Amazon Chicago COVID-19 Tracker

Northwestern Medicine scientists Ramon Lorenzo-Redondo and Dr. Egon Ozer recently visited the airport in Iquitos, a remote Peruvian city deep in the Amazon jungle accessible only by plane or riverboat. They wanted to meet clinicians and scientists who provide care to surrounding communities along the Amazon River.

The reason for the recent trip: Iquitos had a high incidence of COVID-19 at the start of the pandemic, and they wanted to understand how the relative isolation of the big city affected the spread of viral variants in the region. Peru also had the highest COVID-19 mortality rate during the entire pandemic, in particular due to the very high mortality observed during the first phases of the expansion of SARS-CoV-2.

The scientists’ travels across South America, which also included Lima, Peru, and Santa Cruz, Bolivia, are an effort by Robert J. Havey, MD, Institute for Global Health at Northwestern University to expand the global SARS-CoV-2 sequencing network in regions where reporting of viral genetic information is low or almost non-existent. They want to help build the capacity of South American scientists and public health experts to conduct local investigations.


Less than 2% of SARS-CoV-2 sequences come from South America

Lorenzo-Redondo and Ozer are part of a team at the Center for Pathogen Genomics and Microbial Evolution (CPGME), which is part of the Havey Institute for Global Health. The team has been studying the virus in Chicago and around the world since the pandemic began. Their team has already worked with collaborators in Africa – in the countries of Nigeria, Mali and Guinea – to sequence hundreds of COVID-19 specimens from undersampled regions.

“If you look at the global public repository of all SARS-CoV-2 sequences, less than 1% are from the African continent and less than 2% are from South America,” said Ozer, director of CPGME. “Compare that to North America or Europe where a large majority of footage is provided. This leads to huge disparities in knowledge of what is circulating in different parts of the globe.

Create a global collaboration of COVID-19 scientists

Scientists at Northwestern University in Lima, Peru (Source: Northwestern University)

The scientists met with doctors and researchers from hospitals in Peru and Bolivia to provide support for the study of SARS-CoV-2 variants in their regions. This includes shipping some samples to the United States for sequencing, but also providing equipment, supplies, and training to these South American institutions for scientists to track COVID-19 in their country.

The goal is to have a network of collaborations around the world so that scientists can work together and share their expertise and information to respond quickly to new developments in the SARS-CoV-2 pandemic and future outbreaks of emerging or re-emerging pathogens.

“The emergence of a new variant anywhere in the world puts us all at risk,” said Judd Hultquist, assistant professor of infectious disease medicine at Northwestern University Feinberg School of Medicine and associate director of CPGME. “Rapid monitoring internationally is essential so that we are ready when the next variant arises.”

How Omicron’s Early Warning in South Africa Helped the United States

An example of this well-functioning early warning system is the early detection of omicron in South Africa, even before omicron is detected in most countries.

“Because South Africa was sequencing in a timely manner, they were able to sound the alarm a full month before Chicago saw its first case of omicron,” Hultquist said.

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The emergence of a new variant anywhere in the world puts us all at risk. ”

Judd Hulquist
Assistant Professor of Medicine in Infectious Diseases, Northwestern University

This extra time was essential for scientists to learn more about the variant, the risks it posed, and to implement appropriate treatment strategies before it even arrived in the United States.

South African scientists found that many monoclonal antibodies (specific antibodies given to critically ill patients to bind to and neutralize viruses) currently used for COVID-19 patients were not effective for omicron. Thanks to this early warning, American doctors were able to treat patients with the most effective therapies.

The Northwest team is now recapping the history of the pandemic in Chicago since the first case of COVID-19 was detected in the city. “We will analyze clinical outcomes against variants and demographics,” said Lorenzo-Redondo, assistant professor of infectious disease medicine at Feinberg. “We want to bring all the data together to see the factors of the worst outcomes, the differences in variants and how the virus spreads.”

This study will inform other research projects initiated in global health circles.

The aim is to find similarities and differences on these drivers to help design effective prevention strategies of COVID-19, adapted globally and locally, as well as other viral pathogens in the near future.

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