Coronavirus disease (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus with zoonotic origins that was first detected in China in December 2019. Brazil confirmed the first cases on February 26, 2020, in a patient returning from Italy.
Epidemiological situation in Brazil. Official data
To track the number of cases and deaths in Brazil, check out our new COVID-19 Local Information Comparison (CLIC) tool done in collaboration with the Centre for Mathematical Modelling of Infectious Diseases, from the London School of Hygiene and Tropical Medicine. Official case and death counts can be found in the Painel Coronavirus. Now including measures for the effective reproductive number in real-time for all 5568 municipalities and Federal District in Brazil.
First SARS-CoV-2 genomes in Latin America. Read more
We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. The first cases were sequenced and analyzed in only 48 hours.
Routes of COVID-19 introduction in Brazil. Read more
Early in March 2020, as the number of imported SARS-CoV-2 cases was on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.
Between February and March 2019, Brazil received 841,302 international passengers in a total of 84 cities across the country (Figure 1). São Paulo, the largest city in the country, was the final destination of nearly half (46.1%) of the passengers arriving in Brazil, followed by Rio de Janeiro (21%) and Belo Horizonte (4.1%). More than half of the international passengers started their journey in the USA (50.8%) followed by France (7.9%) and Italy (7.5%). The air-travel routes to airports in Brazil with most passengers were USA-São Paulo (23.3%), USA-Rio de Janeiro (9.8%) and Italy-São Paulo (3.4%).
Potential for COVID-19 importation to Brazil. Panel on the left shows the proportion (%) of passengers for the top-20 routes to Brazilian airports from countries that had reported COVID-19 cases by 5th March 2020. Panel on the right side estimated proportion (%) of importations for the top-20 routes from countries that had reported local COVID-19 by 5th March 2020.
Importantly, with the recent reduction in the number of flights leaving from Italy and 51% of flights to Brazil depart from airports in the USA, we should anticipate an increasing proportion of infected travelers arriving from the USA. At a time when the number of SARS-CoV-2 cases is steadily growing in Brazil, our findings highlight the high potential for the introduction of new cases in several cities of Brazil, especially in Sao Paulo and Rio de Janeiro metropolises. Rapid identification of locations where clusters of local transmission might first ignite is critical to better coordinate preparedness, readiness, and response actions. There is a critical need for epidemiological, human mobility, and genetic data to understand virus transmission dynamics across Brazil. Continued integration of these data streams should help guide the deployment of resources to mitigate COVID-19 transmission Brazil. Check out a youtube video from Dr. Chico Camargo explaining our findings (in Portuguese).
Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil. Read more
The first case of COVID-19 was detected in Brazil on 25 February 2020. We report and contextualize epidemiological, demographic and clinical findings for COVID-19 cases during the first 3 months of the epidemic. By 31 May 2020, 514,200 COVID-19 cases, including 29,314 deaths, had been reported in 75.3% (4,196 of 5,570) of municipalities across all five administrative regions of Brazil. The R0 value for Brazil was estimated at 3.1 (95% Bayesian credible interval = 2.4–5.5), with a higher median but overlapping credible intervals compared with some other seriously affected countries. A positive association between higher per-capita income and COVID-19 diagnosis was identified. Furthermore, the severe acute respiratory infection cases with unknown aetiology were associated with lower per-capita income. Co-circulation of six respiratory viruses was detected but at very low levels. These findings provide a comprehensive description of the ongoing COVID-19 epidemic in Brazil and may help to guide subsequent measures to control virus transmission. Our study featured in Globo and Estadao.
Evolution and spread of SARS-CoV-2 in Brazil. Read more
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February to 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within-state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country. Our study featured in Jornal Nacional, G1, and CNN Brasil.
Serial Interval Distribution of SARS-CoV-2 Infection in Brazil. Read more
Current assessments of SARS-CoV-2 transmission dynamics rely on accurate estimates of key epidemiological parameters, including the serial interval, which can be defined as the time between symptom onset of the source and the onset of symptoms of the recipient. Using 65 transmission pairs of SARS-CoV-2 cases reported to the Brazilian Ministry of Health we estimated the first serial interval estimates for SARS-CoV-2 from Latin America. We estimate the mean and standard deviation for the serial interval to be 2.97 and 3.29 days respectively. We also present a model for the serial interval probability distribution using only two parameters.
Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Read more
The herd immunity threshold is the proportion of a population that must be immune to an infectious disease, either by natural infection or vaccination such that, in the absence of additional preventative measures, new cases decline and the effective reproduction number falls below unity. This fundamental epidemiological parameter is still unknown for the recently-emerged COVID-19, and mathematical models have predicted very divergent results. Population studies using antibody testing to infer total cumulative infections can provide empirical evidence of the level of population immunity in severely affected areas. Here we show that the transmission of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of the antibody test. The seroprevalence fell in July and August due to antibody waning. After correcting for this, we estimate a final epidemic size of 66%. Although non-pharmaceutical interventions, plus a change in population behavior, may have helped to limit SARS-CoV-2 transmission in Manaus, the unusually high infection rate suggests that herd immunity played a significant role in determining the size of the epidemic.
Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020 Read more
In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported. We report the phylogenetic context of novel severe acute respiratory syndrome coronavirus 2 B.1.1.7 genomes isolated from 2 patients in Brazil (Figure).
Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence Read more
Our latest comment on the resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence is out now in The Lancet. After initially containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many European and Asian countries had a resurgence of COVID-19 consistent with a large proportion of the population remaining susceptible to the virus after the first epidemic wave. By contrast, in Manaus, Brazil, a study of blood donors indicated that 76% (95% CI 67–98) of the population had been infected with SARS-CoV-2 by October, 2020.
SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil, Rev. Inst. Med. Trop. S. Paulo Read more
Reinfection by the severe acute respiratory syndrome coronavirus type 2 (SARS-COV-2) has been reported in many countries, suggesting that the virus may continue to circulate among humans despite the possibility of local herd immunity due to massive previous infections. The emergence of variants of concern (VOC) that are more transmissible than the previous circulating ones has raised particular concerns on the vaccines effectiveness and reinfection rates. The P.1 lineage was first identified in December 2020 in Manaus city and is now globally spread. We report the first case of reinfection of SARS-CoV-2 caused by the P.1 variant outside of Manaus. The potential of these new variants to escape naturally and vaccine- induced immunity highlights the need for a global vigilance.
Increasing frequency of SARS-CoV-2 lineages B.1.1.7, P.1 and P.2 and identification of a novel lineage harboring E484Q and N501T spike mutations in Minas Gerais, Southeast Brazil, Virological.org, Read more
We report preliminary results of an ongoing investigation of SARS-CoV-2 genomic diversity in the metropolitan region of Belo Horizonte (MRBH), Minas Gerais, Brazil. We sequenced and characterized 85 nearly complete SARS-CoV-2 genome sequences from randomized samples collected between 28 October 2020 and 15 March 2021. Phylogenetic analysis reveals co-circulation of two variants of concern (VOC), B.1.1.7 (n=3, 3.53%) and P.1 (n=30, 35.29%), and variant of interest (VOI) P.2 (n=41, 48.23%). These variants harbor E484K (P.1 and P.2) and N501Y (P.1 and B.1.1.7) mutations that are associated with increased transmissibility or immune escape. The N501Y mutation has also been associated with an increase in COVID-19 hospitalizations and deaths. Notably, we find that between 28 Feb and 15 Mar, 68% of cases were caused by the P.1 lineage in the MRBH. In addition, we report a cluster of two sequences characterized by a unique array of 18 mutations, including new non-synonymous changes in the same critical spike amino acid positions, E484Q and N501T. This lineage seems to have emerged independently from the nationally widespread B.1.1.28, as previously reported for P.1 and P.2, and adds up to the composition of a complex epidemiological scenario of the SARS-CoV-2 pandemic in Brazil.
Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil Read more
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
Respiratory viral shedding in healthcare workers reinfected with SARS-CoV-2, Brazil, 2020, Emerging Infections Diseases, Read more
We documented 4 cases of severe acute respiratory syndrome coronavirus 2 reinfection by non–variant of concern strains among healthcare workers in Campinas, Brazil. We isolated infectious particles from nasopharyngeal secretions during both infection episodes. Improved and continued protection measures are necessary to mitigate the risk for reinfection among healthcare workers
Higher risk of death from COVID-19 in low-income and non-White populations of São Paulo, Brazil, BMJ Global Health, Read more
Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil, and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities.
Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated with Increased COVID-19 Risk in a Population-Based Cohort Study, Clinical Infectious Diseases, Read more
Serologically proven prior dengue infection is associated with increased subsequent risk of clinically apparent COVID-19 in Amazonians, implying that sequential dengue and COVID-19 epidemics may impose an extra burden of disease to affected communities in the tropical and subtropical world.
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2, PLoS Biology, Read more
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in Brazil, Viruses, Read more
The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic. In Brazil, six such lineages cocirculate, one originally from the UK (B.1.1.7), one original from South Africa (B.1.351), and four that emerged within different regions of the country, P.1 (Manaus), P.2 (Rio de Janeiro), N.9 (São Paulo), and N.10 (Maranhão). While reports on the spread of some of these lineages to other Brazilian regions exist, a single report on two cases of lineage B.1.1.7 in São Paulo has been published, and the extent of its geographic spread is currently unknown. Therefore, we conducted a genomic epidemiology study focused on characterizing the dissemination of this lineage in a national context.
Brazil needs a coordinated and cooperative approach to tackle COVID-19, Nature Medicine, Read more
After more than 14 months under siege, Brazilians continue to suffer as they see thousands of people dying every day, killed by the fast-moving respiratory pathogen SARS-CoV-2. Families are struggling to secure their livelihoods, quell hunger and, in some cases, adjust to the long-term toll of having survived infection with SARS-CoV-2. With the surge in cases, overcrowding of hospitals and high lethality, those on the front lines understand that Brazil is at war with COVID-19. The assault has been brutal1. A quarter of all deaths from COVID-19 in Brazil were officially recorded in April 2021. Meanwhile, a SARS-CoV-2 variant of concern, lineage P.1 (B.22.214.171.124), continues to be detected in an ever-increasing share of infections, on the basis of the small number of genomes sequenced across the country. This Commentary discusses the many factors that explain why the toll of the pandemic on Brazil has been so extraordinary, including its close transport connectivity with world markets, the marked socioeconomic vulnerabilities of its many populations, and persistent inequities.
Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study, Lancet Microbe, Read more
Mutations accrued by SARS-CoV-2 lineage P.1—first detected in Brazil in early January, 2021—include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response. We did an immunological study to assess the neutralising effects of antibodies on lineage P.1 and lineage B isolates of SARS-CoV-2, using plasma samples from patients previously infected with or vaccinated against SARS-CoV-2. We found that SARS-CoV-2 lineage P.1 might escape neutralisation by antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2. Continuous genomic surveillance of SARS-CoV-2 combined with antibody neutralisation assays could help to guide national immunisation programmes.
Altered demographic profile of hospitalizations during the second COVID-19 wave in Amazonas, Brazil, The Lancet Regional Health, Read more
Recent months have seen the emergence of SARS-CoV-2 variants with altered epidemiological properties, including increased transmissibility and the ability to partially evade protection immunity from prior infection. These variants have frequently been associated with resurgence of transmission and COVID-19 mortality in settings where they have established. Detailed investigations into the epidemiology of variants of concern (VOC) are crucial to sustained, long-term control of SARS-CoV-2. Despite this, epidemiological studies remain scarce, particularly with regards to clinical outcomes and profiles of disease severity associated with VOC transmission.
Understanding the Potential Impact of Different Drug Properties on SARS-CoV-2 Transmission and Disease Burden: A Modeling Analysis, Clinical Infectious Diseases, Read more
The public health impact of the COVID-19 pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. Using a mathematical model of SARS-CoV-2 transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care. The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R=1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalisation) could have much greater benefits, particularly in resource-poor settings facing large epidemics. Advances in the treatment of COVID-19 to date have been focussed on hospitalised-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.
Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals (Preprint) Read more
The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma’s detection, and were largely transient after Gamma’s detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil’s COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
Tracking the emergence of disparities in the subnational spread of COVID-19 in Brazil using an online application for real-time data visualisation: a longitudinal analysis, The Lancet Regional Health- Americas, Read more
Brazil is one of the countries worst affected by the COVID-19 pandemic with over 20 million cases and 557,000 deaths reported by August 2021. Comparison of real-time local COVID-19 data between areas is essential for understanding transmission, measuring the effects of interventions, and predicting the course of the epidemic, but are often challenging due to different population sizes and structures. We describe the development of a new app for the real-time visualisation of COVID-19 data in Brazil at the municipality level. In the CLIC-Brazil app, daily updates of case and death data are downloaded, age standardised and used to estimate the effective reproduction number (Rt). We show how such platforms can perform real-time regression analyses to identify factors associated with the rate of initial spread and early reproduction number. We also use survival methods to predict the likelihood of occurrence of a new peak of COVID-19 incidence.
Track Omicron’s spread with molecular data, Science, Read more
On 26 November, the newly emerged variant Omicron was designated a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) (1). Rapid polymerase chain reaction (PCR) test results could improve estimates of the prevalence of Omicron around the world. The widely used Thermo Fisher TaqPath COVID-19 PCR assay was valuable in tracking the spread of the Alpha (B.1.1.7) VOC (2) because a deletion of amino acids 69 and 70 in Alpha’s spike gene (Δ69–70) yields a distinct absent S-gene (S–) despite positive test results. The Delta VOC lacks this deletion and is therefore S-gene positive (S+) on TaqPath PCR tests (3). The Omicron VOC shares the spike Δ69–70 deletion with Alpha, which has dropped to negligible levels worldwide. Therefore, the frequency of S– results can be used as a rapid proxy for the frequency of Omicron cases, provided initial detection of local circulation had been confirmed by sequencing.
Global disparities in SARS-CoV-2 genomic surveillance, Preprint, Read more
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020–2021, Emerging Infectious Diseases – Dispatch, Read more
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant has been hypothesized to cause more severe illness than previous variants, especially in children. Successive SARS-CoV-2 IgG serosurveys in the Brazilian Amazon showed that age-specific attack rates and proportions of symptomatic SARS-CoV-2 infections were similar before and after Gamma variant emergence.