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.
- Local tide and geoid corrections significantly improve coastal retracked Jason sea surface heights in the PhilippinesFlores, Paul Caesar; Reyes, Rosalie; Amedo-Repollo, Charina Lyn; Rediang, Abegail; Alfante, Rey Mark; Bauzon, Ma. Divina Angela; Pasaje, Nikki; Bringas, Dennis (Science and Technology Information Institute, 2022-11-08)Retracking algorithms increase the accuracy of coastal sea surface height (SSH) measurements. However, it is still important to validate these retracking estimates with tide gauge (SSHtg) observations. We downloaded the freely available Jason altimeter SSH processed using the XTRACK-ALES algorithm, then detided the SSH using different tide models. The first model is the default tidal correction based on Finite Element Solution 2014 (SSHfes), and the second model is the T_Tide harmonic analysis of the nearest tide gauge (SSHaltimeter). SSHfes showed a very poor correlation (< 0.31) and very high root mean square error (RMSE, > 29 cm). In contrast, SSHaltimeter generally showed a very high correlation (> 0.91) and low RMSE (< 17.4 cm). A further quality check based on the average and standard deviation of the difference between the SSH readings (SSHfes – SSHtg and SSHaltimeter – SSHtg) also showed the superior performance of SSHaltimeter,which scored < 9.3 and < 16.5 cm, respectively; compared to SSHfes, which scored < 9.3 cm and > 27 cm for the same parameters. The poor performance from the SSHfes likely comes from the complex bathymetry and coastal geomorphology of the country, which is not accounted for in the FES. The Philippines generally has a narrow shelf, and the FES tide corrections may be related to deep-water tides rather than the shallow-water tides observed from tide gauges. Despite the high correlation and agreement between the SSHaltimeter and SSHtg, the rate of sea level rise from the SSHaltimeter in some sites is more than twice the rate from SSHtg, which indicates the possible influence of the vertical land movement.
- Ground deformation analysis caused by post-2013 earthquake in Bohol, PhilippinesBauzon, Ma. Divina Angela I.; Reyes, Rosalie B.; Blanco, Ariel C.; Siringan, Fernando P. (Springer Science and Business Media LLC, 2022-08-16)After the 2013 Mw 7.2 earthquake that occurred in Bohol, the shoreline specifically in Loon and Maribojoc was observed to shift seaward due to ground uplift. This study analyzes the post-earthquake shoreline movement, specifically a 12 km coastal strip in Loon and Maribojoc, and ground deformation of the West Bohol area through Sentinel-1 image processing techniques. From October 2014 to April 2018, the DSAS linear regression shoreline rates were − 4.36 m/yr in Loon and − 1.69 m/yr in Maribojoc, indicative of a landward movement of 91.4% and 88.8% of shoreline transects in Loon and Maribojoc, respectively. PSInSAR revealed varying rates of VLM in the study area from October 2014 to December 2018 such that Loon and Maribojoc exhibit a subsidence rate of − 2 to − 8 mm/yr. The correlation between the shoreline retreat and the land subsidence in the study area is 87%, indicating a possible elastic rebound after the earthquake. The portion of Tagbilaran City on its northern side exhibits land subsidence of − 2 to − 6 mm/yr while its southern side exhibits land uplift of 0–2 mm/yr. The relative sea level fall from TGSL measurements indicates an uplift in the location of the tide gauge in Tagbilaran City.
- 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).