1
|
Patiño LH, Ballesteros N, Muñoz M, Ramírez AL, Castañeda S, Galeano LA, Hidalgo A, Paniz-Mondolfi A, Ramírez JD. Global and genetic diversity of SARS-CoV-2 in wastewater. Heliyon 2024; 10:e27452. [PMID: 38463823 PMCID: PMC10923837 DOI: 10.1016/j.heliyon.2024.e27452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
The analysis of SARS-CoV-2 in wastewater has enabled us to better understand the spread and evolution of the virus worldwide. To deepen our understanding of its epidemiological and genomic characteristics, we analyzed 10,147 SARS-CoV-2 sequences from 5 continents and 21 countries that were deposited in the GISAID database up until January 31, 2023. Our results revealed over 100 independent lineages of the virus circulating in water samples from March 2020 to January 2023, including variants of interest and concern. We observed four clearly defined periods of global distribution of these variants over time, with one variant being replaced by another. Interestingly, we found that SARS-CoV-2 water-borne sequences from different countries had a close phylogenetic relationship. Additionally, 40 SARS-CoV-2 water-borne sequences from Europe and the USA did not show any phylogenetic relationship with SARS-CoV-2 human sequences. We also identified a significant number of non-synonymous mutations, some of which were detected in previously reported cryptic lineages. Among the countries analyzed, France and the USA showed the highest degree of sequence diversity, while Austria reported the highest number of genomes (6,296). Our study provides valuable information about the epidemiological and genomic diversity of SARS-CoV-2 in wastewater, which can be employed to support public health initiatives and preparedness.
Collapse
Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Angie Lorena Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Luis Alejandro Galeano
- Grupo de Investigación en Materiales Funcionales y Catálisis (GIMFC), Departamento de Química, Universidad de Nariño, Pasto, 52002, Colombia
| | - Arsenio Hidalgo
- Grupo de Investigación en Salud Pública, Departamento de Matemáticas, Universidad de Nariño, Pasto, 50002, Colombia
| | - Alberto Paniz-Mondolfi
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| |
Collapse
|
2
|
Gräf T, Martinez AA, Bello G, Dellicour S, Lemey P, Colizza V, Mazzoli M, Poletto C, Cardoso VLO, da Silva AF, Motta FC, Resende PC, Siqueira MM, Franco L, Gresh L, Gabastou JM, Rodriguez A, Vicari A, Aldighieri S, Mendez-Rico J, Leite JA. Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean. Nat Commun 2024; 15:1837. [PMID: 38418815 PMCID: PMC10902334 DOI: 10.1038/s41467-024-46143-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
Collapse
Affiliation(s)
- Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Brazil.
| | - Alexander A Martinez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- National Research System (SNI), National Secretary of Research, Technology and Innovation (SENACYT), Panama City, Panama
- Department of Microbiology and Immunology, University of Panama, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Mattia Mazzoli
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vanessa Leiko Oikawa Cardoso
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, FIOCRUZ-Bahia, Salvador, Brazil
| | | | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leticia Franco
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Lionel Gresh
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jean-Marc Gabastou
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Angel Rodriguez
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Andrea Vicari
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Sylvain Aldighieri
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jairo Mendez-Rico
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Juliana Almeida Leite
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA.
| |
Collapse
|
3
|
Rojas-Gulloso A, Sánchez-Lerma L, Montilla M, Morales-Pulecio F, Sarmiento-Rudolf E, Tapia-Reales R. Infectious diseases in migrant pregnant women from an area of the Colombian Caribbean. Travel Med Infect Dis 2023; 55:102629. [PMID: 37586652 DOI: 10.1016/j.tmaid.2023.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
INTRODUCTION Human migration is an activity that affects society in economic and political aspects and as a social determinant because of its differential impact on individual's health. OBJECTIVE To describe the situation of health and infectious diseases of vertical transmission risk in migrant pregnant women from an area of the Colombian Caribbean from 2019 to 2021. METHODS A descriptive cross-sectional study was carried out on pregnant irregular migrants in the Riohacha and Santa Marta municipalities in Colombia. Hemogram, uranalysis, toxoplasma, FTA-ABS, VDRL, rubella, hepatitis B, HIV (TORCHs), vaginal swab, basal glycemia, and transaminases, among other paraclinical tests, were done on pregnant women. Data was arranged, tabulated, and analyzed in SPSS v.23.0. A descriptive statistical analysis with measures of central tendency and dispersion for quantitative variables, and proportions analysis was done for qualitative variables. RESULTS A total of 555 clinical records were analyzed. Of the infectious agents with a risk of vertical transmission, syphilis was the most frequent with 3.6%. Regarding toxoplasmosis, 2.5% were IgM-positive. 4.2% of the pregnant women had IgG antibodies against Rubella and 2 women showed antibodies against HIV. CONCLUSIONS Our results reflect the need for the implementation of educational, prevention, and detection health programs with the aim to decrease the number of prenatal infections in the pregnant migrant population for preventing fatal complications both in mothers and newborns.
Collapse
Affiliation(s)
- A Rojas-Gulloso
- Grupo de Investigación de Ciencias y Pedagogía, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Magdalena, Colombia.
| | - L Sánchez-Lerma
- Grupo de Investigación de Villavicencio-GRIVI, Facultad de Medicina, Universidad Cooperativa de Colombia, Villavicencio, Meta, Colombia
| | - Marcela Montilla
- Grupo de Investigación de Villavicencio-GRIVI, Facultad de Medicina, Universidad Cooperativa de Colombia, Villavicencio, Meta, Colombia
| | - F Morales-Pulecio
- Malteser International America, agencia de ayuda humanitaria de la orden de Malta, Riohacha, La Guajira, Colombia
| | - E Sarmiento-Rudolf
- Malteser International America, agencia de ayuda humanitaria de la orden de Malta, Riohacha, La Guajira, Colombia
| | - Ricardo Tapia-Reales
- Malteser International America, agencia de ayuda humanitaria de la orden de Malta, Riohacha, La Guajira, Colombia
| |
Collapse
|
4
|
Forero-Peña DA, Carrión-Nessi FS, Mendoza-Millán DL, Omaña-Ávila ÓD, Mejía-Bernard MD, Camejo-Ávila NA, Flora-Noda DM, Velásquez VL, Chacón-Labrador FR, Doval-Fernández JM, Maricuto AL, Grillet ME, Hernández-Villena JV, Vincenti-González MF, Paniz-Mondolfi AE, Orejas J, Rodríguez VI, Contreras MB, Guevara RN, Carballo M, Caldera J, Redondo MC, Landaeta ME. First wave of COVID-19 in Venezuela: Epidemiological, clinical, and paraclinical characteristics of first cases. J Med Virol 2021; 94:1175-1185. [PMID: 34761824 PMCID: PMC8662004 DOI: 10.1002/jmv.27449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID‐19) pandemic has particularly affected countries with weakened health services in Latin America, where proper patient management could be a critical step to address the epidemic. In this study, we aimed to characterize and identify which epidemiological, clinical, and paraclinical risk factors defined COVID‐19 infection from the first confirmed cases through the first epidemic wave in Venezuela. A retrospective analysis of consecutive suspected cases of COVID‐19 admitted to a sentinel hospital was carried out, including 576 patient cases subsequently confirmed for severe acute respiratory syndrome coronavirus 2 infection. Of these, 162 (28.1%) patients met the definition criteria for severe/critical disease, and 414 (71.2%) were classified as mild/moderate disease. The mean age was 47 (SD 16) years, the majority of which were men (59.5%), and the most frequent comorbidity was arterial hypertension (23.3%). The most common symptoms included fever (88.7%), headache (65.6%), and dry cough (63.9%). Severe/critical disease affected mostly older males with low schooling (p < 0.001). Similarly, higher levels of glycemia, urea, aminotransferases, total bilirubin, lactate dehydrogenase, and erythrocyte sedimentation rate were observed in severe/critical disease patients compared to those with mild/moderate disease. Overall mortality was 7.6% (44/576), with 41.7% (28/68) dying in hospital. We identified risk factors related to COVID‐19 infection, which could help healthcare providers take appropriate measures and prevent severe clinical outcomes. Our results suggest that the mortality registered by this disease in Venezuela during the first epidemic wave was underestimated. An increase in fatalities is expected to occur in the coming months unless measures that are more effective are implemented to mitigate the epidemic while the vaccination process is ongoing. To the best of our knowledge, our study is the first to assess the epidemiological, clinical, and paraclinical characteristics of COVID‐19 patients in Venezuela. Regarding the occupation, 15% of the patients were healthcare workers. Patients with more year's smoking, bilateral crackles and altered state of consciousness were associated with severe/critical disease. Only 42% of the patients with severe/critical disease criteria were hospitalized, of which 41.7% died.
Collapse
Affiliation(s)
- David A Forero-Peña
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela.,Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela
| | - Fhabián S Carrión-Nessi
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Dr. Francisco Battistini Casalta" Health Sciences School, University of Oriente - Bolivar Nucleus, Ciudad Bolivar, Venezuela
| | - Daniela L Mendoza-Millán
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Óscar D Omaña-Ávila
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Mario D Mejía-Bernard
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Natasha A Camejo-Ávila
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Dr. Francisco Battistini Casalta" Health Sciences School, University of Oriente - Bolivar Nucleus, Ciudad Bolivar, Venezuela
| | - David M Flora-Noda
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - Viledy L Velásquez
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - Fabián R Chacón-Labrador
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Juan M Doval-Fernández
- Department of Infectious Diseases, Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolivar, Venezuela.,Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Andrea L Maricuto
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - María E Grillet
- Vector Biology Laboratory, Institute of Zoology and Tropical Ecology, Central University of Venezuela, Caracas, Venezuela
| | - Juan V Hernández-Villena
- Vector Biology Laboratory, Institute of Zoology and Tropical Ecology, Central University of Venezuela, Caracas, Venezuela
| | - María F Vincenti-González
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - José Orejas
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Verónica I Rodríguez
- Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Mariana B Contreras
- Department of Medicine, "Luis Razetti" School of Medicine, Central University of Venezuela, Caracas, Venezuela
| | - Rafael N Guevara
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - Martín Carballo
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - Jocays Caldera
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - María C Redondo
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| | - María E Landaeta
- Department of Infectious Diseases, University Hospital of Caracas, Caracas, Venezuela
| |
Collapse
|
5
|
Taylor L. The Venezuelan health-care workers secretly collecting COVID stats. Nature 2021; 597:20-21. [PMID: 34433980 DOI: 10.1038/d41586-021-02276-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|