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Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021

Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using gen...

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Autores principales: Capin, Jessel Babe G., Sanque, Angela Jahn C., Eng, Maria Noreen J., Lagare, Arlene, Sepulveda, Maria Corazon B., Murao, Lyre Anni E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10459148/
https://www.ncbi.nlm.nih.gov/pubmed/37632001
http://dx.doi.org/10.3390/v15081658
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author Capin, Jessel Babe G.
Sanque, Angela Jahn C.
Eng, Maria Noreen J.
Lagare, Arlene
Sepulveda, Maria Corazon B.
Murao, Lyre Anni E.
author_facet Capin, Jessel Babe G.
Sanque, Angela Jahn C.
Eng, Maria Noreen J.
Lagare, Arlene
Sepulveda, Maria Corazon B.
Murao, Lyre Anni E.
author_sort Capin, Jessel Babe G.
collection PubMed
description Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using genome sequences from Davao City and nearby provinces. We adapted the RABV ARTIC Protocol for Oxford Nanopore High-Throughput Sequencing to optimize workflow efficiency under limited resources. Comparing new virus samples collected from June 2019 to June 2021 (n = 38) with baseline samples from June 2018 to May 2019 (n = 49), new sub-clades were observed in the phylogenetic tree, suggesting divergence from older variants that were previously undetected. Most of the new viruses belonged to the Asian SEA4_A1.1.1 lineage, but new (SEA4_B1 and SEA4_B1.1) and emerging (SEA4_B1.1_E1) lineages that have never been reported in the Philippines were also identified. The baseline study reported phylogeographic clustering of RABV isolates from the same areas. However, this pattern was disrupted in the current biosurveillance, with variants detected in areas outside the original cluster. Furthermore, our findings revealed significant transmission routes between Davao City and neighboring provinces, contrasting with the predominantly intra-city transmission observed in the baseline study. These results underscore the need for ongoing and timely genomic surveillance to monitor genetic diversity changes and the emergence of novel strains, as well as to track alterations in transmission pathways. Implementing cost-effective next-generation sequencing workflows will facilitate the integration of genomic surveillance into rabies control programs, particularly in resource-limited settings. Collaborations between different sectors can empower local laboratories and experts in genomic technologies and analysis.
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spelling pubmed-104591482023-08-27 Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021 Capin, Jessel Babe G. Sanque, Angela Jahn C. Eng, Maria Noreen J. Lagare, Arlene Sepulveda, Maria Corazon B. Murao, Lyre Anni E. Viruses Article Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using genome sequences from Davao City and nearby provinces. We adapted the RABV ARTIC Protocol for Oxford Nanopore High-Throughput Sequencing to optimize workflow efficiency under limited resources. Comparing new virus samples collected from June 2019 to June 2021 (n = 38) with baseline samples from June 2018 to May 2019 (n = 49), new sub-clades were observed in the phylogenetic tree, suggesting divergence from older variants that were previously undetected. Most of the new viruses belonged to the Asian SEA4_A1.1.1 lineage, but new (SEA4_B1 and SEA4_B1.1) and emerging (SEA4_B1.1_E1) lineages that have never been reported in the Philippines were also identified. The baseline study reported phylogeographic clustering of RABV isolates from the same areas. However, this pattern was disrupted in the current biosurveillance, with variants detected in areas outside the original cluster. Furthermore, our findings revealed significant transmission routes between Davao City and neighboring provinces, contrasting with the predominantly intra-city transmission observed in the baseline study. These results underscore the need for ongoing and timely genomic surveillance to monitor genetic diversity changes and the emergence of novel strains, as well as to track alterations in transmission pathways. Implementing cost-effective next-generation sequencing workflows will facilitate the integration of genomic surveillance into rabies control programs, particularly in resource-limited settings. Collaborations between different sectors can empower local laboratories and experts in genomic technologies and analysis. MDPI 2023-07-30 /pmc/articles/PMC10459148/ /pubmed/37632001 http://dx.doi.org/10.3390/v15081658 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Capin, Jessel Babe G.
Sanque, Angela Jahn C.
Eng, Maria Noreen J.
Lagare, Arlene
Sepulveda, Maria Corazon B.
Murao, Lyre Anni E.
Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title_full Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title_fullStr Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title_full_unstemmed Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title_short Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018–2021
title_sort emerging genomic trends on rabies virus in davao region, philippines, 2018–2021
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10459148/
https://www.ncbi.nlm.nih.gov/pubmed/37632001
http://dx.doi.org/10.3390/v15081658
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