circulation of drug-resistant HIV variants that could render therapy regimens inefficacious in drug experienced HIV patients from Nigeria. We are performing full genome deep-sequencing to analyze the presence of mutations both at the consensus and at minority levels in these patients to understand the effects of suboptimal HIV-1 therapy.

Pediatric SARS-CoV-2 surveillance in Massachusetts, Tennessee, and Illinois

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

In collaboration with Boston Children's Hospital and Vanderbilt University we are performing molecular surveillance of SARS-COV-2 in pediatric population around the country. The CPGME is performing whole genome sequencing and molecular evolution analysis to understand the viral population dynamics in children infected with SARS-CoV-2

Unraveling the Mechanisms of HIV Persistence and Rebound (P01 project)

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

By leveraging new insights and technologies, we are investigating the dynamics of the HIV reservoir at high resolution, including dissecting the role of little known, tissue resident cell targets of HIV infection of myeloid origins. CPGME is sequencing and analyzing viral reservoir intra-host dynamics using PT/CT-guided deep-sequencing approaches.

Viral and Host Dynamics during Respiratory Virus Co-Infection in Children

Northwestern PIs: Judd F Hultquist, PhD, Bria Marielle Coates, MD

This R01-funded collaboration between Northwestern University and Ann & Robert H. Lurie Children’s Hospital of Chicago investigates prevalence of and outcomes in cases of co-infection with SARS-CoV-2, influenza, RSV, or other respiratory viruses in children. The study also seeks to characterize mucosal immune responses to multiple viruses and viral evolution during co-infection.

Molecular Mechanisms of Antimicrobial Resistance in Pseudomonas aeruginosa

Northwestern PI: Egon Ozer, MD, PhD

This study aims to better understand how genetic variation impacts the development of resistance to antibiotics in the bacterial pathogen Pseudomonas aeruginosa. Using computational approaches and genome-wide mutation screens, better models for determining identifying antibiotic resistance for faster and more reliable diagnosis can be developed.

Evolution and Vaccine Resistance in Respiratory Syncytial Virus

Northwestern PIs: Judd F Hultquist, PhD, Ramon Lorenzo Redondo, PhD

Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with the greatest impact on infants, immunocompromised individuals, and older adults. This study investigates temporal and regional variations in RSV genetic diversity and their potential impacts on the virus’ susceptibility to vaccines and therapeutics.