Dataset Information

Transmission dynamics and baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines.

ABSTRACT: The Coronavirus disease 2019 (COVID-19) has exposed many systemic vulnerabilities in many countries' health system, disaster preparedness, and adequate response capabilities. With the early lack of data and information about the virus and the many differing local-specific factors contributing to its transmission, managing its spread had been challenging. The current work presents a modified Susceptible-Exposed-Infectious-Recovered compartmental model incorporating intervention protocols during different community quarantine periods. The COVID-19 reported cases before the vaccine rollout in Davao City, Philippines, are utilized to obtain baseline values for key epidemiologic model parameters. The probable secondary infections (i.e., time-varying reproduction number) among other epidemiological indicators were computed. Results show that the cases in Davao City were driven by the transmission rates, positivity proportion, latency period, and the number of severely symptomatic patients. This paper provides qualitative insights into the transmission dynamics of COVID-19 along with the government's implemented intervention protocols. Furthermore, this modeling framework could be used for decision support, policy making, and system development for the current and future pandemics.

SUBMITTER: Anonuevo LE

PROVIDER: S-EPMC10081793 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Transmission dynamics and baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines.

Añonuevo Loreniel E LE Lachica Zython Paul T ZPT Amistas Deza A DA Lato Jayve Iay E JIE Bontilao Hanna Lyka C HLC Catalan Jolly Mae G JMG Pasion Rachel Joy F RJF Yumang Annabelle P AP Almocera Alexis Erich S AES Arcede Jayrold P JP Mata May Anne E MAE de Los Reyes V Aurelio A AA

PloS one 20230407 4

The Coronavirus disease 2019 (COVID-19) has exposed many systemic vulnerabilities in many countries' health system, disaster preparedness, and adequate response capabilities. With the early lack of data and information about the virus and the many differing local-specific factors contributing to its transmission, managing its spread had been challenging. The current work presents a modified Susceptible-Exposed-Infectious-Recovered compartmental model incorporating intervention protocols during d ...[more]

PMID: 37027359

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Project description: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.

Project description:ObjectivesTo improve on the implementation and uses of HIV pre-exposure prophylaxis (PrEP) programmes, factors affecting HIV PrEP willingness must be investigated. This study aims to determine not only the willingness to use HIV PrEP but also to establish whether awareness and attitude affect this.DesignThis study used a cross-sectional survey research design to examine the awareness, attitude and willingness to use HIV PrEP in Davao City. The survey was adapted from multiple studies and was validated and pilot tested. Statistical analysis included descriptive and inferential statistics like correlation, linear regression and structural modelling.SettingsThis research was conducted in Davao City, Philippines. This is one of the regions in the country with a high HIV incidence. The survey was conducted from March to June 2024.ParticipantsParticipants were at least 18 years of age, currently living in Davao City and a permanent resident of the city.ResultsA total of 258 respondents were gathered in this study, of which 53.10% of all respondents were fully aware of HIV PrEP, while 27.13% were partially aware. The study found the mean attitude and willingness to be 4.21±0.686 and 4.08±0.685, respectively. There was a significant difference in the awareness when grouped according to identity category (X2=24.428; p value=0.002) and highest education attained (X2=15.919; p value=0.044). Being fully aware positively affected willingness to use HIV PrEP by indirectly contributing positively to attitude towards HIV PrEP (β=0.180; p value=0.012).ConclusionGenerally, the awareness, attitude and willingness to use HIV PrEP is high. However, some respondents are hesitant to use HIV PrEP if it is not a hundred percent effective and unable to adhere to it. The results imply a need for action programmes involving various multidisciplinary stakeholders to ensure that the community possesses full awareness, positive attitudes and increased willingness to use HIV PrEP.

Project description:Estimating eco-epidemiological parameters in free-ranging populations can be challenging. As known individuals may be undetected during a field session, or their health status uncertain, the collected data are typically "imperfect". Multi-event capture-mark-recapture (MECMR) models constitute a substantial methodological advance by accounting for such imperfect data. In these models, animals can be "undetected" or "detected" at each time step. Detected animals can be assigned an infection state, such as "susceptible" (S), "infected" (I), or "recovered" (R), or an "unknown" (U) state, when for instance no biological sample could be collected. There may be heterogeneity in the assignment of infection states, depending on the manifestation of the disease in the host or the diagnostic method. For example, if obtaining the samples needed to prove viral infection in a detected animal is difficult, this can result in a low chance of assigning the I state. Currently, it is unknown how much uncertainty MECMR models can tolerate to provide reliable estimates of eco-epidemiological parameters and whether these parameters are sensitive to heterogeneity in the assignment of infection states. We used simulations to assess how estimates of the survival probability of individuals in different infection states and the probabilities of infection and recovery responded to (1) increasing infection state uncertainty (i.e., the proportion of U) from 20 to 90%, and (2) heterogeneity in the probability of assigning infection states. We simulated data, mimicking a highly virulent disease, and used SIR-MECMR models to quantify bias and precision. For most parameter estimates, bias increased and precision decreased gradually with state uncertainty. The probabilities of survival of I and R individuals and of detection of R individuals were very robust to increasing state uncertainty. In contrast, the probabilities of survival and detection of S individuals, and the infection and recovery probabilities showed high biases and low precisions when state uncertainty was >50%, particularly when the assignment of the S state was reduced. Considering this specific disease scenario, SIR-MECMR models are globally robust to state uncertainty and heterogeneity in state assignment, but the previously mentioned parameter estimates should be carefully interpreted if the proportion of U is high.

Dataset Information

Transmission dynamics and baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines.

Publications

Transmission dynamics and baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines.

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