Real-time, rapid detection and sequencing of arboviruses in Brazil

Author(s)

Ingra Morales Claro

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Faculdade de Medicina (FM/SBD)
• Defense date: 2021-10-18

Examining board members

Ester Cerdeira Sabino; Camila Malta Romano; William Marciel de Souza

• Advisor: Ester Cerdeira Sabino

Abstract

Emerging and re-emerging viruses transmitted by arthropods (arboviruses) have always been a global concern for human health. Brazil is a largely tropical country that provides ideal conditions for the existence of many arboviruses that are maintained in a wide variety of zoonotic cycles. In recent years, Brazil has been affected by a wave of serious epidemics, overlapping viruses, mainly caused by the Zika virus (ZIKV), dengue virus (DENV), human immunodeficiency virus (HIV), Ebola virus (EBOV), yellow fever virus (YFV), and Chikungunya virus (CHIKV). The resulting epidemics caused high morbidity, mortality, and economic costs. In addition, there is in Brazil the co-circulation of other arboviruses that are neglected or that are little discussed in the medical literature, which have been responsible for causing small outbreaks or sporadic cases in different regions of the country. However, our understanding of these outbreaks is hampered by the challenge of laboratory diagnosis (often has low specificity and/or requires a priori knowledge of the viruses to be analyzed) and clinical diagnosis (generally fever, headache, joint pain, rashes), which by themselves overlap with those caused by the co-circulation of arthropod-borne viruses, resulting in limited availability of epidemiological surveillance data. Therefore, there is an urgent need to improve our ability to conduct arbovirus surveillance from clinical specimens through better molecular diagnostics. Sequencing tools are approaches that can, in turn, be used to detect and monitor arbovirus diversity, identify emerging strains and control the potential for the introduction of new viruses, being able to prepare or even prevent new outbreaks. In 2016, the ZiBRA (Zika in Brazil Real-Time Analysis) project pioneered a new approach to arbovirus surveillance using portable nanopore-based sequencing technology to obtain complete genomes of the Zika virus in real time - called \"genomic epidemiology \". Being an approach that is still complex and limited by the number of viruses that can be sequenced simultaneously (one reaction for each virus), which greatly increases the cost and does not allow the identification of other viruses that are not being tested in the reaction, this option is still difficult to be adopted as protocol and technology as a routine surveillance tool in research and public health laboratories. In this work, we seek to generate new methodologies that can be used for complete arbovirus surveillance, including a full genome detection and sequencing panel of the main arboviruses of public importance and two metagenomic sequencing approaches for screening and potential discovery of new viruses. In addition, we seek to reduce the cost of arbovirus sequencing to US$ 10 per sample and standardize an improvement in the workflow which will lead to the adoption of this technology by researchers, diagnostic laboratories, and public surveillance laboratories resulting in greater accuracy in the surveillance of arboviruses with the potential for introduction and spread in Brazil and other countries, and accelerate the pace of research on the genetics and epidemiology of arbovirus infections (AU)

• FAPESP's process: 18/17176-8 - Real-time, rapid detection and sequencing of arboviruses in Brazil: Zika, Dengue, Chikungunya and Yellow Fever
• Grantee: Ingra Morales Claro
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)