Luiz Max Carvalho

Fundação Getulio Vargas | FGV · School of Applied Mathematics "EMAp"

Foot-and-mouth disease virus (FMDV) is the causative agent of the most important disease of domestic cattle, foot-and-mouth disease. In Ecuador, FMDV is maintained at an endemic state, with sporadic outbreaks. To unravel the tempo and mode of FMDV spread within the country we conducted a Bayesian phylogeographic analysis using a continuous time Mar...

Sylvatic yellow fever (SYF) is enzootic in Brazil, causing periodic outbreaks in humans living near forest borders or in rural areas. In this study, the cycling patterns of this arbovirosis were analyzed. Spectral Fourier analysis was used to capture the periodicity patterns of SYF in time series. SYF outbreaks have not increased in frequency, only...

Quantifying the attack ratio of disease is key to epidemiological inference and Public Health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial...

Deterministic mathematical models play an important role in our understanding of population growth dynamics. In particular, the effect of temperature on the growth of disease-carrying insects. In this paper we propose a modified Verhulst – logistic growth – equation with temperature-dependent parameters. Namely, the growth rate r and the carrying c...

We estimated within/extra-household SARS-CoV-2 infection risk and associated factors in a household cohort study in one of the most vulnerable neighborhoods in Rio de Janeiro city. Individuals ≥1 years-old with suspected or confirmed COVID-19 in the past 30 days (index cases) and eligible household contacts were enrolled (Nov/2020-Dec/2021) and fol...

Background: Brazil started the COVID-19 mass vaccination in January 2021 with CoronaVac and ChAdOx1, followed by BNT162b2 and Ad26.COV2.S vaccines. By the end of 2021, more than 317 million vaccine doses were administered in the adult population. This study aimed at estimating the effectiveness of the primary series of COVID-19 vaccination and boo...

Correlated proportions appear in many real-world applications and present a unique challenge in terms of finding an appropriate probabilistic model due to their constrained nature. The bivariate beta is a natural extension of the well-known beta distribution to the space of correlated quantities on $[0, 1]^2$. Its construction is not unique, howeve...

It is often the case in Statistics that one needs to compute sums of infinite series, especially in marginalising over discrete latent variables. This has become more relevant with the popularization of gradient-based techniques (e.g. Hamiltonian Monte Carlo) in the Bayesian inference context, for which discrete latent variables are hard or impossi...

Passados os primeiros meses da pandemia do novo coronavírus no Brasil, o Observatório Covid-19 Fiocruz, em parceria com a Editora Fiocruz e com o apoio da Rede SciELO Livros, traz para o público leitor um conjunto de livros instantâneos sobre as análises nele realizadas desde que foi criado para subsidiar o seu combate. Nesta série Informação para...

In a context of community transmission and shortage of vaccines, COVID-19 vaccination should focus on directly reducing the morbidity and mortality caused by the disease. It was thus essential to define priority groups for vaccination by the Brazilian National Immunization Program (PNI in Portuguese), based on the risk of hospitalization and death...

Background. Mass vaccination campaigns started in Brazil on January/2021 with CoronaVac followed by ChAdOx1 nCov-19, and BNT162b2 mRNA vaccines. Target populations initially included vulnerable groups such as people older than 80 years, with comorbidities, of indigenous origin, and healthcare workers. Younger age groups were gradually included. Met...

The power prior is a popular tool for constructing informative prior distributions based on historical data. The method consists of raising the likelihood to a discounting factor in order to control the amount of information borrowed from the historical data. However, one often wishes to assign this discounting factor a prior distribution and estim...

Passados os primeiros meses da pandemia do novo coronavírus no Brasil, o Observatório Covid-19 Fiocruz, em parceria com a Editora Fiocruz e com o apoio da Rede SciELO Livros, traz para o público leitor um conjunto de livros instantâneos sobre as análises nele realizadas desde que foi criado para subsidiar o seu combate. Nesta série Informação para...

Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through time and the distribution of the sampling times depends on the effective population size, explicit statistical mo...

Roughly six months into the COVID-19 pandemic, many countries have managed to contain the spread of the virus by means of strict containment measures including quarantine, tracing and isolation of patients as well strong restrictions on population mobility. Here we propose an extended SEIR model to explore the dynamics of containment and then explo...

The power prior is a popular tool for constructing informative prior distributions based on historical data. The method consists of raising the likelihood to a discounting factor in order to control the amount of information borrowed from the historical data. It is customary to perform a sensitivity analysis reporting results for a range of values...

O presente estudo tem o objetivo de descrever os pacientes hospitalizados por síndrome respiratória aguda grave (SRAG) em decorrência da COVID-19 (SRAG-COVID), no Brasil, quanto às suas características demográficas e comorbidades até a 21ª Semana Epidemiológica de 2020. Buscou-se comparar essas características com as dos hospitalizados por SRAG em...

Trypanosomatids are protozoan parasites that infect thousands of globally dispersed hosts, potentially affecting their physiology. Several species of trypanosomatids are commonly found in phytophagous insects. Leptomonas wallacei is a gut-restricted insect trypanosomatid only retrieved from Oncopeltus fasciatus. The insects get infected by copropha...

Abstract Urban mobility data are important to areas ranging from traffic engineering to the analysis of outbreaks and disasters. In this paper, we study mobility data from a major Brazilian city from a geographical viewpoint using a Complex Network approach. The case study is based on intra-urban mobility data from the Metropolitan area of Rio de J...

The recent years have witnessed a rapid increase in the quantity and quality of genomic data collected from human and animal pathogens, viruses in particular. When coupled with mathematical and statistical models, these data allow us to combine evolutionary theory and epidemiology to understand pathogen dynamics. While these developments led to imp...

Dudas G, Carvalho LM, Rambaut A, Bedford T. 2018. MERS-CoV spillover at the camel-human interface. eLife 7:e31257. doi: 10.7554/eLife.31257.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus from camels causing significant mortality and morbidity in humans in the Arabian Peninsula. The epidemiology of the virus remains poorly understood, and while case-based and seroepidemiological studies have been employed extensively throughout the epidemic, viral sequence d...

MCMC samples from seasonality inference analysis.

XML to run structured coalescent analysis with equal deme sizes between humans and camels and output files.

Output from PHI and 3Seq recombination analyses.

MERS-CoV sequences used in the study.

Strain names, accessions (where available), identified host and reported collection dates for MERS-CoV genomes used in this study.

XML to run structured coalescent analysis on bisected alignment with output files.

XML to run structured coalescent analysis with a relaxed prior and output file.

XML to run discrete trait analysis (DTA) and output files.

Maximum likelihood phylogeny.

Output from ClonalFrameML analysis.

XML to run skygrid analysis on camel-like sequence data and output files.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus from camels causing significant mortality and morbidity in humans in the Arabian Peninsula. The epidemiology of the virus remains poorly understood, and while case-based and seroepidemiological studies have been employed extensively throughout the epidemic, viral sequence d...

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and dem...

Zika virus infection was declared a public health emergency of international concern in February 2016 in response to the outbreak in Brazil and its suspected link with congenital anomalies. In this study, we use notification data and disease natural history parameters to estimate the basic reproduction number (R 0) of Zika in Rio de Janeiro, Brazil...

The magnitude of the 2013–2016 Ebola virus disease (EVD) epidemic enabled an unprecedented number of viral mutations to occur over successive human-to-human transmission events, increasing the probability that adaptation to the human host occurred during the outbreak. We investigated one nonsynonymous mutation, Ebola virus (EBOV) glycoprotein (GP)...

Zika virus infection was declared a public health emergency of international concern in February 2016 in response to the outbreak in Brazil and its suspected link with congenital anomalies. In this study we use early notification data and disease natural history parameters to estimate the basic reproductive number 0. Our estimates of the basic repr...

Objectives: The recent emergence of Zika in Brazil and its association with an increased rate of congenital malformations has raised concerns over its impact on the birth rate in the country. Using data on the incidence of Zika in 2015–2016 and dengue in 2013 and 2015–2016 for the city of Rio de Janeiro (population 6.4 million), a massive increase...

The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude, duration and impact. Extensive collaborative sequencing projects have produced a large collection of over 1600 Ebola virus genomes, representing over 5% of known cases, unmatched for any single human epidemic. In this comprehensive analysis of this entire d...

Hoenen et al. (Reports, 3 April 2015, p. 117; published online 26 March) suggested that the Ebola virus Makona responsible for the West African epidemic evolved more slowly than previously reported. We show that this was based on corrupted data. An erratum provided a rate compatible with the initial and later, more precise, estimates but did not co...

Attaran and colleagues in an open letter to WHO expressed their concern about the upcoming Olympic and Para-lympic Games in Rio de Janeiro and the threat posed by the Zika epidemic (Attaran 2016). We agree that Zika virus is of great public health concern and much remains to be known about this disease. Care should be taken to reduce the risk of in...

The recent emergence of Zika in Brazil and its association with increased congenital malformation rates has raised concerns over its impact on the birth rates in the country. Using data on the incidence of Zika in 2015-2016 and dengue in 2013 and 2015-16 for the city of Rio de Janeiro (pop: 6.4 million), we document a massive increase of Zika in wo...

Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in sever...

Although foot-and-mouth disease virus (FMDV) incidence has decreased in South America over the last years, the pathogen still circulates in the region and the risk of re-emergence in previously FMDV-free areas is a veterinary public health concern. In this paper we merge environmental, epidemiological and genetic data to reconstruct spatiotemporal...

Combining different prior distributions is an important issue in decision theory and Bayesian inference. Logarithmic pooling is a popular method to aggregate expert opinions by using a set of weights that reflect the reliability of each information source. The resulting pooled distribution however heavily depends set of weights given to each opinio...

In this paper we present a multilevel binary model when the outcome is measured with uncertainty. We are interested in obtaining association measures, such as odds ratio, while taking into account specificity and sensitivity of the outcome. Posterior inference is implemented using Hamiltonian Monte Carlo and also integrated nested Laplace approxima...

The Asian/American (AS/AM) genotype of dengue virus type 2 (DENV-2) has been evolving in the Americas over the last 30 years, leading to several waves of dengue epidemics and to the emergence of different viral lineages in the region. In this study, we investigate the spatiotemporal dissemination pattern of the DENV-2 lineages at a regional level....

Background Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulat...

Background: Yellow fever is an acute, frequently fatal, febrile arbovirosis that in Brazil occurs only in the sylvatic form. Sylvatic yellow fever (SYF) appears in sporadic outbreaks over a large area of Brazil. In this paper, we analyze the demographic profile of 831 SYF cases that occurred between 1973 and 2008, to determine which segments of th...

To compare epidemiological aspects of young (15 to 49 years old) and older (more than 50 years old) AIDS patients. We analyzed 511,633 AIDS cases notified to the Brazilian Ministry of Health in the period of 1980-2008 looking at sex, age ranges, educational level and exposure category. Patients were divided into three age groups: under 15, from 15...

Foot-and-mouth disease is the most economically important disease of domestic livestock. In order to obtain insights about the risk of distinct antigenic variants arising, we apply an approach based on complex networks. The network's results show a modularity signature, with se-quences of same year and region linking different modules.