1
|
Valdivia-Carrera CA, Ho-Palma AC, Munguia-Mercado A, Gonzalez-Pizarro K, Ibacache-Quiroga C, Dinamarca A, Stehlík M, Rusiñol M, Girones R, Lopez-Urbina MT, Basaldua Galarza A, Gonzales-Gustavson E. Surveillance of SARS-CoV-2, rotavirus, norovirus genogroup II, and human adenovirus in wastewater as an epidemiological tool to anticipate outbreaks of COVID-19 and acute gastroenteritis in a city without a wastewater treatment plant in the Peruvian Highlands. Sci Total Environ 2023; 905:167161. [PMID: 37730068 DOI: 10.1016/j.scitotenv.2023.167161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated that Wastewater Based Epidemiology is a fast and economical alternative for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level in high-income countries. In the present study, wastewater from a city in the Peruvian Highlands, which lacks a wastewater treatment plant, was monitored for one year to assess the relationship between the concentration of SARS-CoV-2 and the reported cases of COVID-19 in the community. Additionally, we compared the relationship between rotavirus (RV), norovirus genogroup II (NoV GGII), and human adenovirus (HAdV) with the number of reported cases of acute gastroenteritis. Before commencing the analysis of the samples, the viral recovery efficacy of three processing methods was determined in spiked wastewater with SARS-CoV-2. This evaluation demonstrated the highest recovery rate with direct analysis (72.2 %), as compared to ultrafiltration (50.8 %) and skimmed milk flocculation (5.6 %). Wastewater monitoring revealed that 72 % (36/50) of the samples tested positive for SARS-CoV-2, with direct analysis yielding the highest detection frequency and quantification of SARS-CoV-2. Furthermore, a strong correlation was observed between the concentration of SARS-CoV-2 in wastewater and the reported cases of COVID-19, mainly when we shift the concentration of SARS-CoV-2 by two weeks, which allows us to anticipate the onset of the fourth and fifth waves of the pandemic in Peru up to two weeks in advance. All samples processed using the skimmed milk flocculation method tested positive and showed high concentrations of RV, NoV GGII, and HAdV. In fact, the highest RV concentrations were detected up to four weeks before outbreaks of acute gastroenteritis reported in children under four years of age. In conclusion, the results of this study suggest that periodic wastewater monitoring is an excellent epidemiological tool for surveillance and can anticipate outbreaks of infectious diseases, such as COVID-19, in low- and middle-income countries.
Collapse
Affiliation(s)
- Cesar A Valdivia-Carrera
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Ana C Ho-Palma
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru.
| | - Astrid Munguia-Mercado
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru.
| | - Karoll Gonzalez-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Claudia Ibacache-Quiroga
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Alejandro Dinamarca
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Milan Stehlík
- Institute of Statistics, Universidad de Valparaiso, Av. Gran Bretana 1111, Valparaiso, Chile; Linz Institute of Technology & Department of Applied Statistics, Johannes Kepler University in Linz, Altenberger Straße 69, 4040 Linz, Austria.
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Maria T Lopez-Urbina
- Laboratory of Veterinary Epidemiology and Economics, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Anani Basaldua Galarza
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru; Dirección Ejecutiva de Epidemiología, Dirección Regional de Salud, Jr. Julio Cesar Tello 488, Huancayo 12004, Junin, Peru.
| | - Eloy Gonzales-Gustavson
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| |
Collapse
|
2
|
Stehlík M, Kisel'ák J, Dinamarca A, Alvarado E, Plaza F, Medina FA, Stehlíková S, Marek J, Venegas B, Gajdoš A, Li Y, Katuščák S, Bražinová A, Zeintl E, Lu Y. REDACS: Regional emergency-driven adaptive cluster sampling for effective COVID-19 management. Stoch Anal Appl 2022; 41:474-508. [PMID: 37982071 PMCID: PMC10655945 DOI: 10.1080/07362994.2022.2033126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 11/21/2023]
Abstract
As COVID-19 is spreading, national agencies need to monitor and track several metrics. Since we do not have perfect testing programs on the hand, one needs to develop an advanced sampling strategies for prevalence study, control and management. Here we introduce REDACS: Regional emergency-driven adaptive cluster sampling for effective COVID-19 management and control and justify its usage for COVID-19. We show its advantages over classical massive individual testing sampling plans. We also point out how regional and spatial heterogeneity underlines proper sampling. Fundamental importance of adaptive control parameters from emergency health stations and medical frontline is outlined. Since the Northern hemisphere entered Autumn and Winter season (this paper was originally submitted in November 2020), practical illustration from spatial heterogeneity of Chile (Southern hemisphere, which already experienced COVID-19 winter outbreak peak) is underlying the importance of proper regional heterogeneity of sampling plan. We explain the regional heterogeneity by microbiological backgrounds and link it to behavior of Lyapunov exponents. We also discuss screening by antigen tests from the perspective of "on the fly" biomarker validation, i.e., during the screening.
Collapse
Affiliation(s)
- M Stehlík
- Linz Institute of Technology & Department of Applied Statistics, J. Kepler University in Linz, Linz, Austria
- Instituto de Estadística, Universidad de Valparaíso, Valparaíso, Chile
- Facultad de Ingeniería, Universidad Andrés Bello, Valparaíso, Chile
| | - J Kisel'ák
- Institute of Mathematics, Faculty of Science, P.J.Šafárik University, Košice, Slovakia
| | - A Dinamarca
- Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - E Alvarado
- Instituto de Estadística, Universidad de Valparaíso, Valparaíso, Chile
| | - F Plaza
- Instituto de Estadística, Universidad de Valparaíso, Valparaíso, Chile
- Instituto de Fomento Pesquero, Chile
| | - F A Medina
- Biostatistics Program, School of Public Health, University of Chile, Santiago, Chile
| | - S Stehlíková
- Linz Institute of Technology & Department of Applied Statistics, J. Kepler University in Linz, Linz, Austria
| | - J Marek
- University of Pardubice, Pardubice, Czech Republic
| | - B Venegas
- Departamento de Estomatología, Facultad de Ciencias de la Salud, Universidad de Talca, Chile
| | - A Gajdoš
- Facultad de Ingeniería, Universidad Andrés Bello, Valparaíso, Chile
| | - Y Li
- The University of Iowa, Iowa City, Iowa, USA
| | - S Katuščák
- Emeritus Prof.STU, Senior Konzulting, ESK
| | - A Bražinová
- Institute of Epidemiology, Faculty of Medicine in Bratislava, Comenius University, Slovak Republic
| | - E Zeintl
- Linz Institute of Technology & Department of Applied Statistics, J. Kepler University in Linz, Linz, Austria
| | - Y Lu
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| |
Collapse
|
3
|
Affiliation(s)
- M. Stehlík
- Linz Institute of Technology & Department of Applied Statistics, J. Kepler University in Linz, Linz, Austria
- Instituto de Estadística, Universidad de Valparaíso, Valparaíso, Chile
| | - L. M. Grilo
- Instituto Politécnico de Tomar (IPT) & Universidade Aberta, Tomar, Tomar, Portugal
- Centro de Matemática e Aplicaçães (CMA), FCT, Universidade Nova de Lisboa, Lisboa, Portugal
- Centro de Investigação em Cidades Inteligentes (Ci2), IPT & CIICESI / ESTG – P. Porto, Porto, Portugal
| | - P. K. Jordanova
- Faculty of Mathematics and Informatics, Konstantin Preslavsky University of Shumen, Shumen, Bulgaria
| |
Collapse
|
4
|
Mantalos P, Karagrigoriou A, Střelec L, Jordanova P, Hermann P, Kiseľák J, Hudák J, Stehlík M. On improved volatility modelling by fitting skewness in ARCH models. J Appl Stat 2019; 47:1031-1063. [DOI: 10.1080/02664763.2019.1671323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- P. Mantalos
- Department of Economics and Statistics, Linnaeus University, Vaxjo, Sweden
| | - A. Karagrigoriou
- Department of Statistics & Actuarial Financial Mathematics, University of the Aegean, Samos, Greece
| | - L. Střelec
- Department of Statistics and Operation Analysis, Mendel University, Brno, Czech Republic
| | - P. Jordanova
- Faculty of Mathematics and Informatics, Shumen University, Shumen, Bulgaria
| | - P. Hermann
- Department of Applied Statistics, Johannes Kepler University, Linz, Austria
| | - J. Kiseľák
- Department of Applied Statistics, Johannes Kepler University, Linz, Austria
- LIT – Linz Institute of Technology, Johannes Kepler University, Linz, Austria
- Institute of Mathematics, Faculty of Science, P. J. Šafárik University in Košice, Kosice, Slovakia
| | - J. Hudák
- Institute of Mathematics, Faculty of Science, P. J. Šafárik University in Košice, Kosice, Slovakia
| | - M. Stehlík
- Department of Applied Statistics, Johannes Kepler University, Linz, Austria
- LIT – Linz Institute of Technology, Johannes Kepler University, Linz, Austria
- Department of Statistics, University of Valparaíso, Valparaíso, Chile
- Statistics & Actuarial Science Department, The University of Iowa, IA, USA
| |
Collapse
|
5
|
|
6
|
|
7
|
Stehlík M, Aguirre P, Girard S, Jordanova P, Kiseľák J, Torres S, Sadovský Z, Rivera A. On ecosystems dynamics. Ecological Complexity 2017. [DOI: 10.1016/j.ecocom.2016.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
|
9
|
|
10
|
|
11
|
Hermann P, Mrkvička T, Mattfeldt T, Minárová M, Helisová K, Nicolis O, Wartner F, Stehlík M. Fractal and stochastic geometry inference for breast cancer: a case study with random fractal models and Quermass-interaction process. Stat Med 2015; 34:2636-61. [PMID: 25847279 DOI: 10.1002/sim.6497] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/05/2015] [Accepted: 03/12/2015] [Indexed: 11/10/2022]
Abstract
Fractals are models of natural processes with many applications in medicine. The recent studies in medicine show that fractals can be applied for cancer detection and the description of pathological architecture of tumors. This fact is not surprising, as due to the irregular structure, cancerous cells can be interpreted as fractals. Inspired by Sierpinski carpet, we introduce a flexible parametric model of random carpets. Randomization is introduced by usage of binomial random variables. We provide an algorithm for estimation of parameters of the model and illustrate theoretical and practical issues in generation of Sierpinski gaskets and Hausdorff measure calculations. Stochastic geometry models can also serve as models for binary cancer images. Recently, a Boolean model was applied on the 200 images of mammary cancer tissue and 200 images of mastopathic tissue. Here, we describe the Quermass-interaction process, which can handle much more variations in the cancer data, and we apply it to the images. It was found out that mastopathic tissue deviates significantly stronger from Quermass-interaction process, which describes interactions among particles, than mammary cancer tissue does. The Quermass-interaction process serves as a model describing the tissue, which structure is broken to a certain level. However, random fractal model fits well for mastopathic tissue. We provide a novel discrimination method between mastopathic and mammary cancer tissue on the basis of complex wavelet-based self-similarity measure with classification rates more than 80%. Such similarity measure relates to Hurst exponent and fractional Brownian motions. The R package FractalParameterEstimation is developed and introduced in the paper.
Collapse
Affiliation(s)
- Philipp Hermann
- Department of Applied Statistics, Johannes Kepler University Linz, Linz, Austria
| | - Tomáš Mrkvička
- Department of Applied Mathematics and Informatics, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | | | - Mária Minárová
- Department of Mathematics, Slovak University of Technology, Bratislava, Slovak Republic
| | - Kateřina Helisová
- Department of Mathematics, Czech Technical University in Prague, Prague, Czech Republic
| | - Orietta Nicolis
- Institute of Statistics, University of Valparaíso, Valparaíso, Chile
| | - Fabian Wartner
- Department of Applied Statistics, Johannes Kepler University Linz, Linz, Austria
| | - Milan Stehlík
- Department of Applied Statistics, Johannes Kepler University Linz, Linz, Austria.,Departamento de Matemática, Universidad Técnica Federico Santa María, Valparaíso, Chile
| |
Collapse
|
12
|
|
13
|
|
14
|
|
15
|
Lepschy JB, Stehlík M, Minárová M. Fractal analysis for osteoporosis: a likelihood ratio approach. Acta Univ Agric Silvic Mendelianae Brun 2014. [DOI: 10.11118/actaun201058030119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
16
|
|
17
|
|
18
|
|
19
|
|
20
|
Střelec L, Stehlík M. Comparative simulation study of likelihood ratio tests for homogeneity of the exponential distribution. Acta Univ Agric Silvic Mendelianae Brun 2013. [DOI: 10.11118/actaun201260070307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
21
|
|
22
|
|
23
|
|
24
|
|
25
|
|
26
|
Stehlík M, Rodríguez-Díaz JM, Müller WG, López-Fidalgo J. Optimal allocation of bioassays in the case of parametrized covariance functions: an application to Lung’s retention of radioactive particles. TEST-SPAIN 2007. [DOI: 10.1007/s11749-006-0022-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
|