15 April 2021
Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil , Published in Science, Read more
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, 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 mid-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 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against 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.
5 April 2021
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador Preprint in MedRxiv Read more
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
4 March 2021
Dataset on SARS-CoV-2 non-pharmaceutical interventions in Brazilian municipalities, Published in Scientifica Data, Read more
Brazil has one of the fastest-growing COVID-19 epidemics worldwide. Non-pharmaceutical interventions (NPIs) have been adopted at the municipal level with asynchronous actions taken across 5,568 municipalities and the Federal District. This paper systematises the fragmented information on NPIs reporting on a novel dataset with survey responses from 4,027 mayors, covering 72.3% of all municipalities in the country. This dataset responds to the urgency to track and share findings on fragmented policies during the COVID-19 pandemic. Quantifying NPIs can help to assess the role of interventions in reducing transmission. We offer spatial and temporal details for a range of measures aimed at implementing social distancing and the dates when these measures were relaxed by local governments.
4 February 2021
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 Virological.org Read More
Lineages of concern being tracked because they have mutations of interest and evidence of international spread: https://cov-lineages.org/global_report.html
GRINCH includes daily reports on genome and report data associated with cases caused by the B.1.1.7, B.1.351, and P.1 lineages of concern around the world.
27 January 2021
Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence – Published in The Lancet Read more
26 January 2021
Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020, Published in Emerging Infectious Diseases, 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.
25 January 2021
Increasing frequency of the P.1 lineage in Manaus Virological.org Read more
We provide a brief report following up on our previous post. Here we share a frequency table by date of collection for a total of 142 SARS-CoV-2 genome sequences from Manaus, including 115 partial, near-complete, and complete SARS-CoV-2 genome sequences generated by our team from samples collected in December 2020 (n=67, collection dates between 15 December 2020 and 31 December 2020) and January 2021 (n=48, collection dates between 1 Jan 2021 and 9 Jan 2021). Near-complete and complete sequences were classified using pangolin; partial sequences were typed using maximum likelihood phylogenetic analysis with an in-house dataset of near-complete or complete P.1, P.2, and B.1.1.28 sequences.
21 January 2021
Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama Published in Emerging Infectious Diseases Read more
We report an epidemiologic analysis of 4,210 cases of infection with severe acute respiratory syndrome coronavirus 2 and genetic analysis of 313 new near-complete virus genomes in Panama during March 9–April 16, 2020. Although containment measures reduced R0 and Rt, they did not interrupt virus spread in the country.
12 January 2021
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings Virological.org Read more
We have detected a new variant circulating in December in Manaus, Amazonas state, north Brazil, where very high attack rates have been estimated previously. The new lineage, named P.1 (descendent of B.1.1.28), contains a unique constellation of lineage defining mutations, including several mutations of known biological importance such as E484K, K417T, and N501Y. Importantly, the P.1 lineage was identified in 42% (13 out of 31) RT-PCR positive samples collected between 15 to 23 December, but it was absent in 26 publicly available genome surveillance samples collected in Manaus between March to November 2020. These findings indicate local transmission and possibly recent increase in the frequency of a new lineage from the Amazon region. The higher diversity and the earlier sampling dates of P.1. in Manaus corroborates the travel info of recently detected cases in Japan, suggesting the direction of travel was Manaus to Japan. The recent emergence of variants with multiple shared mutations in spike raises concern about convergent evolution to a new phenotype, potentially associated with an increase in transmissibility or propensity for re-infection of individuals.
12 January 2021
Clinical features and natural history of the first 2073 suspected COVID-19 cases in the Corona São Caetano primary care programme: a prospective cohort study, Published in BMJ Open Read More
Despite most cases not requiring hospital care, there are limited community-based clinical data on COVID-19. The Corona São Caetano programme is a primary care initiative providing care to all residents with COVID-19 in São Caetano do Sul, Brazil. It was designed to capture standardised clinical data on community COVID-19 cases. After triage of potentially severe cases, consecutive patients presenting to a multimedia screening platform between 13 April and 13 May 2020 were tested at home with SARS-CoV-2 reverse transcriptase (RT) PCR; positive patients were followed up for 14 days with phone calls every 2 days. RT-PCR-negative patients were offered additional SARS-CoV-2 serology testing to establish their infection status. We describe the clinical, virological and natural history features of this prospective population-based cohort. Of 2073 suspected COVID-19 cases, 1583 (76.4%) were tested by RT-PCR, of whom 444 (28.0%, 95% CI 25.9 to 30.3) were positive; 604/1136 (53%) RT-PCR-negative patients underwent serology, of whom 52 (8.6%) tested SARS-CoV-2 seropositive. The most common symptoms of confirmed COVID-19 were cough, fatigue, myalgia and headache; whereas self-reported fever (OR 3.0, 95% CI 2.4 to 3.9), anosmia (OR 3.3, 95% CI 2.6 to 4.4) and ageusia (OR 2.9, 95% CI 2.3 to 3.8) were most strongly associated with a positive COVID-19 diagnosis by RT-PCR or serology. RT-PCR cycle thresholds were lower in men, older patients, those with fever and arthralgia and closer to symptom onset. The rates of hospitalisation and death among 444 RT-PCR-positive cases were 6.7% and 0.7%, respectively, with older age and obesity more frequent in the hospitalised group. COVID-19 presents in a similar way to other mild community-acquired respiratory diseases, but the presence of fever, anosmia and ageusia can assist the specific diagnosis. Most patients recovered without requiring hospitalisation with a low fatality rate compared with other hospital-based studies.
31 December 2020
First report of the SARS-CoV-2 B.1.1.7 lineage in Brazil Emerging Infectious Diseases Read more
We report the first two cases caused by the SARS-CoV-2 B.1.1.7 (also known as Variant of Concern 202012/01, VOC) lineage in Brazil. The findings come less than 36 hours upon sample collection. Samples were immediately analyzed using a portable DNA sequencer as part of genomic surveillance activities from the Brazil-UK CADDE project. Sequencing and phylogenetic analysis confirm two separate introductions of the VOC lineage in Brazil, possibly from the UK. One case reported no travel outside of Brazil. Given the higher transmissibility of the VOC compared to non-VOC lineages, increased genomic surveillance is urgently needed to investigate the extent of VOC circulation in the country.
8 December 2020
Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic, Published in Science Read more
SARS-CoV-2 spread rapidly in the Brazilian Amazon and the attack rate there is an estimate of the final size of a largely unmitigated epidemic. We use a convenience sample of blood donors to show that by June, one month after the epidemic peak in Manaus, capital of Amazonas state, 44% of the population had detectable IgG antibodies. Correcting for cases without a detectable antibody response and antibody waning, we estimate a 66% attack rate in June, rising to 76% in October. This is higher than in São Paulo, in southeastern Brazil, where the estimated attack rate in October is 29%. These results confirm that, when poorly controlled, COVID-19 can infect a high fraction of the population causing high mortality.
03 November 2020
A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages, Published in Molecular Biology and Evolution Read more
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analyzed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyze the spatio-temporal dispersal history and dynamics of SARS-CoV-2 lineages. As a proof of concept, we focus on the Belgian epidemic, which has had one of the highest spatial densities of available SARS-CoV-2 genomes. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.
4 September 2020
Evolution and epidemic spread of SARS-CoV-2 in Brazil, Published in Science, Read more
Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 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 and 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 traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.
7 August 2020
Fatal outcome of chikungunya virus infection in Brazil, Published in Clinical Infectious Diseases Read more
A retrospective investigation was undertaken to describe clinical, epidemiological, and virus genomic features associated with deaths caused by CHIKV in Ceará state, northeast Brazil. Sera, cerebrospinal fluid (CSF), and tissue samples from 100 fatal cases with suspected arbovirus infection were tested for CHIKV, dengue (DENV), and Zika virus (ZIKV). 68 fatal cases had CHIKV infection confirmed by RT-qPCR (52.9%), viral antigen (41.1%), and/or specific-IgM (63.2%). Co-detection of CHIKV with DENV was found in 22% of fatal cases, ZIKV in 2.9%, and DENV and ZIKV in 1.5%. A total of 39 CHIKV-deaths presented with neurological signs and symptoms and CHIKV-RNA was found in the CSF of 92.3% of these patients. Fatal outcomes were associated with irreversible multiple organ dysfunction syndrome. Patients with diabetes appear to die at a higher frequency during the sub-acute phase. Genetic analysis showed the circulation of two CHIKV-East Central South African (ECSA) lineages in Ceará and revealed no unique virus genomic mutation associated with fatal outcome.
31 July 2020
Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil, Nature Human Behaviour, 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.
10 July 2020
Interfaces for spillover transmission for coronaviruses, Published in Estudos Avancados, Read more
The current path of human development generates deleterious environmental impacts, which have a negative impact on health; among them, the intensified transmission of infectious diseases, epidemics, and pandemics, such as covid-19. The way we usually deal with biodiversity and ecosystems, combined with the effects of climate change, makes for interfaces and pathways that favor diversification, spillover, and the circulation of viruses. By these means, Sars-CoV-2 may invade Brazilian biomes, transforming, for instance, the Amazon rain forest into a huge reservoir from where coronavirus may return even more aggressive to health.
25 Jul 2020
Serial Interval Distribution of SARS-CoV-2 Infection in Brazil, Journal Travel Medicine, 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. We estimate the serial interval of SARS-CoV-2 from 65 infector–infectee pairs from Brazil. The median serial interval in our data was estimated at 3 (standard deviation = 3.29) days.
30 May 2020
Genomic evidence of yellow fever virus in Aedes scapularis, southeastern Brazil, 2016, Acta Tropica Read more
The southeastern region of Brazil has recently experienced the largest yellow fever disease outbreak in decades. Since July 2016 epizootic events were reported in São Paulo state’s north region, where 787 Culicidae were captured as part of public health surveillance efforts and tested using real-time quantitative PCR. One Aedes scapularis pool collected in November 2016 in an agriculture area in Urupês city tested positive for YFV-RNA. Using a validated multiplex PCR approach we were able to recover a complete virus genome sequence from this pool. Phylogenetic analysis of the novel strain and publicly available data indicates that the belongs to the South American genotype 1 clade circulating in Sao Paulo state and is basal to the recent outbreak clade in southeast Brazil. Our findings highlight the need of additional studies, including vector competence studies, to disentangle the role of Aedes scapularis in yellow fever transmission in the Americas.
11 May 2020
Importation and early local transmission of COVID-19 in Brazil, 2020, Revista Instituto Medicina Tropical, 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. Our study provides a snapshot of the early establishment of the COVID-19 pandemic in Brazil, characterized by multiple independent introductions from Italy, followed by local transmission of the virus in Sao Paulo. Phylogenetic analyses are broadly consistent with the patients’ self-reported traveling histories. We show that the two genomes associated with local transmission are linked to a patient infected in Italy and are identical to other Italian genomes collected in the same time window. Given the within-outbreak rate of evolutionary change estimated for SARS-CoV-2, we caution against inferring directionality of transmission based on genetic data alone. Such inferences can further be overshadowed by incomplete sampling due to delays, reflecting the lack of equitable access to diagnosis and genomic sequencing.
15 March 2020
Routes for COVID-19 importation in Brazil, Journal Travel Medicine, Read more
To better understand the potential for SARS-CoV-2 introductions to Brazil, we estimate the relative risk of COVID-19 introduction to Brazilian cities by taking into account SARS-CoV-2 incidence per international traveller arriving at an airport in Brazil. We estimate that 54.8% of all imported cases would be expected to come from travellers infected in Italy and 9.3% and 8.3% of the cases would be from travellers infected in China and France, respectively. The route Italy–São Paulo was estimated to comprise 24.9% of total infected travellers flying to Brazil during this period. Moreover, we estimate that Italy has been the source location for five of the top 10 importation routes for infected travellers into Brazil based on the current epidemiological scenario. Consistent with this, at least 48% (n = 14/29) of the reported imported cases in Brazil have a history of travelling to Italy prior to the onset of symptoms, as of 9 March 2020. Six (23.1%) of the confirmed cases that acquired the virus in Italy have been identified in São Paulo.
28 February 2020
First cases of coronavirus disease (COVID-19) in Brazil, Virological, Read more
We provide a brief report and phylogenetic analysis of the confirmed COVID-2 cases in Brazil. From 488 suspected cases, two have so far tested positive for COVID-19. These two cases both traveled to Northern Italy. Detailed clinical and epidemiological descriptions for suspected and confirmed patients, including for the two patients reported here, are available from the National Public Health Emergency Alert and Response Network from the Brazilian Ministry of Health. Full report available in Virological.org.
7 August 2020
Genomic Surveillance of Yellow Fever Virus Epidemic Waves in São Paulo, Brazil, 2016 – 2018, PLoS Pathogens, Read more
Since July 2016, southeast Brazil has experienced the largest yellow fever virus (YFV) outbreak in decades. Using our validated portable sequencing protocols, we generated 46 complete novel YFV genomes and investigate the geographical and temporal distribution of observed cases in non-human primates in Sao Paulo state. We find that most cases in Sao Paulo result from a single introduction from Minas Gerais that spread at a rate of 1 km per day, consistent with a scenario of continued spread in non-human primate communities and sylvatic vector across forested patches, with occasional spillover to unvaccinated human populations.
18 November 2019
This study uses portable sequencing validated protocols to rapidly generate the first virus genome data from 20 cases occurring in Araraquara and São José do Rio Preto, São Paulo state, Brazil. We find that the 2019 dengue outbreak in Brazil in this region is caused by a newly introduced DENV serotype 2 genotype III (Asian/American) that is replacing previously-circulating DENV2 lineages.
14 February 2020
The evolutionary dynamics of Oropouche Virus in South America, Journal of Virology, Read more
The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Our results show that differing evolutionary processes on the three segments that encompass the viral genome of OROV lead to variable evolutionary rates and divergence dates that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.
31 January 2020
Sabia virus infections in yellow fever suspected cases in Sao Paulo, Brazil Preliminary Report Read more
We provide a brief report on two Sabia virus cases detected in Sao Paulo, Brazil, in December 2019. We used CADDE’s novel metagenomic protocol and design new PCR diagnostic primers and probes that can cover a larger diversity of SABV strains in Brazil. A preliminary report on our results can be found here.
18 February 2020
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region, Cell Reports, Read more
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.