1
|
Fu S, Zhang Y, Li Y, Zhang Z, Du C, Wang R, Peng Y, Yue Z, Xu Z, Hu Q. Estimating epidemic trajectories of SARS-CoV-2 and influenza A virus based on wastewater monitoring and a novel machine learning algorithm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175830. [PMID: 39197755 DOI: 10.1016/j.scitotenv.2024.175830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/20/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
The COVID-19 pandemic has altered the circulation of non-SARS-CoV-2 respiratory viruses. In this study, we carried out wastewater surveillance of SARS-CoV-2 and influenza A virus (IAV) in three key port cities in China through real-time quantitative PCR (RT-qPCR). Next, a novel machine learning algorithm (MLA) based on Gaussian model and random forest model was used to predict the epidemic trajectories of SARS-CoV-2 and IAV. The results showed that from February 2023 to January 2024, three port cities experienced two waves of SARS-CoV-2 infection, which peaked in late-May and late-August 2023, respectively. Two waves of IAV were observed in the spring and winter of 2023, respectively with considerable variations in terms of onset/offset date and duration. Furthermore, we employed MLA to extract the key features of epidemic trajectories of SARS-CoV-2 and IAV from February 3rd, to October 15th, 2023, and thereby predicted the epidemic trends of SARS-CoV-2 and IAV from October 16th, 2023 to April 22nd, 2024, which showed high consistency with the observed values. These collective findings offer an important understanding of SARS-CoV-2 and IAV epidemics, suggesting that wastewater surveillance together with MLA emerges as a powerful tool for risk assessment of respiratory viral diseases and improving public health preparedness.
Collapse
Affiliation(s)
- Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
| | - Yixiang Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Chen Du
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Yuejing Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zhijiao Yue
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zheng Xu
- Southern University of Sciences and Technology Yantian Hospital, Shenzhen 518081, China; Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
| |
Collapse
|
2
|
Ang LW, Mak TM, Cui L, Leo YS, Lee VJM, Lin RTP. Characterisation of respiratory syncytial virus activity in children and adults presenting with acute respiratory illness at primary care clinics in Singapore, 2014-2018. Influenza Other Respir Viruses 2020; 14:412-419. [PMID: 32090482 PMCID: PMC7298310 DOI: 10.1111/irv.12730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/08/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is an important respiratory pathogen that affects people of all ages. OBJECTIVES We examined the patterns of RSV circulation in 2014-2018, and investigated their age-specific differences in tropical Singapore. METHODS Nasopharyngeal and/or throat swabs were taken from outpatient attendees for the national influenza virological surveillance among those who presented with acute respiratory illness in the community. Specimens tested negative for influenza were then tested for RSV and other respiratory pathogens. RESULTS Among 8436 influenza-negative specimens tested during the five-year period, 5.8% (95% confidence interval 5.3%-6.3%) were positive for RSV. The peak of RSV activity occurred around middle of the year. The age-specific proportion of RSV detections showed a reverse J-shaped pattern; RSV positivity was the highest in young children ≤2 years of age (10.9%), followed by those aged 3-5 years (6.4%) and persons aged ≥65 years (5.3%), while the nadir was observed in the age group of 15-24 years (1.2%). RSV type A was predominantly circulating in children ≤5 years of age from 2014 to 2015 and 2017, whereas in 2016, they were more affected by type B. CONCLUSION Respiratory syncytial virus was more frequently detected among the two age groups that have been recommended for influenza vaccination; persons ≥65 years of age and children 6 months to <5 years of age. Characterisation of RSV activity in the community helps to better inform public health policies for effective prevention and control interventions.
Collapse
Affiliation(s)
- Li Wei Ang
- National Centre for Infectious Diseases, Singapore City, Singapore.,Public Health Group, Ministry of Health, Singapore City, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore City, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore City, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore City, Singapore
| | | | | |
Collapse
|
3
|
Al Amad MA, Al Mahaqri AA, Al Serouri AA, Khader YS. Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016. INQUIRY: The Journal of Health Care Organization, Provision, and Financing 2019; 56:46958019850731. [PMID: 31137990 PMCID: PMC6542124 DOI: 10.1177/0046958019850731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In 2010, Yemen started the surveillance for severe acute respiratory infections (SARIs) by establishing 2 sentinel sites in Sana’a and Aden city. This study aims to determine the proportions of influenza and noninfluenza viruses among SARI patients and to determine the severity of SARI and its associated factors. The data of SARI patients who were admitted to SARI surveillance sites at Al Johory hospital in Sana’a and Al Wahdah hospital in Aden city during the period 2011-2016 were analyzed. The proportions of positive influenza viruses (type A, B) and noninfluenza viruses (respiratory syncytial, adenovirus, human parainfluenza, and human metapneumovirus), intensive care unit (ICU) admission rate, and fatality rate among SARI patients were calculated. A total of 1811 of SARI patients were admitted during 2011-2016. Of those, 78% were <15 years old. A total of 89 (5%) patients had influenza viruses and 655 (36%) had noninfluenza viruses. The overall ICU admission rate was 40% and the case-fatality rate was 8%. Infection by influenza type (A, B) and mixed (adenovirus, human parainfluenza) was significantly associated with lower ICU admission. Age <15 years old, infection with influenza B, pre-existence of chronic diseases, and admission to Aden site were significantly associated with higher fatality rate among patients. In conclusion; SARI patients in Yemen had a high ICU admission and case-fatality rates. Influenza type B, chronic diseases, and admission to Aden site are associated with higher fatality rate. Expanding surveillance sites and panel of laboratory tests to involve other pathogens will help to provide accurate diagnosis for SARI etiology and give more comprehensive picture. Training staff for SARI case management will help to reduce severe outcomes.
Collapse
Affiliation(s)
| | | | | | - Yousef S Khader
- 3 Jordan University of Science and Technology, Irbid, Jordan
| |
Collapse
|
4
|
Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010-2015. J Infect 2019; 79:373-382. [PMID: 31323249 PMCID: PMC7112594 DOI: 10.1016/j.jinf.2019.07.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/17/2019] [Accepted: 07/12/2019] [Indexed: 01/09/2023]
Abstract
OBJECTIVES To improve our understanding of the global epidemiology of common respiratory viruses by analysing their contemporaneous incidence at multiple sites. METHODS 2010-2015 incidence data for influenza A (IAV), influenza B (IBV), respiratory syncytial (RSV) and parainfluenza (PIV) virus infections were collected from 18 sites (14 countries), consisting of local (n = 6), regional (n = 9) and national (n = 3) laboratories using molecular diagnostic methods. Each site submitted monthly virus incidence data, together with details of their patient populations tested and diagnostic assays used. RESULTS For the Northern Hemisphere temperate countries, the IAV, IBV and RSV incidence peaks were 2-6 months out of phase with those in the Southern Hemisphere, with IAV having a sharp out-of-phase difference at 6 months, whereas IBV and RSV showed more variable out-of-phase differences of 2-6 months. The tropical sites Singapore and Kuala Lumpur showed fluctuating incidence of these viruses throughout the year, whereas subtropical sites such as Hong Kong, Brisbane and Sydney showed distinctive biannual peaks for IAV but not for RSV and PIV. CONCLUSIONS There was a notable pattern of synchrony of IAV, IBV and RSV incidence peaks globally, and within countries with multiple sampling sites (Canada, UK, Australia), despite significant distances between these sites.
Collapse
|
5
|
Wen X, Huang Q, Tao H, Zou W, Gao M, Guo H, Yao X, Cui D, Wang X. Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study. BMC Infect Dis 2019; 19:32. [PMID: 30621623 PMCID: PMC6325799 DOI: 10.1186/s12879-018-3668-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/28/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs.
Collapse
Affiliation(s)
- Xiaohong Wen
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Qiuling Huang
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Hong Tao
- Department of Laboratory & Pharmacy, Suzhou Vocational Health College, Suzhou, 215009, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Huihui Guo
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Xing Yao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Dawei Cui
- Department of Blood Transfusion, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Xiang Wang
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China.
| |
Collapse
|
6
|
Respiratory Viruses in a Primary Health Care Facility in Amsterdam, the Netherlands. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2018. [DOI: 10.1097/ipc.0000000000000604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
7
|
Tang JW, Lam TT, Zaraket H, Lipkin WI, Drews SJ, Hatchette TF, Heraud JM, Koopmans MP. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. THE LANCET. INFECTIOUS DISEASES 2017; 17:e320-e326. [PMID: 28457597 PMCID: PMC7164797 DOI: 10.1016/s1473-3099(17)30238-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 01/13/2023]
Abstract
Together with influenza, the non-influenza RNA respiratory viruses (NIRVs), which include respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus, represent a considerable global health burden, as recognised by WHO's Battle against Respiratory Viruses initiative. By contrast with influenza viruses, little is known about the contemporaneous global diversity of these viruses, and the relevance of such for development of pharmaceutical interventions. Although far less advanced than for influenza, antiviral drugs and vaccines are in different stages of development for several of these viruses, but no interventions have been licensed. This scarcity of global genetic data represents a substantial knowledge gap and impediment to the eventual licensing of new antiviral drugs and vaccines for NIRVs. Enhanced genetic surveillance will assist and boost research and development into new antiviral drugs and vaccines for these viruses. Additionally, understanding the global diversity of respiratory viruses is also part of emerging disease preparedness, because non-human coronaviruses and paramyxoviruses have been listed as priority concerns in a recent WHO research and development blueprint initiative for emerging infectious diseases. In this Personal View, we explain further the rationale for expanding the genetic database of NIRVs and emphasise the need for greater investment in this area of research.
Collapse
Affiliation(s)
- Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK; Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, UK.
| | - Tommy T Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, American University of Beirut, Beirut, Lebanon
| | - W Ian Lipkin
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Steven J Drews
- Alberta Provincial Laboratory for Public Health, University of Alberta, Edmonton, AB, Canada
| | - Todd F Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| |
Collapse
|
8
|
Hung IFN, Zhang AJ, To KKW, Chan JFW, Zhu SHS, Zhang R, Chan TC, Chan KH, Yuen KY. Unexpectedly Higher Morbidity and Mortality of Hospitalized Elderly Patients Associated with Rhinovirus Compared with Influenza Virus Respiratory Tract Infection. Int J Mol Sci 2017; 18:ijms18020259. [PMID: 28134768 PMCID: PMC5343795 DOI: 10.3390/ijms18020259] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 11/17/2022] Open
Abstract
Rhinovirus is a common cause of upper and lower respiratory tract infections in adults, especially among the elderly and immunocompromised. Nevertheless, its clinical characteristics and mortality risks have not been well described. A retrospective analysis on a prospective cohort was conducted in a single teaching hospital center over a one-year period. We compared adult patients hospitalized for pneumonia caused by rhinovirus infection with those hospitalized for influenza infection during the same period. All recruited patients were followed up for at least 3 months up to 15 months. Independent risk factors associated with mortality for rhinovirus infection were identified. Between 1 March 2014 and 28 February 2015, a total of 1946 patients were consecutively included for analysis. Of these, 728 patients were hospitalized for rhinovirus infection and 1218 patients were hospitalized for influenza infection. Significantly more rhinovirus patients were elderly home residents and had chronic lung diseases (p < 0.001), whereas more influenza patients had previous stroke (p = 0.02); otherwise, there were no differences in the Charlson comorbidity indexes between the two groups. More patients in the rhinovirus group developed pneumonia complications (p = 0.03), required oxygen therapy, and had a longer hospitalization period (p < 0.001), whereas more patients in the influenza virus group presented with fever (p < 0.001) and upper respiratory tract symptoms of cough and sore throat (p < 0.001), and developed cardiovascular complications (p < 0.001). The 30-day (p < 0.05), 90-day (p < 0.01), and 1-year (p < 0.01) mortality rate was significantly higher in the rhinovirus group than the influenza virus group. Intensive care unit admission (odds ratio (OR): 9.56; 95% confidence interval (C.I.) 2.17–42.18), elderly home residents (OR: 2.60; 95% C.I. 1.56–4.33), requirement of oxygen therapy during hospitalization (OR: 2.62; 95% C.I. 1.62–4.24), and hemoglobin level <13.3 g/dL upon admission (OR: 2.43; 95% C.I. 1.16–5.12) were independent risk factors associated with 1-year mortality in patients hospitalized for rhinovirus infection. Rhinovirus infection in the adults was associated with significantly higher mortality and longer hospitalization when compared with influenza virus infection. Institutionalized older adults were particularly at risk. More stringent infection control among health care workers in elderly homes could lower the infection rate before an effective vaccine and antiviral become available.
Collapse
Affiliation(s)
- Ivan F N Hung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Pokfulam, Hong Kong SAR, China.
| | - Anna Jinxia Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Kelvin K W To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Jasper F W Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Shawn H S Zhu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Ricky Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Tuen-Ching Chan
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Pokfulam, Hong Kong SAR, China.
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu's Centre for Infection and Division of Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
| |
Collapse
|