West Nile Virus in Brazil

Abstract

Background: West Nile virus (WNV) was first sequenced in Brazil in 2019, when it was isolated from a horse in the Espírito Santo state. Despite multiple studies reporting serological evidence suggestive of past circulation since 2004, WNV remains a low priority for surveillance and public health, such that much is still unknown about its genomic diversity, evolution, and transmission in the country. Methods: A combination of diagnostic assays, nanopore sequencing, phylogenetic inference, and epidemiological modeling are here used to provide a holistic overview of what is known about WNV in Brazil. Results: We report new genetic evidence of WNV circulation in southern (Minas Gerais, São Paulo) and northeastern (Piauí) states isolated from equine red blood cells. A novel, climate-informed theoretical perspective of the potential transmission of WNV across the country highlights the state of Piauí as particularly relevant for WNV epidemiology in Brazil, although it does not reject possible circulation in other states. Conclusion: Our output demonstrates the scarceness of existing data, and that although there is sufficient evidence for the circulation and persistence of the virus, much is still unknown on its local evolution, epidemiology, and activity. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics with spill-over potential to humans.

Keywords: Brazil; West Nile virus; genomic monitoring; molecular detection.

Figure 1

Investigation of WNV infections in Brazil, between July 2018 and September 2020, and estimated transmission potential. (A,B) Agarose gel electrophoresis of amplicons from assay for WNV. (A) nested RT-PCR. MW (Molecular weight ladder), 100 bp DNA Ladder RTU, Kasvi; 1—plasma of horse from São Paulo; 2—buffy coat of horse from São Paulo; 3—washed RBC of horse from São Paulo; 4—blank negative control using during the nested RT-PCR; 5 and 6—positive control (synthetic gene); NTC, no template control (using since the extraction); expected amplicon size: 370 bp. (B) Multiplex PCR. MW (Molecular weight ladder), Fluorescent 100 bp DNA Ladder, Cellco, Jena Bioscience; 1—horse form Minas Gerais (pair primers); 2—horse form Minas Gerais (odd primers); 3—horse form Sao Paulo (pair primers); 4—horse form Sao Paulo (impair primers); 5—horse form Piaui (pair primers); 6—horse form Piaui (odd primers); NTC, no template control (using since the extraction); expected amplicon size: 400 bp. (C) Midpoint rooted maximum-likelihood phylogeny of WNV genomes, showing major lineages. The scale bar is in units of substitutions per site (s/s). Support for branching structure is shown by bootstrap values at nodes. (D) Time-resolved maximum likelihood tree showing the WNV strains belonged to the 1a lineage. Colors indicate geographic location of sampling. The new Brazilian WNV strains are shown with text in red.

Figure 2

Data-driven epidemiological perspective of WNV in Brazil. (A) Mapping of historic evidence for WNV circulation in Brazil, for which the color and symbol legend on the bottom left of the panel define the animal source and methodology. Data are based on a literature review up to 2019 [24], in addition with recently published reports in 2020–2021 [24] and the new data generated in this study. (B) Mean estimated transmission potential of WNV (index P) over the period 2015–2019. The color scale on the bottom left of the panel shows the range of the presented values. The black borders mark the boundaries of the Piauí and Espiríto Santo states. (C) Proportion of months for which the transmission potential of WNV (index P) was above the value 1, over the period 2015–2019. The color scale on the bottom left of the panel shows the range of the presented values. The black borders mark the boundaries of the Piauí and Espiríto Santo states. (D) Time series of suspected reported West Nile fever cases (bars) and estimated transmission potential of WNV (index P, blue line) for the Piauí state. Index P is the average per month, across all data points within the boundaries of the state. (E) Time series of suspected reported West Nile fever cases (bars) and estimated transmission potential of WNV (index P, green line) for the Espiríto Santo state. Index P is the average per month, across all data points within the boundaries of the state. (F) Spatial snapshot of estimated transmission potential of WNV (index P) for the month of March 2016. Color scale on the right shows the range of the presented values. (G) Same as F but for June 2016. (H) Same as F but for September 2016. (I) Same as F but for December 2016.