The Medical Research Council (MRC) and the São Paulo Research Foundation (FAPESP) are funding research efforts at the CADDE in Brazil.
The researchers generated the first COVID-19 genomes from South America and tracked the in-country spread.
The Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) team comprises of Brazilian and UK scientists. The team sequenced the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Brazil within 48 hours of the first confirmed case in early March 2020.
The data was shared with other researchers through a global data-sharing platform for all influenza viruses and the coronavirus causing COVID-19.
Tracking the spread of the virus
Computer modelling helped the team track the global spread of the virus and showed two independent virus introductions to Brazil, from travel through Europe.
The CADDE scientists then tracked the virus’s spread into five regions and confirmed local transmission in six states by the end of March 2020.
Read more about the COVID-19 circulation in Brazil on the CADDE website.
Travel data helps estimate COVID-19 importations
The researchers at CADDE estimated the number of people entering the country with COVID-19 based on travel data. This estimation was called ‘COVID-19 importations’.
Brazil’s economy is heavily based on tourism, so COVID-19 importations were a major concern for the efforts in Brazil.
Between February and March 2019, Brazil received almost 1 million international passengers from around the world. São Paulo, the largest city in the country, was the final destination of nearly half the people arriving in Brazil, followed by Rio de Janeiro and Belo Horizonte.
In 2019, more than half of the international passengers started their journey in the US, followed by France and Italy.
Understanding this travel pattern was key to tracking and estimating the potential COVID-19 importations to Brazil during the 2020 pandemic.
Tracking the evolution of variants
SARS-CoV-2 was first detected in the city of Manaus in Brazil on 13 March 2020. By October 2020, three out of four residents in Manaus had already been infected with SARS-CoV-2. However, this did not lead to herd immunity, as just a few months later a second wave of the virus reinfected the population, causing even more illness and death.
CADDE scientists quickly mobilised and focused their resources on this second wave. They began analysing patient samples collected between November and December 2020.
CADDE scientists sequenced genomes from 184 patient samples collected from Manaus and identified the cause for this resurgence as a new variant, known as P.1.
Genomic sequencing of the P.1 variant showed that it had mutations that allowed it to reinfect previously infected people and was twice as transmissible as earlier variants. It was therefore designated as a ‘variant of concern’.
CADDE scientists detected the first P.1 variant case by genomic surveillance on 6 December 2020, and further evolutionary analysis from the team suggests that P.1 emerged, undetected, in mid-November 2020.
These findings highlight the importance of genomic surveillance and international data sharing for detecting and characterising emerging SARS-CoV-2 variants quickly. Genomic surveillance is essential for responding to pandemics by:
- providing a deeper understanding of how viruses mutate
- helping understand how transmission rates change
- highlighting the potential for more serious infections
- providing better strategies for tracking and treating emerging variants.
Lessons from Zika
The Zika epidemic in 2015 provided an opportunity to build and mobilise genomic surveillance capability in Brazil. Until then, genomic sequencing was mostly carried out in larger biomedical research institutions that used bulky sequencing machines, where samples had to be brought to the lab for analysis.
Funded by MRC and other partners, the ZiBRA (Zika in Brazil Real Time Analysis) project used a ‘mobile lab’ with genomic sequencing capability to analyse Zika virus samples to provide important epidemiological information about the spread of the disease.
These mobile labs were able to carry out genomic sequencing ‘in situ’, travelling to more remote parts of the country to analyse samples in the field, and getting a clearer picture of the epidemic.
Professor Nuno Faria said:
Working on Zika, and the ZiBRA project was really important in setting us up for our COVID-19 work. Although SARS-CoV-2 is a respiratory virus and Zika is a mosquito-borne virus, there were key similarities in our approach at a broader level.
Genomic data from viral outbreaks are usually very sparse in the beginning, and thanks to ZiBRA we were able to train lots of people, up to hundreds of young researchers, in using these techniques of genomic sequencing.
We developed partnerships with the team at the Ministry of Health and informal connections with the Pan American Health Organisation. These networks and others helped us to rapidly share findings from a given location with partners from all over the world and share protocols for sequencing, and that helped with the first detection of SARS-CoV-2 in Latin America.
The international collaborative networks, expertise, and sequencing protocols developed during the ZiBRA project laid the groundwork for the CADDE scientists when faced with tracking the spread of another infectious disease in the form of COVID-19.
Last updated: 2 March 2022