Viruses

Research

15 pages, 854 KiB

Open AccessArticle

Interpretation of COVID-19 Epidemiological Trends in Mexico Through Wastewater Surveillance Using Simple Machine Learning Algorithms for Rapid Decision-Making

by Arnoldo Armenta-Castro, Orlando de la Rosa, Alberto Aguayo-Acosta, Mariel Araceli Oyervides-Muñoz, Antonio Flores-Tlacuahuac, Roberto Parra-Saldívar and Juan Eduardo Sosa-Hernández

Viruses 2025, 17(1), 109; https://doi.org/10.3390/v17010109 - 15 Jan 2025

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Abstract

Detection and quantification of disease-related biomarkers in wastewater samples, denominated Wastewater-based Surveillance (WBS), has proven a valuable strategy for studying the prevalence of infectious diseases within populations in a time- and resource-efficient manner, as wastewater samples are representative of all cases within the [...] Read more.

Detection and quantification of disease-related biomarkers in wastewater samples, denominated Wastewater-based Surveillance (WBS), has proven a valuable strategy for studying the prevalence of infectious diseases within populations in a time- and resource-efficient manner, as wastewater samples are representative of all cases within the catchment area, whether they are clinically reported or not. However, analysis and interpretation of WBS datasets for decision-making during public health emergencies, such as the COVID-19 pandemic, remains an area of opportunity. In this article, a database obtained from wastewater sampling at wastewater treatment plants (WWTPs) and university campuses in Monterrey and Mexico City between 2021 and 2022 was used to train simple clustering- and regression-based risk assessment models to allow for informed prevention and control measures in high-affluence facilities, even if working with low-dimensionality datasets and a limited number of observations. When dividing weekly data points based on whether the seven-day average daily new COVID-19 cases were above a certain threshold, the resulting clustering model could differentiate between weeks with surges in clinical reports and periods between them with an 87.9% accuracy rate. Moreover, the clustering model provided satisfactory forecasts one week (80.4% accuracy) and two weeks (81.8%) into the future. However, the prediction of the weekly average of new daily cases was limited (R² = 0.80, MAPE = 72.6%), likely because of insufficient dimensionality in the database. Overall, while simple, WBS-supported models can provide relevant insights for decision-makers during epidemiological outbreaks, regression algorithms for prediction using low-dimensionality datasets can still be improved. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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16 pages, 3301 KiB

Open AccessArticle

Activity of Various Cathepsin Proteases and Enrichment of Klotho Protein in the Urine and Urinary Extracellular Vesicles After SARS-CoV-2 Infection

by Niharika Bala, Ramish H. Rafay, Sarah C. Glover and Abdel A. Alli

Viruses 2025, 17(1), 25; https://doi.org/10.3390/v17010025 - 28 Dec 2024

Viewed by 614

Abstract

Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for causing the Coronavirus disease 2019 (COVID-19) outbreak. While mutations cause the emergence of new variants, the ancestral SARS-CoV-2 strain is unique among other strains. Methods: Various clinical parameters, the activity of cathepsin [...] Read more.

Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for causing the Coronavirus disease 2019 (COVID-19) outbreak. While mutations cause the emergence of new variants, the ancestral SARS-CoV-2 strain is unique among other strains. Methods: Various clinical parameters, the activity of cathepsin proteases, and the concentration of various proteins were measured in urine samples from COVID-19-negative participants and COVID-19-positive participants. Urinary extracellular vesicles (uEVs) were isolated from urine samples from the two groups and used for proteomic analysis and subsequent pathway analyses. Results: Activity levels of cathepsin S and L were greater in the urine of COVID-19-positive participants. The concentration of C-reactive protein, transmembrane serine protease 2, and klotho protein were significantly greater in the urine of COVID-19-positive participants. There was a greater amount of uEVs in the COVID-19 group and klotho protein was found to be enriched in uEVs from the COVID-19 group. Pathway analyses of the proteomics data showed most of the identified proteins were involved in signal transduction, stress response, protein metabolism, and transport. The identified proteins were predominantly associated with cellular membranes and with function of the cytoskeleton, enzyme regulation, and signal transduction. Conclusions: Taken together, our data identify novel urinary biomarkers that could be used to further investigate the long-term effects of SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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14 pages, 4107 KiB

Open AccessArticle

Characterization and Fluctuations of an Ivermectin Binding Site at the Lipid Raft Interface of the N-Terminal Domain (NTD) of the Spike Protein of SARS-CoV-2 Variants

by Marine Lefebvre, Henri Chahinian, Bernard La Scola and Jacques Fantini

Viruses 2024, 16(12), 1836; https://doi.org/10.3390/v16121836 - 27 Nov 2024

Viewed by 1536

Abstract

Most studies on the docking of ivermectin on the spike protein of SARS-CoV-2 concern the receptor binding domain (RBD) and, more precisely, the RBD interface recognized by the ACE2 receptor. The N-terminal domain (NTD), which controls the initial attachment of the virus to [...] Read more.

Most studies on the docking of ivermectin on the spike protein of SARS-CoV-2 concern the receptor binding domain (RBD) and, more precisely, the RBD interface recognized by the ACE2 receptor. The N-terminal domain (NTD), which controls the initial attachment of the virus to lipid raft gangliosides, has not received the attention it deserves. In this study, we combined molecular modeling and physicochemical approaches to analyze the mode of interaction of ivermectin with the interface of the NTD-facing lipid rafts of the host cell membrane. We characterize a binding area that presents point mutations and deletions in successive SARS-CoV-2 variants from the initial strain to omicron KP.3 circulating in many countries in 2024. We show that ivermectin has exceptional flexibility, allowing the drug to bind to the spike protein of all variants tested. The energy of interaction is specific to each variant, allowing a classification according to their affinity for ivermectin in the following ascending order: Omicron KP.3 < Delta < Omicron BA.5 < Alpha < Wuhan (B.1) < Omicron BA.1. The binding site of ivermectin is subject to important variations of the NTD, including the Y144 deletion. It overlaps with the ganglioside binding domain of the NTD, as demonstrated by docking and physicochemical studies. These results suggest a new mechanism of antiviral action for ivermectin based on competitive inhibition for initial virus attachment to lipid rafts. The current KP.3 variant is still recognized by ivermectin, although with an affinity slightly lower than the Wuhan strain. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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11 pages, 1455 KiB

Open AccessArticle

Modeling the Dynamic of Multiwave Diseases: The Model of Hand, Foot and Mouth Disease

by Patrice Ravel, Nghia Ngu Duy, Guilhem Kister, Le Thi Song Huong, Ankit Dwivedi, Christian A. Devaux, Tran Nhu Duong, Nguyen Tran Hien, Laurent Gavotte, Emmanuel Cornillot and Roger Frutos

Viruses 2024, 16(8), 1217; https://doi.org/10.3390/v16081217 - 29 Jul 2024

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Abstract

An HFMD outbreak spread over the city of Hải Phòng from summer 2011 to autumn 2012. This epidemic was chosen because it was the very first HFMD epidemic in North Vietnam, eliminating thus interferences with previous outbreaks. This epidemic displayed three separate waves. [...] Read more.

An HFMD outbreak spread over the city of Hải Phòng from summer 2011 to autumn 2012. This epidemic was chosen because it was the very first HFMD epidemic in North Vietnam, eliminating thus interferences with previous outbreaks. This epidemic displayed three separate waves. A complete dataset was collected for more than 9500 patients during this period, which enabled us to analyze this epidemic at different scales. Access to the healthcare system was crucial during this period, which was possible due to a reorganization of the system in February–March 2012. An analysis at the commune level enabled us to track the epidemic along certain communication routes. The three-waves structure reveals a wide disparity at the district level. We developed a mathematical model showing high accuracy at the adjustment of data for both the total number of cases and for the number of cases per week. As a consequence, the model was able to accurately determine the dates of the beginning and end of each wave and to show that they overlapped. Using mathematical functions associated with this model, it was possible to calculate the probability for a patient to belong to a specific wave. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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22 pages, 11640 KiB

Open AccessArticle

A T-Cell-Derived 3-Gene Signature Distinguishes SARS-CoV-2 from Common Respiratory Viruses

by Yang Li, Xinya Tao, Sheng Ye, Qianchen Tai, Yu-Ang You, Xinting Huang, Mifang Liang, Kai Wang, Haiyan Wen, Chong You, Yan Zhang and Xiaohua Zhou

Viruses 2024, 16(7), 1029; https://doi.org/10.3390/v16071029 - 26 Jun 2024

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Abstract

Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with [...] Read more.

Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with integrated bioinformatics and machine learning. We collected 3730 blood samples from both asymptomatic and symptomatic individuals infected with SARS-CoV-2, seasonal human coronavirus (sHCoVs), influenza virus (IFV), respiratory syncytial virus (RSV), or human rhinovirus (HRV) across 15 cohorts. First, we identified an enhanced cellular immune response but limited interferon activities in SARS-CoV-2 infection, especially in asymptomatic cases. Second, we identified a SARS-CoV-2-specific 3-gene signature (CLSPN, RBBP6, CCDC91) that was predominantly expressed by T cells, could distinguish SARS-CoV-2 infection, including Omicron, from other common respiratory viruses regardless of symptoms, and was predictive of SARS-CoV-2 infection before detectable viral RNA on RT-PCR testing in a longitude follow-up study. Thereafter, a user-friendly online tool, based on datasets collected here, was developed for querying a gene of interest across multiple viral infections. Our results not only identify a unique host response to the viral pathogenesis in SARS-CoV-2 but also provide insights into developing effective tools against viral pandemics from the host perspective. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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15 pages, 8013 KiB

Open AccessArticle

An In Silico Analysis of PCR-Based Monkeypox Virus Detection Assays: A Case Study for Ongoing Clinical Surveillance

by Kuncheng Song, Hayden N. Brochu, Qimin Zhang, Jonathan D. Williams and Lakshmanan K. Iyer

Viruses 2023, 15(12), 2327; https://doi.org/10.3390/v15122327 - 27 Nov 2023

Cited by 1 | Viewed by 2840

Abstract

The 2022 global Mpox outbreak swiftly introduced unforeseen diversity in the monkeypox virus (MPXV) population, resulting in numerous Clade IIb sublineages. This propagation of new MPXV mutations warrants the thorough re-investigation of previously recommended or validated primers designed to target MPXV genomes. In [...] Read more.

The 2022 global Mpox outbreak swiftly introduced unforeseen diversity in the monkeypox virus (MPXV) population, resulting in numerous Clade IIb sublineages. This propagation of new MPXV mutations warrants the thorough re-investigation of previously recommended or validated primers designed to target MPXV genomes. In this study, we explored 18 PCR primer sets and examined their binding specificity against 5210 MPXV genomes, representing all the established MPXV lineages. Our results indicated that only five primer sets resulted in almost all perfect matches against the targeted MPXV lineages, and the remaining primer sets all contained 1–2 mismatches against almost all the MPXV lineages. We further investigated the mismatched primer-genome pairs and discovered that some of the primers overlapped with poorly sequenced and assembled regions of the MPXV genomes, which are consistent across multiple lineages. However, we identified 173 99% genome-wide conserved regions across all 5210 MPXV genomes, representing 30 lineages/clades with at least 80% lineage-specific consensus for future primer development and primer binding evaluation. This exercise is crucial to ensure that the current detection schemes are robust and serve as a framework for primer evaluation in clinical testing development for other infectious diseases. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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Review

Jump to: Research, Other

12 pages, 1028 KiB

Open AccessReview

Breaking the Barrier: SARS-CoV-2 Infections in Wild and Companion Animals and Their Implications for Public Health

by Zhandos Abay, Sandugash Sadikaliyeva, Ainur Nurpeisova, Kuanysh Jekebekov, Kamshat Shorayeva, Bolat Yespembetov, Sergazy Nurabayev, Aslan Kerimbayev, Berik Khairullin, Hansang Yoo, Lespek Kutumbetov, Markhabat Kassenov and Kunsulu Zakarya

Viruses 2024, 16(6), 956; https://doi.org/10.3390/v16060956 - 13 Jun 2024

Cited by 2 | Viewed by 1629

Abstract

The emergence of the novel coronavirus SARS-CoV-2 has led to significant interest in its potential transmission between animals and humans, especially pets. This review article summarises the literature on coronavirus infections in domestic animals, emphasising epidemiology, transmission dynamics, clinical manifestations, and public health [...] Read more.

The emergence of the novel coronavirus SARS-CoV-2 has led to significant interest in its potential transmission between animals and humans, especially pets. This review article summarises the literature on coronavirus infections in domestic animals, emphasising epidemiology, transmission dynamics, clinical manifestations, and public health implications. This article highlights current understandings of the relationship between infections in companion animals and humans, identifies research gaps, and suggests directions for future research. Cases of disease in cats, dogs, and other domestic animals, often occurring through close contact with infected owners, are reviewed, raising concerns about possible zoonotic and reverse zoonotic transmission. Precautions and recommendations for pet owners and healthcare workers are also discussed. The scientific evidence presented in the article highlights the need for a One Health approach that considers the health of people, animals, and the environment to combat future pandemics. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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Other

Jump to: Research, Review

23 pages, 942 KiB

Open AccessSystematic Review

Epidemiological and Clinical Characteristics of Mpox in Cisgender and Transgender Women and Non-Binary Individuals Assigned to the Female Sex at Birth: A Comprehensive, Critical Global Perspective

by Nicola Luigi Bragazzi, Woldegebriel Assefa Woldegerima, Jianhong Wu, Manlio Converti, Lukasz Szarpak, Andrea Crapanzano, Marwan Odeh, Raymond Farah and Rola Khamisy-Farah

Viruses 2024, 16(3), 325; https://doi.org/10.3390/v16030325 - 21 Feb 2024

Cited by 3 | Viewed by 2830

Abstract

The 2022–2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox [...] Read more.

The 2022–2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox infections, particularly among women, to address a notable knowledge gap. This review systematically gathers and analyzes the scientific literature and case reports concerning Mpox infections in women, covering a broad geographical spectrum including regions such as Argentina, Brazil, Colombia, Nigeria, Europe, Vietnam, and the United States. The analysis delves into various aspects of Mpox in women, including clinical features, epidemiology, psychological impacts, preparedness strategies, and case studies, with particular attention to pregnant women and those with underlying health conditions. Empirical data from multiple studies underscore the unique epidemiological and clinical patterns of Mpox in women. In the United States, a small percentage of Mpox cases were reported among cisgender women, with a notable portion involving non-Hispanic Black or African American, non-Hispanic White, and Hispanic or Latino ethnicities. The primary transmission route was identified as sexual or close intimate contact, with the virus predominantly manifesting on the legs, arms, and genital areas. Further, a study in Spain highlighted significant disparities in diagnosis delays, transmission modes, and clinical manifestations between genders, indicating a different risk profile and disease progression in women. Additionally, a case from Vietnam, linked to a new Mpox sub-lineage in women, emphasized the role of women in the transmission dynamics and the importance of genomic monitoring. This review emphasizes the necessity for inclusive surveillance and research to fully understand Mpox dynamics across diverse population groups, including women. Highlighting gender and sexual orientation in public health responses is crucial for an effective approach to managing the spread and impact of this disease. The findings advocate for a gender-diverse assessment in health services and further research to explore the nuances of Mpox transmission, behavior, and progression among different groups, thereby enhancing the global response to Mpox and similar public health challenges. Full article

(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)

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