Journal Articles - UP - MSI
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- Multifaceted assessment of wastewater-based epidemiology for SARS-CoV-2 in selected urban communities in Davao City, Philippines: A pilot studyOtero, Maria Catherine B.; Murao, Lyre Anni E.; Limen, Mary Antoinette G.; Caalim, Daniel Rev A.; Gaite, Paul Lorenzo A.; Bacus, Michael G.; Acaso, Joan T.; Miguel, Refeim M.; Corazo, Kahlil; Knot, Ineke E.; Sajonia, Homer; de los Reyes, Francis L.; Jaraula, Caroline Marie B.; Baja, Emmanuel S.; Del Mundo, Dann Marie N. (MDPI, 2022-07-19)Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical–anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.The authors thank the Davao City Health Office, the local government units under the City Government of Davao, the partner hospitals for their support and assistance, and Diana Aga for discussions on sample collection and analyses. The authors would also like to thank the members of the Bortz Virology Laboratory at the University of Alaska Anchorage- Ralf Dagdag and Matthew Redlinger, Amanda Warr from the Roslin Institute, Nicole Wheeler from the University of Birmingham, Lara Urban, co-founder of PuntSeq, and Joe Russell from MRI Global for their expert advice in nanopore and wastewater sequencing.
- Shallow structures, interactions, and recurrent vertical motions of active faults in Lingayen Gulf, PhilippinesFlores, Paul Caesar M.; Siringan, Fernando P.; Mateo, Zenon Richard P.; Marfito, Bryan J.; Sarmiento, Keanu Jershon S.; Abigania, Maria Isabel T.; Daag, Arturo S.; Maac-Aguilar, Yolanda (Elsevier, 2023-06-01)The surface trace of the East Zambales Fault (EZF) and its associated faults in the Lingayen Gulf have been previously mapped but no other characteristics were reported. This study utilized seismic reflection, multi-beam bathymetry, and side scan sonar to characterize the offshore EZF in terms of magnitudes of vertical displacement. Sequence stratigraphy and radiocarbon dates provided age constraints on the recurrence interval within the Holocene. The EZF extends for ∼ 57 km into the gulf, follows a north-northwest trend, and bounds the karstic terrane (west) and fluvio-deltaic deposits (east). Sinistral motion is indicated by: 1) normal and reverse drag geometries, 2) reversal in the sense of throw with depth, 3) flower structure, and 4) right-stepping and the uplift of a pressure ridge named Pudoc Bathymetric High. The Central Lingayen Gulf Fault (CLGF), to the east of EZF, follows the same trend. The Lingayen Gulf Transverse Fault (LGTF), oriented east–west, forms a flower structure with the CLGF. The EZF, CLGF, and LGTF combined form the Lingayen Gulf Fault System, which divides the gulf into five fault blocks where uplift and subsidence locally occurred. A paleo-delta at −60 m yielded an age of 6.8 kyBP, indicating it was formed during the first Holocene highstand. With natural compaction considered, fault-associated subsidence of 46–53 m may have occurred. The average Holocene vertical displacement is 2.1–2.2 m, which translates to a recurrence interval of 320–270 years for the fault system. The faults can likely generate earthquakes with magnitudes 7.5 (EZF), 6.7 (CLGF), and 6.6 (LGTF).This work was supported by grants to F. P. Siringan by the Department of Science and Technology – Philippine Council for Industry, Energy and Emerging Technology Research and Development through the Mapping of Active Offshore Faults for Resilient Coasts Project; and the Department of Environment and Natural Resources – Biodiversity Management Bureau through the Coral Reef Visualization and Assessment - Deep Coral Mapping Project. We are thankful to Deo Carlo Llamas for the meaningful discussions about the current knowledge of the East Zambales Fault. We also thank the anonymous reviewers who provided significant insights for the improvement of this manuscript.