Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

Giovanetti, Marta; Faria, Nuno Rodrigues; Lourenço, José; Jesus, Jaqueline Góes de; Xavier, Joilson; Claro, Ingra Morales; Kraemer, Moritz U. G.; Fonseca, Vagner; Dellicour, Simon; Thézé, Julien; Salles, Flavia da Silva; Gräf, Tiago; Silveira, Paola Paz; Nascimento, Valdinete Alves do; Souza, Victor Costa de; Iani, Felipe Campos de Melo; Castilho-Martins, Emerson Augusto; Cruz, Laura N.; Wallau, Gabriel Luz; Fabri, Allison; Levy, Flávia Mauad; Quick, Joshua; Azevedo, Vasco; Aguiar, Renato Santana; Oliveira, Túlio de; Menezes, Camila Bôtto de; Castilho, Márcia da Costa; Terra, Tirza Matos; Silva, Marineide Souza da; Filippis, Ana María Bispo de; Abreu, André Luiz de; Oliveira, Wanderson Kleber de; Croda, Júlio; Albuquerque, Carlos Frederico Campelo de; Nunes, Márcio Roberto Teixeira; Sabino, Éster Cerdeira; Loman, Nicholas J.; Naveca, Felipe Gomes; Pybus, Oliver G.; Alcântara, Luíz Carlos Júnior

doi:10.1016/j.celrep.2020.01.085

Cited by 41 publications

(32 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Suitability measures are an increasingly common, data-driven practice in mosquito-borne disease epidemiology, relying on meteorological variables as drivers of mosquito population dynamics and virusmosquito transmission efficiency [23,24,35]. We have validated the suitability index P in previous research, by successfully characterising the transmission potential of Aedes-borne pathogens, such as dengue virus in Brazil and Myanmar, Zika, dengue and chikungunya viruses in Honduras [33,36], and Zika virus in the Amazon region [34].…”

Section: Introductionmentioning

confidence: 99%

“…In this study we set out to characterise in detail the transmission potential of WNV in Israel using a mosquito-borne suitability measure termed the index P [33,34]. Suitability measures are an increasingly common, data-driven practice in mosquito-borne disease epidemiology, relying on meteorological variables as drivers of mosquito population dynamics and virusmosquito transmission efficiency [23,24,35].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background Climate is a major factor in the epidemiology of West Nile virus (WNV), a pathogen increasingly pervasive worldwide. Cases increased during 2018 in Israel, the United States and Europe. Aim We set to retrospectively understand the spatial and temporal determinants of WNV transmission in Israel, as a case study for the possible effects of climate on virus spread. Methods We employed a suitability index to WNV, parameterising it with prior knowledge pertaining to a bird reservoir and Culex species, using local time series of temperature and humidity as inputs. The predicted suitability index was compared with confirmed WNV cases in Israel (2016–2018). Results The suitability index was highly associated with WNV cases in Israel, with correlation coefficients of 0.91 (p value = 4 × 10− 5), 0.68 (p = 0.016) and 0.9 (p = 2 × 10− 4) in 2016, 2017 and 2018, respectively. The fluctuations in the number of WNV cases between the years were explained by higher area under the index curve. A new WNV seasonal mode was identified in the south-east of Israel, along the Great Rift Valley, characterised by two yearly peaks (spring and autumn), distinct from the already known single summer peak in the rest of Israel. Conclusions By producing a detailed geotemporal estimate of transmission potential and its determinants in Israel, our study promotes a better understanding of WNV epidemiology and has the potential to inform future public health responses. The proposed approach further provides opportunities for retrospective and prospective mechanistic modelling of WNV epidemiology and its associated climatic drivers.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Genomic surveillance could be a powerful tool in the implementation of the national COVID-19 control strategy in Thailand. ARTIC multiplex tiling PCR allows whole-genome sequencing with minuscule amount of material by generating genome-wide overlapping amplicons, which has led to its success during the Zika virus outbreak investigation in Brazil ( Quick et al, 2017 , Giovanetti et al, 2020 ). Using leftover RNA samples from a standard RT-PCR diagnosis, the genomic information of SARS-CoV-2 can be decoded in less than a week.…”

Section: Introductionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

et al. 2021

View full text Add to dashboard Cite

“…Perhaps most impressively the MinION decreased the diagnosis time in a 62-year-old female patient with bacterial sepsis from 6.25 days to just 19 h [26]. The MinION's portability and ability to base call in real time has also made it popular for tracking disease outbreaks [24,27,28], including recent outbreaks of ebola [24], zika [28] and COVID-19 [29,30] as well as more isolated outbreaks of human metapneumovirus [31] and the fungal pathogen Candida auris [32].…”

Section: Introductionmentioning

confidence: 99%

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Lamb

Hayes

Nguyen

et al. 2020

Genes

View full text Add to dashboard Cite

Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: ‘crush-side genotyping’ for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.

show abstract

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

Cited by 41 publications

References 60 publications

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Contact Info

Product

Resources

About