scholarly journals Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Bandar Alosaimi ◽  
Asif Naeem ◽  
Majed F. Alghoribi ◽  
Lilian Okdah ◽  
Maaweya E. Hamed ◽  
...  
Keyword(s):  
Surveillance Systems ◽  
Case Definitions ◽  
Structural Mapping ◽  
Policy Makers ◽  
Influenza Like Illness ◽  
Spike Gene ◽  
Ambulatory Patients ◽  
Community Transmission ◽  
Next Generation Sequencing Ngs ◽  
Epidemiological Link

In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

scholarly journals Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples

2021 ◽  
Author(s):  
Rajindra Napit ◽  
Prajwol Manandhar ◽  
Ashok Chaudhary ◽  
Bishwo Shrestha ◽  
Ajit Poudel ◽  
...  
Keyword(s):  
Viral Evolution ◽  
Rapid Identification ◽  
Surveillance Systems ◽  
Environmental Surveillance ◽  
Spike Gene ◽  
Global Database ◽  
Resource Limited ◽  
Frameshift Deletion ◽  
Community Transmission ◽  
Load Intensity

Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized, and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.

Derivation of New Surveillance System for Influenza-like Illness Using Claims Data 2014-2018 in Korea (Preprint)

2020 ◽  
Author(s):  
HeeKyung Choi ◽  
Won Suk Choi ◽  
Euna Han
Keyword(s):  
Surveillance System ◽  
Claims Data ◽  
Health Concern ◽  
Influenza Surveillance ◽  
Utilization Review ◽  
Surveillance Systems ◽  
Influenza Like Illness ◽  
System P ◽  
National Patient ◽  
Antitussive Agents

BACKGROUND Influenza is an important public health concern. A national surveillance system that easily and rapidly detects influenza epidemics is lacking. OBJECTIVE We assumed that the rate of influenza-like illness (ILI) related-claims is similar to the current ILI surveillance system. METHODS We used the Health Insurance Review and Assessment Service-National Patient Samples (HIRA-NPS), 2014-2018. We defined ILI-related claims as outpatient claims that contain both antipyretic and antitussive agents and calculated the weekly rate of ILI-related claims. We compared ILI-related claims and weekly ILI rates from clinical sentinel surveillance data. RESULTS We observed a strong correlation between the two surveillance systems each season. The absolute thresholds for the four-years were 84.64 and 86.19 cases claims per 1,000 claims for claims data and 12.27 and 16.82 per 1,000 patients for sentinel data (Figure 5). Both the claims and sentinel data surpassed the epidemic thresholds each season. The peak epidemic in the claims data was reached one to two weeks later than in the sentinel data. The epidemic patterns were more similar in the 2016-2017 and 2017-2018 seasons than the 2014-2015 and 2015-2016 seasons. CONCLUSIONS Based on hospital reports, ILI-related claims rates were similar to the ILI surveillance system. ILI claims data can be loaded to a drug utilization review system in Korea to make an influenza surveillance system.

scholarly journals A large outbreak of influenza A and B on a cruise ship causing widespread morbidity

2003 ◽  
Vol 130 (2) ◽  
pp. 263-271 ◽  
Author(s):  
J. M. L. BROTHERTON ◽  
V. C. DELPECH ◽  
G. L. GILBERT ◽  
S. HATZI ◽  
P. D. PARASKEVOPOULOS ◽  
...  
Keyword(s):  
Influenza Vaccination ◽  
Influenza A ◽  
Surveillance Systems ◽  
Cruise Ship ◽  
Influenza Like Illness ◽  
Antiviral Therapies ◽  
Intervention Measures ◽  
Large Outbreak ◽  
And Control ◽  
Control Study

In September 2000 an outbreak of influenza-like illness was reported on a cruise ship sailing between Sydney and Noumea with over 1100 passengers and 400 crew on board. Laboratory testing of passengers and crew indicated that both influenza A and B had been circulating on the ship. The cruise coincided with the peak influenza period in Sydney. Morbidity was high with 40 passengers hospitalized, two of whom died. A questionnaire was sent to passengers 3 weeks after the cruise and 836 of 1119 (75%) responded. A total of 310 passengers (37%) reported suffering from an influenza-like illness (defined as cough, fever, myalgia and weakness) and 528 (63%) had seen a doctor for illness related to the cruise. One-third of passengers reported receipt of influenza vaccination in 2000; however neither their rates of influenza-like illness nor hospitalization were significantly different from those in unvaccinated passengers. A case–control study also found no significant protective effect of influenza vaccination. With the increasing popularity of cruise vacations, such outbreaks are likely to affect increasing numbers of people. Whilst influenza vaccination of passengers and crew may afford some protection, uptake and effectiveness may not be sufficient to prevent outbreaks. Surveillance systems and early intervention measures, such as antiviral therapies, should be considered to detect and control such outbreaks.

scholarly journals Prevalence, incidence and bothersomeness of urinary incontinence in pregnancy: a systematic review and meta-analysis

2021 ◽  
Author(s):  
Heidi F. A. Moossdorff-Steinhauser ◽  
Bary C. M. Berghmans ◽  
Marc E. A. Spaanderman ◽  
Esther M. J. Bols
Keyword(s):  
Systematic Review ◽  
Urinary Incontinence ◽  
Pregnant Women ◽  
Health Care Providers ◽  
Meta Analysis ◽  
Care Providers ◽  
Case Definitions ◽  
Monthly Basis ◽  
Policy Makers ◽  
In Pregnancy

Abstract Introduction and hypothesis Urinary incontinence (UI) is a common and embarrassing complaint for pregnant women. Reported prevalence and incidence figures show a large range, due to varying case definitions, recruited population and study methodology. Precise prevalence and incidence figures on (bothersome) UI are of relevance for health care providers, policy makers and researchers. Therefore, we conducted a systematic review and meta-analysis to investigate the prevalence and incidence of UI in pregnancy in the general population for relevant subgroups and assessed experienced bother. Methods All observational studies published between January 1998 and October 2018 reporting on prevalence and/or incidence of UI during pregnancy were included. All women, regardless of weeks of gestation and type of UI presented in all settings, were of interest. A random-effects model was used. Subgroup analyses were conducted by parity, trimester and subtype of UI. Results The mean (weighted) prevalence based on 44 included studies, containing a total of 88.305 women, was 41.0% (range of 9–75%). Stress urinary incontinence (63%) is the most prevalent type of UI; 26% of the women reported daily loss, whereas 40% reported loss on a monthly basis. Bother was experienced as mild to moderate. Conclusions UI is very prevalent and rising with the weeks of gestation in pregnancy. SUI is the most common type and in most cases it was a small amount. Bother for UI is heterogeneously assessed and experienced as mild to moderate by pregnant women.

Increase in paratyphoid fever cases in Japanese travellers returning from Cambodia in 2013

2015 ◽  
Vol 144 (3) ◽  
pp. 602-606 ◽  
Author(s):  
T. SAITOH ◽  
M. MORITA ◽  
T. SHIMADA ◽  
H. IZUMIYA ◽  
A. KANAYAMA ◽  
...  
Keyword(s):  
Country Of Origin ◽  
Laboratory Data ◽  
Surveillance Systems ◽  
Clonal Identity ◽  
Paratyphoid Fever ◽  
Microbiological Analyses ◽  
Epidemiological Link ◽  
Unusual Increase

SUMMARYIn 2013, an unusual increase of paratyphoid fever cases in travellers returning from Cambodia was reported in Japan. From December 2012 to September 2013, 18 cases ofSalmonellaParatyphi A infection were identified. Microbiological analyses revealed that most isolates had the same clonal identity, although the epidemiological link between these cases remains unclear. It was inferred that the outbreak was caused by a common and persistent source in Cambodia that was likely to have continued during 2014. The information of surveillance and laboratory data from cases arising in travellers from countries with limited surveillance systems should be timely shared with the country of origin.

scholarly journals Age- and Influenza Activity-Stratified Case Definitions of Influenza-Like Illness: Experience from Hospital-Based Influenza Surveillance in South Korea

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e84873 ◽  
Author(s):  
Tae Un Yang ◽  
Hee Jin Cheong ◽  
Joon Young Song ◽  
Jin Soo Lee ◽  
Seong-Heon Wie ◽  
...  
Keyword(s):  
South Korea ◽  
Illness Experience ◽  
Influenza Surveillance ◽  
Case Definitions ◽  
Influenza Like Illness ◽  
Influenza Activity

Clinical Predictors for Laboratory-Confirmed Influenza Infections: Exploring Case Definitions for Influenza-Like Illness

2015 ◽  
Vol 36 (3) ◽  
pp. 241-248 ◽  
Author(s):  
Shital C. Shah ◽  
Dino P. Rumoro ◽  
Marilyn M. Hallock ◽  
Gordon M. Trenholme ◽  
Gillian S. Gibbs ◽  
...  
Keyword(s):  
Influenza A ◽  
Medical Center ◽  
Academic Medical Center ◽  
Clinical Signs ◽  
Case Definition ◽  
Chief Complaint ◽  
Nasopharyngeal Swab ◽  
Clinical Predictors ◽  
Case Definitions ◽  
Influenza Like Illness

OBJECTIVETo identify clinical signs and symptoms (ie, “terms”) that accurately predict laboratory-confirmed influenza cases and thereafter generate and evaluate various influenza-like illness (ILI) case definitions for detecting influenza. A secondary objective explored whether surveillance of data beyond the chief complaint improves the accuracy of predicting influenza.DESIGNRetrospective, cross-sectional study.SETTINGLarge urban academic medical center hospital.PARTICIPANTSA total of 1,581 emergency department (ED) patients who received a nasopharyngeal swab followed by rRT-PCR testing between August 30, 2009, and January 2, 2010, and between November 28, 2010, and March 26, 2011.METHODSAn electronic surveillance system (GUARDIAN) scanned the entire electronic medical record (EMR) and identified cases containing 29 clinical terms relevant to influenza. Analyses were conducted using logistic regressions, diagnostic odds ratio (DOR), sensitivity, and specificity.RESULTSThe best predictive model for identifying influenza for all ages consisted of cough (DOR=5.87), fever (DOR=4.49), rhinorrhea (DOR=1.98), and myalgias (DOR=1.44). The 3 best case definitions that included combinations of some or all of these 4 symptoms had comparable performance (ie, sensitivity=89%–92% and specificity=38%–44%). For children <5 years of age, the addition of rhinorrhea to the fever and cough case definition achieved a better balance between sensitivity (85%) and specificity (47%). For the fever and cough ILI case definition, using the entire EMR, GUARDIAN identified 37.1% more influenza cases than it did using only the chief complaint data.CONCLUSIONSA simplified case definition of fever and cough may be suitable for implementation for all ages, while inclusion of rhinorrhea may further improve influenza detection for the 0–4-year-old age group. Finally, ILI surveillance based on the entire EMR is recommended.Infect Control Hosp Epidemiol 2015;00(0): 1–8

scholarly journals Epidemiology and Viral Etiology of the Influenza-Like Illness in Corsica during the 2012–2013 Winter: An Analysis of Several Sentinel Surveillance Systems

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e100388 ◽  
Author(s):  
Laëtitia Minodier ◽  
Christophe Arena ◽  
Guillaume Heuze ◽  
Marc Ruello ◽  
Jean Pierre Amoros ◽  
...  
Keyword(s):  
Sentinel Surveillance ◽  
Surveillance Systems ◽  
Viral Etiology ◽  
Influenza Like Illness

scholarly journals Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States

2021 ◽  
Author(s):  
Jessica T Davis ◽  
Matteo Chinazzi ◽  
Nicola Perra ◽  
Kunpeng Mu ◽  
Ana Pastore y Piontti ◽  
...  
Keyword(s):  
United States ◽  
Early Stage ◽  
The United States ◽  
International Travel ◽  
Surveillance Systems ◽  
Model Driven ◽  
Global Dynamic ◽  
The Us ◽  
Community Transmission ◽  
Spatio Temporal

Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1-3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.

Sign in / Sign up

Export Citation Format

Share Document