Professor Nuno R. Faria

Hill SC, Vasconcelos J, Neto Z, Jandondo D, Ze-Ze L, Aguiar RS, Xavier J, Theze J, Mirandela M, Micolo Candido AL, Vaz F, Sebastiao CDS, Wu C-H, Kraemer MUG, Melo A, Schamber-Reis BLF, de Azevedo GS, Tanuri A, Higa LM, Clemente C, da Silva SP, Candido DDS, Claro IM, Quibuco D, Domingos C, Pocongo B, Watts AG, Khan K, Junior Alcantara LC, Sabino EC, Lackritz E, Pybus OG, Alves M-J, Afonso J, Faria NRet al., 2019, Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation, LANCET INFECTIOUS DISEASES, Vol: 19, Pages: 1138-1147, ISSN: 1473-3099

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• Citations: 44

Oboist U, Perez PN, Villabona-Arenas CJ, Theze J, Faria NR, Lourenco Jet al., 2019, MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index, Methods in Ecology and Evolution, Vol: 10, Pages: 1357-1370, ISSN: 2041-210X

Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open‐source, ready to use and freely available software tools exist.We developed the M osquito‐borne V iral S uitability E stimator (MVSE ) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate‐driven mathematical expression for the basic reproductive number of mosquito‐borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe.We describe the background theory, empirical support and biological interpretation of the index P. Using real‐world examples spanning multiple epidemiological contexts, we further demonstrate MVSE 's basic functionality, research and educational potentials.

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Nazziwa J, Faria N, Chaplin B, Rawizza H, Dakum P, Abimiku A, Charurat M, Ndembi N, Esbjörnsson Jet al., 2019, A3 Molecular epidemiology of HIV-1 in Nigeria, Virus evolution, Vol: 5, ISSN: 2057-1577

Abstract Nigeria has been reported to have the highest number of AIDS-related deaths in the world. In this study, we aimed to use molecular epidemiology to investigate the HIV-1 diversity and phylodynamics in Nigeria. We analyzed 1,442 HIV-1 pol sequences collected from 1999 to 2014 from seven geopolitical zones in Nigeria. The main circulating strains, CRF02_AG (44.1% of the analyzed sequences), Subtype G (8.3%), and CRF43_02G (16.4%), were introduced to Nigeria in the 1960s, 1970s, and 1980s, respectively. The number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. We also found a significant number of unique recombinant forms (22.7%), the majority of which were recombinants between the two or three of the main circulating strains described above. In addition, phylogeographic analysis indicates multiple occasions of HIV-1 transmission between Lagos and Abuja (two of the main cities in Nigeria). Our results may be relevant for HIV-1 intervention and contribute in making informed decisions in strategies aiming at reducing further spread of HIV-1 in Nigeria.

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Candido DDS, Pybus OG, Faria NR, 2019, Genomic epidemiology quantifies gaps in Aedes-borne virus transmission in the Americas, Publisher: OXFORD UNIV PRESS, Pages: S12-S12

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Giovanetti M, de Jesus JG, Joshua Q, Claro IM, Junior JX, Hill SC, Renato S, Paz P, Lourenco J, Dellicour S, Sabino E, Loman NJ, Naveca F, Pybus OG, Faria NR, Carlos Junior Alcantara Let al., 2019, A32 Genomic surveillance of Zika virus transmission in the Amazonas State, Brazil, Virus evolution, Vol: 5, ISSN: 2057-1577

Abstract Zika virus (ZIKV) has caused an unprecedented epidemic linked to severe congenital syndromes. Transmission of ZIKV in the Americas was first confirmed in May 2015 in northeast Brazil, though the virus was likely introduced 1–2 years prior to its detection. Manaus, the capital city of the Amazonas State, the largest territory of any state in Brazil and the main economic center in the northern region, reported between 2016 and 2017 more than 2,327 suspected cases of ZIKV infection. To gain insights into the timing, source, and likely route(s) of ZIKV introduction in the Amazonas State, we tracked the virus by sequencing ZIKV genomes from infected patients. Using nanopore sequencing technology, we generated 56 Brazilian ZIKV genomes from Manaus city in the Amazonas state, sampled from human cases. On the basis of available sequences of isolates from the Americas, the Manaus sequences, we analyzed fell within a single strongly supported monophyletic clade (bootstrap support = 99%, posterior support = 1.00) that belongs to the Asian genotype. Genetic analysis suggests the outbreak most likely originated from transmission cycles not previously identified in North Brazil and not from a separate introduction into the Americas. Molecular dating analysis indicates that the outbreak was caused by a single founder strain that is estimated to have arrived in Manaus around February 2015. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Manaus. Geographical analysis further indicates that the Northern part of the Manaus regions has a high transmission potential for ZIKV. Our work illustrates that near-real time genomics in the field can augment traditional approaches to infectious disease surveillance and control. Estimated dates for the international spread of ZIKV from the north region indicate the persistence of the virus transmission in recipient regions. Our study provides an understanding of how ZIKV

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da Silva Cândido D, Pybus OG, Faria NR, 2019, A38 Genomic epidemiology quantifies gaps in Aedes-borne virus transmission in the Americas, Virus evolution, Vol: 5, ISSN: 2057-1577

Abstract The rapid spread and severity of pathogens, such as Zika (ZIKV) and Chikungunya (CHIKV) viruses in the Americas, demonstrate the need for a better understanding of when and where outbreaks emerge. Sequence evolution of these viral pathogens occurs simultaneously with geographic spread, which allows phylodynamic processes to be recovered from genomic data. Here, we used time-calibrated phylogeographic analyses implemented in a Bayesian phylogenetic framework to characterize the date of introduction of ZIKV, CHIKV, dengue, and yellow fever viruses in different geographic regions of the Americas. To estimate ‘surveillance gaps’, we compared the estimated dates of introduction of these pathogens to the first confirmations of virus circulation in the region. Datasets included all publicly available geo-referenced and time-stamped genetic data from the Americas. A series of environmental and ecological covariates will be tested to infer what factors are associated with the delayed detection of arbovirus transmission in each geographic region. These results will provide important information on where to concentrate surveillance strengthening measures in order to prevent future mosquito-borne virus epidemics.

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Giovanetti M, de Jesus JG, Joshua Q, Claro IM, Xavier Junior J, Hill SC, Renato S, Paz P, Lourenco J, Dellicour S, Sabino E, Loman NJ, Naveca F, Pybus OG, Faria NR, Junior Alcantara LCet al., 2019, Genomic surveillance of Zika virus transmission in the Amazonas State, Brazil, Publisher: OXFORD UNIV PRESS, Pages: S10-S10

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de Jesus JG, Dutra KR, da Silva Salles FC, Claro IM, Terzian AC, da Silva Candido D, Hill SC, Thézé J, DAgostini TL, Felix AC, Negri Reis AF, Alcantara LCJ, Abreu AL, Croda JHR, de Oliveira WK, de Filipis AMB, dos Santos Camis MDCR, Romano CM, Loman NJ, Pybus OG, Sabino EC, Nogueira ML, Faria NRet al., 2019, Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

<jats:title>Abstract</jats:title><jats:p>Over 400 million people are estimated to be at risk of acquiring dengue virus (DENV). Despite efforts to mitigate the impact of DENV epidemics, the virus remains a public health problem in the Americas: more than one million DENV cases were reported in the continent between January and July 2019 DENV was first detected in Brazil in 1982, and Brazil has reported 88% (1,127,244 cases) of all DENV cases in the Americas during 2019 to date. São Paulo state in the southeast of Brazil has reported nearly half of all DENV infections in the country. Here we characterised the genetic diversity of DENV strains circulating in São Paulo state in 2019, at the epicentre of the ongoing DENV epidemic. Using portable nanopore sequencing we generated 20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Notably, phylogenetic analysis indicated that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Our genetic analysis further indicates that the introduction and onwards spread of the outbreak lineage (named here DENV2-III BR-4) indicates a new DENV2 lineage replacement in Brazil. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.</jats:p><jats:sec><jats:title>Author Summary</jats:title><jats:p>Dengue

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Giovanetti M, de Mendonça MCL, Fonseca V, Mares-Guia MA, Fabri A, Xavier J, de Jesus JG, Gräf T, dos Santos Rodrigues CD, dos Santos CC, Sampaio SA, Chalhoub FLL, de Bruycker Nogueira F, Theze J, Romano APM, Ramos DG, de Abreu AL, Oliveira WK, do Carmo Said RF, de Alburque CFC, de Oliveira T, Fernandes CA, Aguiar SF, Chieppe A, Sequeira PC, Faria NR, Cunha RV, Alcantara LCJ, de Filippis AMBet al., 2019, Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies

<jats:title>ABSTRACT</jats:title><jats:p>The recent re-emergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the virus’ rapid dissemination in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil we generated 18 complete and near-complete genomes from the peak of the epidemic curve from non-human primates (NHPs) and human infected cases across Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the timing, source and likely routes of yellow fever virus transmission and dispersion during the one of the largest outbreaks ever registered in Brazil. We showed that the recent YFV epidemic spillover southwards several times from Minas Gerais to Espírito Santo and Rio de Janeiro states in 2016 to 2019. The quick production and analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce that real-time and continued genomic surveillance strategies can assist in the monitoring and public health responses of arbovirus epidemics.</jats:p><jats:sec><jats:title>IMPORTANCE</jats:title><jats:p>Arbovirus infections in Brazil including Yellow Fever, Dengue, Zika and Chikungunya result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by limited availability of real time genomic data. In this study, we investigated the genetic diversity and spatial distribution of YFV during the current outbreak in southeastern Brazil. To gain insights into the routes of YFV introduction and dispersion, we tracked the virus by sequencing YFV genomes sampled from non-human primates and infected patients from the southeastern region. Our study provides an understanding of how YFV initiates transmission in new Brazilian regions and illustrates that near-real

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Vasylyeva TI, du Plessis L, Pineda-Pena AC, Kuehnert D, Lemey P, Vandamme A-M, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NRet al., 2019, Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology, JOURNAL OF INFECTIOUS DISEASES, Vol: 220, Pages: 233-243, ISSN: 0022-1899

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• Citations: 16

Gutierrez B, Wise E, Pullan S, Logue C, Bowden TA, Trueba G, Nunes M, Faria NR, Pybus OGet al., 2019, The evolutionary dynamics of Oropouche Virus (OROV) in South America

<jats:title>Abstract</jats:title><jats:p>The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,<jats:italic>Oropouche orthobunyavirus</jats:italic>(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.</jats:p>

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Xavier J, Giovanetti M, Fonseca V, Theze J, Graf T, Fabri A, de Jesus JG, Lima de Mendonca MC, dos Santos Rodrigues CD, Mares-Guia MA, dos Santos CC, de Oliveira Tosta SF, Candido D, Ribeiro Nogueira RM, de Abreu AL, Oliveira WK, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Sequeira PC, Faria NR, Bispo de Filippis AM, Junior Alcantara LCet al., 2019, Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil, PLOS ONE, Vol: 14, ISSN: 1932-6203

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• Citations: 23

Hanke K, Faria NR, Kuehnert D, Yousef KP, Hauser A, Meixenberger K, Hofmann A, Bremer V, Bartmeyer B, Pybus O, Kuecherer C, von Kleist M, Bannert Net al., 2019, Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany, JOURNAL OF VIROLOGY, Vol: 93, ISSN: 0022-538X

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• Citations: 7

Hill SC, de Souza RP, Thézé 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 Goes J, Quick J, Fernandes NCCA, Guerra JM, Réssio RA, Giovanetti M, Alcantara LCJ, Cirqueira CS, Delgado JD, Macedo FLL, Timenetsky MCST, de Paula R, Spinola R, Telles de Deus JT, Mucci LF, Tubaki RM, Menezes RMT, Ramos PL, Abreu AL, Cruz LN, Loman N, Dellicour S, Pybus OG, Sabino EC, Faria NRet al., 2019, Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

<jats:title>Abstract</jats:title><jats:p>São Paulo (SP), a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in SP, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in SP, we generated and analysed virus genomic data and epizootic case data from NHP in SP. We report the occurrence of three spatiotemporally distinct phases of the outbreak in SP prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in SP, mostly sampled from non-human primates between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo state at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of SP state. Our results shed light on the sylvatic transmission of yellow fever in highly fragmented forested regions in SP state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.</jats:p><

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Kraemer MUG, Reiner RC, Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Weaver ND, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding Net al., 2019, Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus., Nat Microbiol, Vol: 4

In the version of this Article originally published, the affiliation for author Catherine Linard was incorrectly stated as '6Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK'. The correct affiliation is '9Spatial Epidemiology Lab (SpELL), Universite Libre de Bruxelles, Brussels, Belgium'. The affiliation for author Hongjie Yu was also incorrectly stated as '11Department of Statistics, Harvard University, Cambridge, MA, USA'. The correct affiliation is '15School of Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China'. This has now been amended in all versions of the Article.

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Kraemer MUG, Reiner RC, Brady O, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Weaver N, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay S, Golding Net al., 2019, Past and future spread of the arbovirus vectors <i>Aedes aegypti</i> and <i>Aedes albopictus</i>, NATURE MICROBIOLOGY, Vol: 4, Pages: 854-863, ISSN: 2058-5276

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• Citations: 474

Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowe A, Abecasis A, Deforche K, Santiago GA, de Siqueira IC, San EJ, Machado KCB, Azevedo V, Bispo-de Filippis AM, da Cunha RV, Pybus OG, Vandamme A-M, Alcantara LCJ, de Oliveira Tet al., 2019, A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes, PLOS NEGLECTED TROPICAL DISEASES, Vol: 13, ISSN: 1935-2735

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• Citations: 25

Hill SC, de Vasconcelos JN, Granja BG, Theze J, Jandondo D, Neto Z, Mirandela M, Sebastiao CDS, Micolo Candido AL, Clemente C, da Silva SP, de Oliveira T, Pybus OG, Faria NR, Afonso JMet al., 2019, Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018, EMERGING INFECTIOUS DISEASES, Vol: 25, Pages: 784-787, ISSN: 1080-6040

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• Citations: 25

Kraemer MUG, Golding N, Bisanzio D, Bhatt S, Pigott DM, Ray SE, Brady OJ, Brownstein JS, Faria NR, Cummings DAT, Pybus OG, Smith DL, Tatem AJ, Hay SI, Reiner RCet al., 2019, Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings, SCIENTIFIC REPORTS, Vol: 9, ISSN: 2045-2322

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• Citations: 63

Naveca FG, Claro I, Giovanetti M, de Jesus JG, Xavier J, de Melo Iani FC, do Nascimento VA, de Souza VC, Silveira PP, Lourenco J, Santillana M, Kraemer MUG, Quick J, Hill SC, Theze J, de Oliveira Carvalho RD, Azevedo V, da Silva Salles FC, Teixeira Nunes MR, Lemos PDS, Candido DDS, Pereira GDC, Assuncao Oliveira MA, Ribeiro Meneses CA, Maito RM, Santa Brigida Cunha CR, de Sousa Campos DP, Castilho MDC, da Silva Siqueira TC, Terra TM, Campelo de Albuquerque CF, da Cruz LN, de Abreu AL, Martins DV, de Moraes Vanlume Simoes DS, de Aguiar RS, Bessa Luz SL, Loman N, Pybus OG, Sabino EC, Okumoto O, Junior Alcantara LC, Faria NRet al., 2019, Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon, PLOS NEGLECTED TROPICAL DISEASES, Vol: 13, ISSN: 1935-2735

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• Citations: 33

Vasylyeva TI, Liulchuk M, du Plessis L, Fearnhill E, Zadorozhna V, Babii N, Scherbinska A, Novitsky V, Pybus OG, Faria NRet al., 2019, The Changing Epidemiological Profile of HIV-1 Subtype B Epidemic in Ukraine, AIDS RESEARCH AND HUMAN RETROVIRUSES, Vol: 35, Pages: 155-163, ISSN: 0889-2229

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• Citations: 3

Hill SC, Vasconcelos J, Neto Z, Jandondo D, Zé-Zé L, Aguiar RS, Xavier J, Thézé J, Mirandela M, Cândido ALM, Vaz F, Sebastião CDS, Wu C-H, Kraemer M, Melo A, Schamber-Reis BLF, de Azevedo GS, Tanuri A, Higa LM, Clemente C, da Silva SP, da Silva Candido D, Claro IM, Domingos Quibuco N, Domingos C, Pocongo B, Watts AG, Khan K, Alcantara LCJ, Sabino EC, Lackritz E, Pybus OG, Alves M-J, Afonso J, Faria NRet al., 2019, Emergence of the Zika virus Asian lineage in Angola

<jats:sec><jats:title>Research In Context</jats:title><jats:sec><jats:title>Evidence before this study</jats:title><jats:p>We searched PubMed without language restrictions using the keywords ‘Zika’ and ‘Africa’ for papers published to October 2018. We also checked available ‘Situation Report’ publications from WHO for evidence of Zika virus (ZIKV) or congenital Zika disease in Africa. ZIKV African lineage has been detected within Africa since the mid 20<jats:sup>th</jats:sup> century, yet evidence for spread of the ZIKV Asian lineage within Africa is limited. Two countries in Africa (Cabo Verde and Angola) have reported ZIKV cases that are believed to be caused by a newly introduced Asian lineage virus. Sequence data are critical for confirming and understanding the spread of ZIKV Asian lineage within Africa, but these data are currently limited to a single 193bp fragment of the ZIKV NS1 gene from Angola. In addition, whilst epidemiological data on ZIKV and suspected microcephaly cases have been reported in detail from Cabo Verde, data from Angola are extremely limited.</jats:p></jats:sec><jats:sec><jats:title>Added value of this study</jats:title><jats:p>We provide a detailed report of detected ZIKV acute cases and suspected microcephaly cases in Angola. We sequence ZIKV genomes from three acutely infected cases. These represent the first three Asian lineage genomes available from Africa, one of which was acquired from a baby with confirmed microcephaly. Analysis of these sequences suggests that ZIKV may have been introduced to Angola between July 2015 and June 2016, after which it likely circulated for at least one year. This provides the first genetic confirmation of autochthonous ZIKV Asian lineage transmission within Africa. We suggest that the virus was more likely introduced to Angola directly from Brazil, rather than from Cabo Verde.

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Kraemer MUG, Cummings DAT, Funk S, Reiner RC, Faria NR, Pybus OG, Cauchemez Set al., 2019, Reconstruction and prediction of viral disease epidemics, EPIDEMIOLOGY AND INFECTION, Vol: 147, ISSN: 0950-2688

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• Citations: 23

Naveca FG, Claro I, Giovanetti M, de Jesus JG, Xavier J, Iani FCDM, do Nascimento VA, de Souza VC, Silveira PP, Lourenço J, Santillana M, Kraemer MUG, Quick J, Hill SC, Theze J, Carvalho RDDO, Azevedo V, Sales FCDS, Nunes MRT, Lemos PDS, Candido DDS, Pereira GDC, Oliveira MAA, Meneses CAR, Maito RM, Cunha CRSB, Campos DPDS, Castilho MDC, Siqueira TCDS, Terra TM, Albuquerque CFCD, Cruz LND, Abreu ALD, Martins DV, Simoes DSDMV, Aguiar RS, Luz SLB, Loman N, Pybus OG, Sabino EC, Okumoto O, Alcantara LCJ, Faria NRet al., 2018, Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

<jats:p>BackgroundSince its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country.Methodology/Principal FindingsWe report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. In just 48 hours, we generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima.Conclusions/SignificanceThis study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of t

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Flammer PG, Dellicour S, Preston SG, Rieger D, Warren S, Tan CKW, Nicholson R, Prichystalova R, Bleicher N, Wahl J, Faria NR, Pybus OG, Pollard M, Smith ALet al., 2018, Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lubeck, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 285, ISSN: 0962-8452

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• Citations: 14

Giovanetti M, Goes de Jesus J, Lima de Maia M, Junior JX, Castro Amarante MF, Viana P, Khouri Barreto F, de Cerqueira EM, Pedreira Santos N, Barreto Falcao M, Machado Costa MC, Barros Faical AV, Andrade de Melo AL, Santos Amorim L, de Siqueira IC, Macarenhas DL, Bispo de Filippis AM, Faria NR, Xavier Acosta A, Junior Alcantara LCet al., 2018, Genetic evidence of Zika virus in mother's breast milk and body fluids of a newborn with severe congenital defects, CLINICAL MICROBIOLOGY AND INFECTION, Vol: 24, Pages: 1111-1112, ISSN: 1198-743X

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• Citations: 12

do Rosario MS, Giovanetti M, Pereira de Jesus PA, Farias DS, Faria NR, de Lima CPS, da Silva SP, Nunes MR, Junior Alcantara LC, de Siqueira ICet al., 2018, Opsoclonus-myoclonus-ataxia syndrome associated with chikungunya and dengue virus co-infection, INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, Vol: 75, Pages: 11-14, ISSN: 1201-9712

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• Citations: 11

Hill SC, Vasconcelos JND, Granja BG, Thézé J, Jandondo D, Neto Z, Mirandela M, Sebastião CDS, Micolo Cândido AL, Clemente C, Silva SPD, Oliveira TD, Pybus OG, Faria NR, Afonso JMet al., 2018, Early genomic detection of the Cosmopolitan Genotype of Dengue Virus 2 in Angola, 2018

<jats:title>Abstract</jats:title><jats:p>We used portable genome sequencing to investigate reported dengue virus transmission in Angola. Our results reveal autochthonous transmission of dengue serotype 2 (Cosmopolitan genotype) in Jan 2018.</jats:p>

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Nazziwa J, Faria N, Chaplin B, Rawizza H, Dakum P, Abimiku A, Charurat M, Ndembi N, Esbjörnsson Jet al., 2018, Characterisation of the HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread

<jats:title>ABSTRACT</jats:title><jats:p>Nigeria has been reported to have the highest number of AIDS-related deaths in the world. In this study, we aimed to determine the HIV-1 genetic diversity and phylodynamics in Nigeria. We analysed 1442 HIV-1<jats:italic>pol</jats:italic>sequences collected 1999-2014 from four geopolitical zones in Nigeria. Phylogenetic analysis showed that the main circulating strains was the circulating recombinant strain (CRF) 02_AG (44% of the analysed sequences), subtype G (8%), and CRF43_02G (16%); and that these were introduced in Nigeria in the 1960s, 1970s and 1980s, respectively. The number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. We also found a significant number of unique recombinant forms (22.7%). The majority of those were recombinants between two or three of the main circulating strains. Seven of those recombinants may represent novel CRFs. Finally, phylogeographic analysis suggested multiple occasions of HIV-1 transmissions between Lagos and Abuja (two of the main cities in Nigeria), that HIV-1 epidemic started in these cities, and then dispersed into rural areas.</jats:p><jats:sec><jats:title>IMPORTANCE</jats:title><jats:p>Nigeria has the second largest HIV-1 epidemic in the world with the highest number of AIDS-related deaths. The few previous reports have focused on local HIV-1 subtype/CRF distributions in different Nigerian regions, and the molecular epidemiology of HIV-1 in Nigeria as a whole is less well characterized. In this study, we describe the HIV-1 spatiotemporal dynamics of the five dominating transmission clusters representing the main characteristics of the epidemiology. Our results may contribute to inform prevention strategies against further spread of HIV-1 in Nigeria.</jats:p></jats:sec>

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Faria NR, Kraemer MUG, Hill SC, de Jesus JG, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Theze J, Carvalho RDO, Baele G, Wu C-H, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenco J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonca MCL, dos Santos CC, dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OGet al., 2018, Genomic and epidemiological monitoring of yellow fever virus transmission potential, Science, Vol: 361, Pages: 894-899, ISSN: 0036-8075

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.

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