Imperial College London

Professor Nuno R. Faria

Faculty of MedicineSchool of Public Health

Professor in Virus Genomic Epidemiology
 
 
 
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Contact

 

+44 (0)20 7594 3560n.faria

 
 
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Location

 

Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

212 results found

Amorim MR, Souza WM, Barros ACG, Toledo-Teixeira DA, Bispo-dos-Santos K, Simeoni CL, Parise PL, Vieira A, Forato J, Claro IM, Mofatto LS, Barbosa PP, Brunetti NS, Franca ESS, Pedroso GA, Carvalho BFN, Zaccariotto TR, Krywacz KCS, Vieira AS, Mori MA, Farias AS, Pavan MHP, Bachur LF, Cardoso LGO, Spilki FR, Sabina EC, Faria NR, Santos MNN, Angerami R, Leme PAF, Schreiber A, Moretti ML, Granja F, Proenca-Modena JLet al., 2021, Respiratory Viral Shedding in Healthcare Workers Reinfected with SARS-CoV-2, Brazil, 2020, EMERGING INFECTIOUS DISEASES, Vol: 27, Pages: 1737-1740, ISSN: 1080-6040

Journal article

Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FS, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlueter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Proenca-Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu C-H, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino ECet al., 2021, Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil, Science, Vol: 372, Pages: 815-821, ISSN: 0036-8075

Cases of severe acute respiratory syndrome coronavirus 2 (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 (angiotensin-converting enzyme 2) 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- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 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.

Journal article

Prete CA, Buss LF, Buccheri R, Abrahim CMM, Salomon T, Crispim MAE, Oikawa MK, Grebe E, da Costa AG, Fraiji NA, Carvalho MDPSS, Whittaker C, Alexander N, Faria NR, Dye C, Nascimento VH, Busch MP, Sabino ECet al., 2021, Reinfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazil

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The city of Manaus, north Brazil, was stricken by a second epidemic wave of SARS-CoV-2 despite high seroprevalence estimates, coinciding with the emergence of the Gamma (P.1) variant. Reinfections were postulated as a partial explanation for the second surge. However, accurate calculation of reinfection rates is difficult when stringent criteria as two time-separated RT-PCR tests and/or genome sequencing are required. To estimate the proportion of reinfections caused by the Gamma variant during the second wave in Manaus and the protection conferred by previous infection, we analyzed a cohort of repeat blood donors to identify anti-SARS-CoV-2 antibody boosting as a means to infer reinfection.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We tested serial blood samples from unvaccinated repeat blood donors in Manaus for the presence of anti-SARS-CoV-2 IgG antibody. Donors were required to have three or more donations and at least one donation during each epidemic wave. Donors were tested with two assays that display waning in early convalescence, enabling the detection of reinfection-induced boosting. The serial samples were used to divide donors into six groups defined based on the inferred sequence of infection and reinfection with non-Gamma and Gamma variants.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>From 3,655 repeat blood donors, 238 met all inclusion criteria, and 223 had enough residual sample volume to perform both serological assays. Using a strict serological definition of reinfection, we found 13.6% (95% CI 7.0% - 24.5%) of all presumed Gamma infections that were observed in 2021 were reinfections. If we also include cases of probable or possible reinfections, these percentages increase respectively to 22.7% (95% CI

Journal article

Mee P, Alexander N, Mayaud P, Colon Gonzalez FDJ, Abbott S, de Souza Santos AA, Acosta AL, Parag KV, Pereira RHM, Prete CA, Sabino EC, Faria NR, Brady OJet al., 2021, 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

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Brazil is one of the countries worst affected by the COVID-19 pandemic with over 20 million cases and 557,000 deaths reported. 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.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>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 reproduction number (<jats:italic>R</jats:italic><jats:sub><jats:italic>t</jats:italic></jats:sub>). 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.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>After an initial introduction in São Paulo and Rio de Janeiro states in early March 2020, the epidemic spread to Northern states and then to highly populated coastal regions and the Central-West. Municipalities with higher metrics of social development experienced earlier arrival of COVID-19 (decrease of 11·1 days [95% CI:13·2,8·9] in the time to arrival for each 10% increase in the social development index). Differences in the initial epidemic intensity (mean<jats:italic>Rt</jats:italic>) were largely driven by geographic location and the date of local onset.</jats:p></jats:

Journal article

Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh NDet al., 2021, Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2, PLOS BIOLOGY, Vol: 19, ISSN: 1544-9173

Journal article

Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander A-L, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas Pet al., 2021, Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

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.

Working paper

Li SL, Pereira RHM, Prete Jr CA, Zarebski AE, Emanuel L, Alves PJH, Peixoto PS, Braga CK, de Souza Santos AA, de Souza WM, Barbosa RJ, Buss LF, Mendrone A, de Almeida-Neto C, Ferreira SC, Salles NA, Marcilio I, Wu C-H, Gouveia N, Nascimento VH, Sabino EC, Faria NR, Messina JPet al., 2021, Higher risk of death from COVID-19 in low-income and non-White populations of SAo Paulo, Brazil, BMJ GLOBAL HEALTH, Vol: 6, ISSN: 2059-7908

Journal article

Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, De Maio N, Faria NR, Hadfield J, Hayette M-P, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes Pet al., 2021, A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages, Molecular Biology and Evolution, Vol: 38, Pages: 1608-1613, ISSN: 0737-4038

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 spatiotemporal 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.

Journal article

Acosta AL, Xavier F, Saraiva A, Sabino J, Faria N, Sabino E, Salum MAMet al., 2021, Coronavirus from cities to forests: mapping vulnerable interfaces and hotspots for SARS-CoV-2 spillover from humans to biodiversity, The Lancet. Planetary health, Vol: 5, Pages: S15-S15, ISSN: 2542-5196

<h4>Background</h4> With the continuous spreading of SARS-CoV-2 globally, the probability for interactions between humans who are infected and wildlife tends to grow intensely, as well as the likelihood of viral spillover from humans to biodiversity. This aspect is of great concern for wildlife conservation and human health, because the list of highly susceptible animal groups that have contracted SARS-CoV-2 (bats, mustelids, and primates) is large and, once infected, these groups can act as vectors and reservoirs, becoming a substrate for viral mutations and recombinations and boosting the risk of new strains emerging, which can return to humans as new diseases. Little is known about the inducing factors facilitating coronavirus spillover from one species to another, but it can be argued that interface zones between wild fauna and humans, which are narrow edges between anthropic (cities, roads, parks, ecotourism sites, and agricultural frontiers) and sylvatic habitat, are zones of increased interaction between humans and wild animals, and thus have a higher probability of viral spillover events than other areas. In a similar context, the habitat compression by forest fragmentation also brings species and infected beings closer, reducing their home ranges and intensifying the risk of spillover among wild populations. Therefore, on the basis of the premise for zoonosis—the greater human–animal interaction, the greater risk of viral spillover—we aimed to identify the most and least susceptible areas to viral spillover in Brazil. <h4>Methods</h4> We developed an approach combining ecological modelling (Biomod2: modelling habitat suitability for 158 bat and 49 primate species) and geographical information systems (by using demographic indicators, roads, and related variables) to map the most and least susceptible areas to spillover in Brazil. This map indicates priority areas for serological surveillance of fauna for monitoring

Journal article

Vogels CBF, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ, NGS-SA, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh NDet al., 2021, PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern., medRxiv

With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , 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 UK 4,5 could be serendipitously detected by the ThermoFisher 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 that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three 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 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.

Journal article

de Souza Santos AA, Candido DDS, de Souza WM, Buss L, Li SL, Pereira RHM, Wu C-H, Sabino EC, Faria NRet al., 2021, Dataset on SARS-CoV-2 non-pharmaceutical interventions in Brazilian municipalities, Scientific Data, Vol: 8, ISSN: 2052-4463

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.

Journal article

Prete CA, Buss L, Dighe A, Porto VB, da Silva Candido D, Ghilardi F, Pybus OG, de Oliveira WK, Croda JHR, Sabino EC, Faria NR, Donnelly CA, Nascimento VHet al., 2021, Serial interval distribution of SARS-CoV-2 infection in Brazil, JOURNAL OF TRAVEL MEDICINE, Vol: 28, ISSN: 1195-1982

Journal article

Claro IM, da Silva Sales FC, Ramundo MS, Candido DS, Silva CAM, de Jesus JG, Manuli ER, de Oliveira CM, Scarpelli L, Campana G, Pybus OG, Sabino EC, Faria NR, Levi JEet al., 2021, Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020, EMERGING INFECTIOUS DISEASES, Vol: 27, Pages: 970-972, ISSN: 1080-6040

Journal article

du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole A, Nicholls SM, Parag K, Scher E, Vasylyeva T, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OGet al., 2021, Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK, SCIENCE, Vol: 371, Pages: 708-+, ISSN: 0036-8075

Journal article

Sabino EC, Buss LF, Carvalho MPS, Prete CA, Crispim MAE, Fraiji NA, Pereira RHM, Parag KV, Peixoto PDS, Kraemer MUG, Oikawa MK, Salomon T, Cucunuba ZM, Castro MC, Santos AADS, Nascimento VH, Pereira HS, Ferguson NM, Pybus OG, Kucharski A, Busch MP, Dye C, Faria NRet al., 2021, Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence, LANCET, Vol: 397, Pages: 452-455, ISSN: 0140-6736

Journal article

Franco D, Gonzalez C, Abrego LE, Carrera J-P, Diaz Y, Caicedo Y, Moreno A, Chavarria O, Gondola J, Castillo M, Valdespino E, Gaitán M, Martínez-Mandiche J, Hayer L, Gonzalez P, Lange C, Molto Y, Mojica D, Ramos R, Mastelari M, Cerezo L, Moreno L, Donnelly CA, Pascale JM, Faria NR, Lopez-Verges S, Martinez AA, Gorgas COVID19 team and Panama COVID19 Laboratory Networket al., 2021, Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama., Emerging Infectious Diseases, Vol: 27, Pages: 612-615, ISSN: 1080-6040

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.

Journal article

Li G, Liu Y, Jing X, Wang Y, Miao M, Tao L, Zhou Z, Xie Y, Huang Y, Lei J, Gong G, Jin P, Hao Y, Faria NR, De Clercq E, Zhang Met al., 2021, Mortality risk of COVID-19 in elderly males with comorbidities: a multi-country study, AGING-US, Vol: 13, Pages: 27-60, ISSN: 1945-4589

Journal article

Buss LF, Prete CA, Abrahim CMM, Mendrone A, Salomon T, de Almeida-Neto C, França RFO, Belotti MC, Carvalho MPSS, Costa AG, Crispim MAE, Ferreira SC, Fraiji NA, Gurzenda S, Whittaker C, Kamaura LT, Takecian PL, da Silva Peixoto P, Oikawa MK, Nishiya AS, Rocha V, Salles NA, de Souza Santos AA, da Silva MA, Custer B, Parag KV, Barral-Netto M, Kraemer MUG, Pereira RHM, Pybus OG, Busch MP, Castro MC, Dye C, Nascimento VH, Faria NR, Sabino ECet al., 2021, Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic., Science, Vol: 371, Pages: 288-292, ISSN: 1095-9203

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly in Manaus, the capital of Amazonas state in northern Brazil. The attack rate there is an estimate of the final size of the largely unmitigated epidemic that occurred in Manaus. We use a convenience sample of blood donors to show that by June 2020, 1 month after the epidemic peak in Manaus, 44% of the population had detectable immunoglobulin G (IgG) antibodies. Correcting for cases without a detectable antibody response and for 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 was 29%. These results confirm that when poorly controlled, COVID-19 can infect a large proportion of the population, causing high mortality.

Journal article

Faria NM, 2021, Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings

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.

Working paper

de Souza WM, Amorim MR, Sesti-Costa R, Coimbra LD, Toledo-Teixeira DAD, Parise PL, Barbosa PP, Bispo-dos-Santos K, Mofatto LS, Simeoni CL, Brunetti NS, Claro IM, Duarte ASS, Coletti TM, Zangirolami AB, Costa-Lima C, Gomes ABSP, Buscaratti LI, Sales FC, Costa VA, Franco LAM, Candido DS, Pybus OG, de Jesus JG, Silva CAM, Ramundo MS, Ferreira GM, Pinho MC, Souza LM, Rocha EC, Andrade PS, Crispim MAE, Maktura GC, Manuli ER, Santos MNN, Camilo CC, Angerami RN, Moretti ML, Spilki FR, Arns CW, Addas-Carvalho M, Benites BD, Mori MA, Gaburo N, Dye C, Wu C-H, Marques-Souza H, Marques RE, Farias A, Diamond MS, Faria NR, Sabino EC, Granja F, Proenca-Modena JLet al., 2021, Levels of SARS-CoV-2 Lineage P.1 Neutralization by Antibodies Elicited after Natural Infection and Vaccination, SSRN Electronic Journal

Journal article

Romano CM, Felix AC, de Paula AV, de Jesus JG, Andrade PS, Candido D, de Oliveira FM, Ribeiro AC, da Silva FC, Inemami M, Costa AA, Leal COD, Figueiredo WM, Pannuti CS, de Souza WM, Faria NR, Sabino ECet al., 2021, SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil, REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO, Vol: 63, ISSN: 0036-4665

Journal article

, 2021, SURTO HOSPITALAR DE COVID‐19 NUMA ÁREA ADMINISTRATIVA DO INSTITUTO CENTRAL DO HC‐FMUSP, The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases, Vol: 25, Pages: 101065-101065, ISSN: 1413-8670

Journal article

O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, COVID-19 Genomics UK COG-UK consortium, Network for Genomic Surveillance in South Africa NGS-SA, Brazil-UK CADDE Genomic Network, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Swiss Viollier Sequencing Consortium, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha Rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium DCGC, Communicable Diseases Genomic Network CDGN, Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases KDCA, de Oliveira T, Faria N, Rambaut A, Kraemer MUGet al., 2021, Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch., Wellcome Open Res, Vol: 6, ISSN: 2398-502X

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Journal article

Li SL, Pereira RHM, Prete CA, Zarebski AE, Emanuel L, Alves PJH, Peixoto PS, Braga CKV, de Souza Santos AA, de Souza WM, Barbosa RJ, Buss LF, Mendrone A, de Almeida-Neto C, Ferreira SC, Salles NA, Marcilio I, Wu C-H, Gouveia N, Nascimento VH, Sabino EC, Faria NR, Messina JPet al., 2020, Social and racial inequalities in COVID-19 risk of hospitalisation and death across São Paulo state, Brazil

<jats:title>Summary</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>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.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We conducted a cross-sectional study using hospitalised severe acute respiratory infections (SARI) notified from March to August 2020, in the<jats:italic>Sistema de Monitoramento Inteligente de São Paulo</jats:italic>(SIMI-SP) database. We examined the risk of hospitalisation and death by race and socioeconomic status using multiple datasets for individual-level and spatio-temporal analyses. We explained these inequalities according to differences in daily mobility from mobile phone data, teleworking behaviour, and comorbidities.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>Throughout the study period, patients living in the 40% poorest areas were more likely to die when compared to patients living in the 5% wealthiest areas (OR: 1·60, 95% CI: 1·48 – 1·74) and were more likely to be hospitalised between April and July, 2020 (OR: 1·08, 95% CI: 1·04 – 1·12). Black and<jats:italic>Pardo</jats:italic>individuals were more likely to be hospitalised when compared to White individuals (OR: 1·37, 95% CI: 1·32 – 1·41; OR: 1·23, 95% CI: 1·21 – 1·25, respectively), and were more likely to die (OR: 1·14, 95% CI: 1·07 – 1·21; 1·09, 95% CI: 1·05 – 1·13, respectively).</jats:p></jats:sec><jats:sec><jats

Journal article

du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, OToole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OGet al., 2020, Establishment &amp; lineage dynamics of the SARS-CoV-2 epidemic in the UK

<jats:title>Abstract</jats:title><jats:p>The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in &gt;1000 lineages; those introduced prior to national lockdown were larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.</jats:p>

Journal article

Buss LF, Prete CA, Abrahim CMM, Mendrone A, Salomon T, de Almeida-Neto C, França RFO, Belotti MC, Carvalho MPSS, Costa AG, Crispim MAE, Ferreira SC, Fraiji NA, Gurzenda S, Whittaker C, Kamaura LT, Takecian PL, Oikawa MK, Nishiya AS, Rocha V, Salles NA, de Souza-Santos AA, da Silva MA, Custer B, Barral-Netto M, Kraemer MUG, Pereira RHM, Pybus OG, Busch MP, Castro MC, Dye C, Nascimento VH, Faria NR, Sabino ECet al., 2020, COVID-19 herd immunity in the Brazilian Amazon

<jats:title>Abstract</jats:title><jats:p>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<jats:sup>1</jats:sup>. This fundamental epidemiological parameter is still unknown for the recently-emerged COVID-19, and mathematical models have predicted very divergent results<jats:sup>2,3</jats:sup>. 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.</jats:p>

Journal article

Goes de Jesus J, Gräf T, Giovanetti M, Mares-Guia MA, Xavier J, Lima Maia M, Fonseca V, Fabri A, Dos Santos RF, Mota Pereira F, Ferraz Oliveira Santos L, Reboredo de Oliveira da Silva L, Pereira Gusmão Maia Z, Gomes Cerqueira JX, Thèze J, Abade L, Cordeiro MDCS, Torquato SSC, Santana EB, de Jesus Silva NS, Dourado RSO, Alves AB, do Socorro Guedes A, da Silva Filho PM, Rodrigues Faria N, de Albuquerque CFC, de Abreu AL, Martins Romano AP, Croda J, do Carmo Said RF, Cunha GM, da Fonseca Cerqueira JM, Mello ALESD, de Filippis AMB, Alcantara LCJet al., 2020, Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil, PLoS Neglected Tropical Diseases, Vol: 14, ISSN: 1935-2727

Yellow fever virus (YFV) causes a clinical syndrome of acute hemorrhagic hepatitis. YFV transmission involves non-human primates (NHP), mosquitoes and humans. By late 2016, Brazil experienced the largest YFV outbreak of the last 100 years, with 2050 human confirmed cases, with 681 cases ending in death and 764 confirmed epizootic cases in NHP. Among affected areas, Bahia state in Northeastern was the only region with no autochthonous human cases. By using next generation sequence approach, we investigated the molecular epidemiology of YFV in NHP in Bahia and discuss what factors might have prevented human cases. We investigated 47 YFV positive tissue samples from NHP cases to generate 8 novel YFV genomes. ML phylogenetic tree reconstructions and automated subtyping tools placed the newly generated genomes within the South American genotype I (SA I). Our analysis revealed that the YFV genomes from Bahia formed two distinct well-supported phylogenetic clusters that emerged most likely of an introduction from Minas Gerais and Espírito Santo states. Vegetation coverage analysis performed shows predominantly low to medium vegetation coverage in Bahia state. Together, our findings support the hypothesis of two independent YFV SA-I introductions. We also highlighted the effectiveness of the actions taken by epidemiological surveillance team of the state to prevented human cases.

Journal article

Franco D, Gonzalez C, Abrego LE, Carrera JP, Diaz Y, Caisedo Y, Moreno A, Chavarria O, Gondola J, Castillo M, Valdespino E, Gaitán M, Martínez-Mandiche J, Hayer L, Gonzalez P, Lange C, Molto Y, Mojica D, Ramos R, Mastelari M, Cerezo L, Moreno L, Donnelly CA, Faria NR, Pascale JM, Lopez-Verges S, Martinez AAet al., 2020, Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama

<jats:title>Summary</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease control strategies. We investigated the early transmission patterns of the virus and the outcomes of mitigation measures in the country.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We collected information from epidemiological surveillance, including contact tracing, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number (Rt) using date of symptom onset in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country.</jats:p></jats:sec><jats:sec><jats:title>Interpretation</jats:title><jats:p>These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission clusters is crucial to interrupt local transmission of SARS-CoV-2 in a region.</jats:p></jats:sec>

Journal article

de Souza WM, Buss LF, Candido DDS, Carrera J-P, Li S, Zarebski AE, Pereira RHM, Prete CA, de Souza-Santos AA, Parag KV, Belotti MCTD, Vincenti-Gonzalez MF, Messina J, da Silva Sales FC, Andrade PDS, Nascimento VH, Ghilardi F, Abade L, Gutierrez B, Kraemer MUG, Braga CKV, Aguiar RS, Alexander N, Mayaud P, Brady OJ, Marcilio I, Gouveia N, Li G, Tami A, de Oliveira SB, Porto VBG, Ganem F, de Almeida WAF, Fantinato FFST, Macario EM, de Oliveira WK, Nogueira ML, Pybus OG, Wu C-H, Croda J, Sabino EC, Faria NRet al., 2020, Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil, NATURE HUMAN BEHAVIOUR, Vol: 4, Pages: 856-+, ISSN: 2397-3374

Journal article

Hill SC, de Souza R, Theze J, Claro I, Aguiar RS, Abade L, Santos FCP, Cunha MS, Nogueira JS, Salles FCS, Rocco IM, Maeda AY, Vasami FGS, du Plessis L, Silveira PP, de Jesus JG, Quick J, Fernandes NCCA, Guerra JM, Ressio RA, Giovanetti M, Alcantara LCJ, Cirqueira CS, Diaz-Delgado J, Macedo FLL, Timenetsky MDCST, de Paula R, Spinola R, de Deus JT, Mucci LF, Tubaki RM, de Menezes RMT, Ramos PL, de Abreu AL, Cruz LN, Loman N, Dellicour S, Pybus OG, Sabino EC, Faria NRet al., 2020, Genomic Surveillance of Yellow Fever Virus Epizootic in Sao Paulo, Brazil, 2016-2018, PLOS PATHOGENS, Vol: 16, ISSN: 1553-7366

Journal article

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