Imperial College London

Dr Nuno R. Faria

Faculty of MedicineSchool of Public Health

Reader in Viral Evolution
 
 
 
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Contact

 

n.faria

 
 
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Location

 

Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

137 results found

Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ, Network for Genomic Surveillance in South Africa, 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 Biol, Vol: 19

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 Coronavirus Disease 2019 (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.

Journal article

Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FCS, 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 MUG, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Proença-Modena JL, 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 EC, 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 FSV, de Lima AB, Silva JDP, Zauli DAG, de S Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, 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

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.

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., medRxiv

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.

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

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

Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NRet al., 2021, Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil., Infect Genet Evol, Vol: 91

Autochthonous Zika virus (ZIKV) transmission in Brazil was first identified in April 2015 in Brazil, with the first ZIKV-associated microcephaly cases detected in October 2015. Despite efforts on understanding ZIKV transmission in Brazil, little is known about the virus epidemiology and genetic diversity in Minas Gerais (MG), the second most populous state in the country. We report molecular and genomic findings from the main public health laboratory in MG. Until January 2020, 26,817 ZIKV suspected infections and 86 congenital syndrome cases were reported in MG state. We tested 8552 ZIKV and microcephaly suspected cases. Ten genomes were generated on-site directly from clinical samples. A total of 1723 confirmed cases were detected in Minas Gerais, with two main epidemic waves; the first and larger epidemic wave peaked in March 2016, with the second smaller wave that peaked in March 2017. Dated molecular clock analysis revealed that multiple introductions occurred in Minas Gerais between 2014 and 2015, suggesting that the virus was circulating unnoticed for at least 16 months before the first confirmed laboratory case that we retrospectively identified in December 2015. Our findings highlight the importance of continued genomic surveillance strategies combined with traditional epidemiology to assist public health laboratories in monitoring and understanding the diversity of circulating arboviruses, which might help attenuate the public health impact of infectious diseases.

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

Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey Pet al., 2021, Relax, keep walking-a practical guide to continuous phylogeographic inference with BEAST., Mol Biol Evol

Spatially-explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented ten years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyse the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.

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

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

Lima STSD, Souza WMD, Cavalcante JW, da Silva Candido D, Fumagalli MJ, Carrera J-P, Simões Mello LM, de Carvalho Araújo FM, Cavalcante Ramalho IL, de Almeida Barreto FK, de Melo Braga DN, Simião AR, Miranda da Silva MJ, Oliveira RDMAB, Lima CPS, Sousa Lins CD, Barata RR, Melo MNP, de Souza MPC, Franco LM, Távora FRF, Queiroz Lemos DR, Alencar CHMD, Jesus RD, Souza Fonseca VD, Dutra LH, Abreu ALD, Araújo ELL, Ribas Freitas AR, Gonçalves Vianez Júnior JLDS, Pybus OG, Moraes Figueiredo LT, Faria NR, Teixeira Nunes MR, Góes Cavalcanti LPD, Miyajima Fet al., 2020, Fatal outcome of chikungunya virus infection in Brazil., Clinical Infectious Diseases, ISSN: 1058-4838

BACKGROUND: Chikungunya virus (CHIKV) emerged in the Americas in 2013 and has caused ~2.1 million cases and over 600 deaths. A retrospective investigation was undertaken to describe clinical, epidemiological and virus genomic features associated with deaths caused by CHIKV in Ceará state, northeast Brazil. METHODS: 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). Clinical, epidemiological and death reports were obtained for patients with confirmed CHIKV infection. Logistic regression analysis was undertaken to identify independent factors associated with risk of death during CHIKV infection. Phylogenetic analysis was conducted using whole genomes from a subset of cases. RESULTS: 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 were 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 circulation of two CHIKV-East Central South African (ECSA) lineages in Ceará and revealed no unique virus genomic mutation associated with fatal outcome. CONCLUSION: The investigation of the largest cross-sectional cohort of CHIKV-deaths to date reveals that CHIKV-ECSA strains can cause death in individuals from both risk and non-risk groups, including young adults.

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

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

Deng X, Gu W, Federman S, Du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan C-Y, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CYet al., 2020, Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California, Science, Vol: 369, Pages: 582-587, ISSN: 0036-8075

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Journal article

Candido DDS, Claro IM, de Jesus JG, Souza WMD, Moreira FRR, Dellicour S, Mellan T, du Plessis L, Pereira RHM, Sales FCDS, Manuli ER, Theze J, Almeida L, de Menezes MT, Voloch CM, Fumagalli MJ, Coletti TDM, Silva CAM, Ramundo MS, Amorim MR, Hoeltgebaum H, Mishra S, Gill M, Carvalho LM, Buss LF, Prete CA, Ashworth J, Nakaya H, Peixoto PDS, Brady O, Nicholls S, Tanuri A, Rossi AD, Braga CKV, Gerber AL, Guimaraes AP, Gaburo N, Alencar CS, Ferreira ACDS, Lima CX, Levi JE, Granato C, Ferreira GM, Francisco RDS, Granja F, Garcia MT, Moretti ML, Perroud MW, Castineiras TMPP, Lazari CDS, Hill S, Santos AADS, Simeoni CL, Forato J, Sposito AC, Schreiber AZ, Santos MNN, Sa CZ, Souza RP, Resende Moreira LC, Teixeira MM, Hubner J, Leme PAF, Moreira RG, Nogueira ML, Ferguson N, Costa SF, Proenca-Modena JL, Vasconcelos AT, Bhatt S, Lemey P, Wu C-H, Rambaut A, Loman N, Aguiar RS, Pybus O, Sabino EC, Faria NR, CADDE-Genomic-Network, Candido DS, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, Mellan TA, du Plessis L, Pereira RHM, Sales FCS, Manuli ER, Theze J, Almeida L, Menezes MT, Voloch CM, Fumagalli MJ, Coletti TM, Silva CAM, Ramundo MS, Amorim MR, Hoeltgebaum HH, Mishra S, Gill MS, Carvalho LM, Buss LF, Prete Jr CA, Ashworth J, Nakaya H, Peixoto PS, Brady OJ, Nicholls SM, Tanuri A, Rossi AD, Braga CK, Gerber AL, Guimaraes APDC, Gaburo Jr N, Alencar CS, Ferreira ACS, Lima CX, Levi JE, Granato C, Ferreira GM, Francisco Jr RS, Granja F, Garcia MT, Moretti ML, Perroud Jr MW, Castineiras TMPP, Lazari CS, Hill SC, de Souza Santos AA, Simeoni CL, Forato J, Sposito AC, Schreiber AZ, Santos MNN, de Sa CZ, Souza RP, Resende-Moreira LC, Teixeira MM, Hubner J, Leme PAF, Moreira RG, Nogueira ML, Ferguson NM, Costa SF, Proenca-Modena JL, Vasconcelos ATR, Bhatt S, Lemey P, Wu C-H, Rambaut A, Loman NJ, Aguiar RS, Pybus OG, Sabino EC, Faria NRet al., 2020, Evolution and epidemic spread of SARS-CoV-2 in Brazil, Science, Vol: 369, Pages: 1255-1260, ISSN: 0036-8075

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for Sao Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0 - -1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.

Journal article

Prete CA, Buss L, Porto VB, Candido DDS, Ghilardi F, Dighe A, Donnelly CA, Pybus OG, Brady O, Croda JHR, Faria NR, Sabino EC, Nascimento VHet al., 2020, Serial Interval Distribution of SARS-CoV-2 Infection in Brazil, Journal of Travel Medicine, ISSN: 1195-1982

<jats:p>Using 65 transmission pairs of SARS-CoV-2 reported to the Brazilian Ministry of Health 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.</jats:p>

Journal article

Mavian C, Pond SK, Marini S, Magalis BR, Vandamme A-M, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovao NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT-Y, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi Met al., 2020, Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 117, Pages: 12522-12523, ISSN: 0027-8424

Journal article

Lu J, du Plessis L, Liu Z, Hill V, Kang M, Lin H, Sun J, Francois S, Kraemer MUG, Faria NR, McCrone JT, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, Bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus OG, Ke Cet al., 2020, Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China, CELL, Vol: 181, Pages: 997-+, ISSN: 0092-8674

Journal article

Mellan TA, Hoeltgebaum HH, Mishra S, Whittaker C, Schnekenberg RP, Gandy A, Unwin HJT, Vollmer MAC, Coupland H, Hawryluk I, Faria NR, Vesga J, Zhu H, Hutchinson M, Ratmann O, Monod M, Ainslie KEC, Baguelin M, Bhatia S, Boonyasiri A, Brazeau N, Charles G, Cucunuba Z, Cuomo-Dannenburg G, Dighe A, Eaton J, Elsland SLV, Gaythorpe KAM, Green W, Knock E, Laydon D, Lees JA, Mousa A, Nedjati-Gilani G, Nouvellet P, Parag KV, Thompson HA, Verity R, Walters CE, Wang H, Wang Y, Watson OJ, Whittles L, Xi X, Dorigatti I, Walker P, Ghani AC, Riley S, Ferguson NM, Donnelly CA, Flaxman S, Bhatt Set al., 2020, Subnational analysis of the COVID-19 epidemic in Brazil

<jats:label>1</jats:label><jats:title>Abstract</jats:title><jats:p>Brazil is currently reporting the second highest number of COVID-19 deaths in the world. Here we characterise the initial dynamics of COVID-19 across the country and assess the impact of non-pharmaceutical interventions (NPIs) that were implemented using a semi-mechanistic Bayesian hierarchical modelling approach. Our results highlight the significant impact these NPIs had across states, reducing an average <jats:italic>R<jats:sub>t</jats:sub> &gt;</jats:italic> 3 to an average of 1.5 by 9-May-2020, but that these interventions failed to reduce <jats:italic>R<jats:sub>t</jats:sub></jats:italic> &lt; 1, congruent with the worsening epidemic Brazil has experienced since. We identify extensive heterogeneity in the epidemic trajectory across Brazil, with the estimated number of days to reach 0.1% of the state population infected since the first nationally recorded case ranging from 20 days in São Paulo compared to 60 days in Goiás, underscoring the importance of sub-national analyses in understanding asynchronous state-level epidemics underlying the national spread and burden of COVID-19.</jats:p>

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., 2020, A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages, Publisher: Cold Spring Harbor Laboratory

<jats:p>Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (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 analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. 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.</jats:p>

Working paper

de Oliveira SB, Pôrto VBG, Ganem F, Mendes FM, Almiron M, de Oliveira WK, Fantinato FFST, de Almeida WAF, de Macedo Borges AP, Pinheiro HNB, Oliveira RDS, Andrews JR, Faria NR, Lopes MB, de Araújo WN, Diaz-Quijano FA, Nakaya HI, Croda Jet al., 2020, Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data

<jats:title>Abstract</jats:title><jats:p>Social distancing measures have emerged as the predominant intervention for containing the spread of COVID-19, but evaluating adherence and effectiveness remains a challenge. We assessed the relationship between aggregated mobility data collected from mobile phone users and the time-dependent reproduction number R(t), using severe acute respiratory illness (SARI) cases reported by São Paulo and Rio de Janeiro. We found that the proportion of individuals staying home all day (isolation index) had a strong inverse correlation with R(t) (rho&lt;-0.7) and was predictive of COVID-19 transmissibility (p&lt;0.0001). Furthermore, indexs of 46.7% had the highest accuracy (93.9%) to predict R(t) below one. This metric can be monitored in real time to assess adherence to social distancing measures and predict their effectiveness for controlling SARS-CoV-2 transmission.</jats:p><jats:sec><jats:title>One Sentence Summary</jats:title><jats:p>Mobility data to monitoring social distancing in the COVID-19 outbreak</jats:p></jats:sec>

Journal article

Kraemer MUG, Yang C-H, Gutierrez B, Wu C-H, Klein B, Pigott DM, du Plessis L, Faria NR, Li R, Hanage WP, Brownstein JS, Layan M, Vespignani A, Tian H, Dye C, Pybus OG, Scarpino SVet al., 2020, The effect of human mobility and control measures on the COVID-19 epidemic in China, SCIENCE, Vol: 368, Pages: 493-+, ISSN: 0036-8075

Journal article

Cunha MS, Faria NR, Caleiro GS, Candido DS, Hill SC, Claro IM, da Costa AC, Nogueira JS, Maeda AY, da Silva FG, de Souza RP, Spinola R, Tubaki RM, Tironi de Menezes RM, Abade L, Mucci LF, Sampaio Tavares Timenetsky MDC, Sabino Eet al., 2020, Genomic evidence of yellow fever virus in Aedes scapularis, southeastern Brazil, 2016, ACTA TROPICA, Vol: 205, ISSN: 0001-706X

Journal article

de Souza WM, Buss LF, Candido DDS, Carrera J-P, Li S, Zarebski AE, Vincenti-Gonzalez MF, Messina J, Silva Sales FCD, Santos Andrade PD, Prete CA, Nascimento VH, Ghilardi F, Moraes Pereira RH, Souza Santos AAD, Abade L, Gutierrez B, Kraemer MUG, Aguiar RS, Alexander N, Mayaud P, Brady OJ, de Souza IOM, Gouveia N, Li G, Tami A, de Oliveira SB, Gomes Porto VB, Ganem F, de Almeida WAF, Tardetti Fantinato FFS, Macário EM, de Oliveira WK, Pybus OG, Wu C-H, Croda J, Sabino EC, Faria NRet al., 2020, Epidemiological and clinical characteristics of the early phase of the COVID-19 epidemic in Brazil

<jats:title>Summary</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The first case of COVID-19 was detected in Brazil on February 25, 2020. We report the epidemiological, demographic, and clinical findings for confirmed COVID-19 cases during the first month of the epidemic in Brazil.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Individual-level and aggregated COVID-19 data were analysed to investigate demographic profiles, socioeconomic drivers and age-sex structure of COVID-19 tested cases. Basic reproduction numbers (<jats:italic>R</jats:italic><jats:sub><jats:italic>0</jats:italic></jats:sub>) were investigated for São Paulo and Rio de Janeiro. Multivariate logistic regression analyses were used to identify symptoms associated with confirmed cases and risk factors associated with hospitalization. Laboratory diagnosis for eight respiratory viruses were obtained for 2,429 cases.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>By March 25, 1,468 confirmed cases were notified in Brazil, of whom 10% (147 of 1,468) were hospitalised. Of the cases acquired locally (77·8%), two thirds (66·9% of 5,746) were confirmed in private laboratories. Overall, positive association between higher per capita income and COVID-19 diagnosis was identified. The median age of detected cases was 39 years (IQR 30-53). The median <jats:italic>R</jats:italic><jats:sub><jats:italic>0</jats:italic></jats:sub> was 2·9 for São Paulo and Rio de Janeiro. Cardiovascular disease/hypertension were associated with hospitalization. Co-circulation of six respiratory viruses, including influenza A and B and human rhinovirus was detected in low levels.</jats:p></jats:sec><jats:sec><jats:title>Interpretation<

Journal article

Lu J, Plessis LD, Liu Z, Hill V, Kang M, Lin H, Sun J, François S, Kraemer MUG, Faria NR, McCrone JT, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus OG, Ke Cet al., 2020, Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

<jats:title>Summary</jats:title><jats:p>COVID-19 is caused by the SARS-CoV-2 coronavirus and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China’s most populous province, during early 2020 resulted in 1,388 reported RNA positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain due to low virus genetic variation early in the pandemic. Our results illustrate how the timing, size and duration of putative local transmission chains were constrained by national travel restrictions and by the province’s large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required as the number of cases imported from other countries is increasing.</jats:p><jats:sec><jats:title>Highlights</jats:title><jats:list list-type="bullet"><jats:list-item><jats:p>1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19<jats:sup>th</jats:sup> March 2020</jats:p></jats:list-item><jats:list-item><jats:p>Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples.</jats:p></jats:list-item><jats:list-item><jats:p>Genomic analyses reveal multiple virus importations into Guangdong Province, resulting in genetically distinct clusters that require careful interpretation.</jats:p></jats:list-item><jats:list-item><jats:p>Large-scale epidemiological surve

Journal article

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