scholarly journals A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community

2022 ◽  
Author(s):  
Jade Daigle ◽  
Kathleen Racher ◽  
Justin Hazenberg ◽  
Allan Yeoman ◽  
Heather Hannah ◽  
...  
Keyword(s):  
Public Health ◽  
Limit Of Detection ◽  
Detection Threshold ◽  
Rapid Test ◽  
Clinical Testing ◽  
Remote Communities ◽  
Public Health Response ◽  
Public Health Action ◽  
Remote Community ◽  
Surveillance Programs

Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories. Importance: Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert. The advantages of an easy-to-use wastewater test for SARS-CoV-2 are clear – it supports surveillance in remote communities, improves access to testing, and provides faster results allowing for an immediate public health response. The application of wastewater rapid testing in a remote community facilitated the detection of a COVID-19 cluster and triggered public health action, clearly demonstrating the utility of this technology. Wastewater surveillance will become increasingly important in the post-vaccination pandemic landscape as individuals with asymptomatic/mild infections continue transmitting SARS-CoV-2 but are unlikely to be tested.

scholarly journals A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community

2021 ◽  
Author(s):  
Jade Daigle ◽  
Kathleen Racher ◽  
Justin Hazenberg ◽  
Allan Yeoman ◽  
Heather Hannah ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Detection Threshold ◽  
Clinical Testing ◽  
Viable Option ◽  
Remote Community ◽  
Remote Areas ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Surveillance Programs ◽  
Wastewater Samples

Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories.

Cross-contamination in molecular laboratories: A challenge to COVID-19 testing in Bangladesh

2021 ◽  
Vol 2 (5) ◽  
Author(s):  
Mohammad Jahidur Rahman Khan ◽  
◽  
Selim Reza ◽  
Farzana Mim ◽  
Md Abdullah Rumman ◽  
...  
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Diagnostic Errors ◽  
Laboratory Diagnosis ◽  
Cross Contamination ◽  
Rt Pcr ◽  
Public Health Response ◽  
Surveillance Programs ◽  
The Government

Rapid and accurate laboratory diagnosis of SARS-CoV-2 infection is crucial for the management of COVID-19 patients and control of the spread of the virus. At the start of the COVID-19 pandemic, Bangladesh had only one government molecular laboratory where real-time RT-PCR will be performed to diagnose SARS-CoV-2 infection. With the increasing number of suspected cases requiring confirmation diagnostic testing, there was a requirement to quickly expand capacity for large-scale testing. The government of Bangladesh established over 100 molecular laboratories within one year to test COVID-19. To fulfil the requirement for expanded testing, the government was compelled to recruit laboratory employees with inadequate experience, technical knowledge, and skills in molecular assays, particularly in processing specimens, interpreting results, recognizing errors, and troubleshooting. As a result, the risk of diagnostic errors, such as cross-contamination, is increased, as is that the risk of false-positive results, which might risk the patient’s health and undermine the efficacy of public health policies, public health response, surveillance programs, and restrictive measures aimed toward containing the outbreak. This review article aims to explain different sources of crosscontamination in the COVID-19 RT-PCR laboratories and the way to forestall them in efficient and practical ways.

scholarly journals Use of a Rapid Test for Diagnosis of Dengue during Suspected Dengue Outbreaks in Resource-Limited Regions

2016 ◽  
Vol 54 (8) ◽  
pp. 2090-2095 ◽  
Author(s):  
Elizabeth A. Hunsperger ◽  
Tyler M. Sharp ◽  
Paul Lalita ◽  
Kini Tikomaidraubuta ◽  
Yolanda Rebello Cardoso ◽  
...  
Keyword(s):  
Public Health ◽  
Sensitivity And Specificity ◽  
Nonstructural Protein ◽  
Clinical Care ◽  
Rapid Test ◽  
Enzyme Linked Immunosorbent Assay ◽  
Major Public Health Problem ◽  
Public Health Response ◽  
Nonstructural Protein 1 ◽  
Dengue Outbreaks

Dengue is major public health problem, globally. Timely verification of suspected dengue outbreaks allows for public health response, leading to the initiation of appropriate clinical care. Because the clinical presentation of dengue is nonspecific, dengue diagnosis would benefit from a sensitive rapid diagnostic test (RDT). We evaluated the diagnostic performance of an RDT that detects dengue virus (DENV) nonstructural protein 1 (NS1) and anti-DENV IgM during suspected acute febrile illness (AFI) outbreaks in four countries. Real-time reverse transcription-PCR and anti-DENV IgM enzyme-linked immunosorbent assay were used to verify RDT results. Anti-DENV IgM RDT sensitivity and specificity ranged from 55.3 to 91.7% and 85.3 to 98.5%, respectively, and NS1 sensitivity and specificity ranged from 49.7 to 92.9% and 22.2 to 89.0%, respectively. Sensitivity varied by timing of specimen collection and DENV serotype. Combined test results moderately improved the sensitivity. The use of RDTs identified dengue as the cause of AFI outbreaks where reference diagnostic testing was limited or unavailable.

scholarly journals COVID-19, Australia: Epidemiology Report 12: Reporting week ending 23:59 AEST 19 April 2020

2020 ◽  
Vol 44 ◽  
Author(s):  
Keyword(s):  
Public Health ◽  
Disease Transmission ◽  
Case Fatality ◽  
The United States ◽  
International Travel ◽  
World Health ◽  
Public Health Response ◽  
Public Health Action ◽  
Case Ascertainment ◽  
Overseas Travel

Confirmed cases in Australia notified up to 19 April 2020: notifications = 6,606; deaths = 69. The reduction in international travel and domestic movement, social distancing measures and public health action have likely slowed the spread of the disease. Notifications in Australia remain predominantly among people with recent overseas travel, with some locally-acquired cases being detected. Most locally-acquired cases can be linked back to a confirmed case, with a small portion unable to be epidemiologically linked. The distribution of overseas-acquired cases to locally-acquired cases varies by jurisdiction. The crude case fatality rate (CFR) in Australia remains low (1.0%) compared to the World Health Organization’s globally-reported rate (6.8%) and to other comparable high-income countries such as the United States of America (4.7%) and the United Kingdom (13.5%). The low CFR is likely reflective of high case ascertainment including detection of mild cases. High case ascertainment enables public health response and reduction of disease transmission. Internationally, cases continue to increase. The rates of increase have started to slow in several regions, although it is too soon to tell whether this trend will be sustained. Interpretation of international epidemiology should be conducted with caution as it differs from country to country depending not only on the disease dynamics, but also on differences in case detection, testing and implemented public health measures.

The Burden of Antimicrobial Resistant Infections in Wales: a population-level modelling analysis

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
H Wang ◽  
P P M Thomas
Keyword(s):  
Public Health ◽  
Relative Deprivation ◽  
Infection Type ◽  
Surveillance Data ◽  
Health Board ◽  
Local Health ◽  
Public Health Response ◽  
Public Health Action ◽  
Public Health Burden ◽  
Health Action

Abstract Background Antimicrobial Resistance (AMR) threatens the sustainability of an effective, global public health response to infectious disease. This study uses routine surveillance data to estimate the public health burden (PHB) of AMR infections in Wales for the period 2017-19, with further stratification by Age, Sex, local Health Board (HB) area and relative deprivation, to guide public health action. Methods Welsh AMR Surveillance data, collected as part of the European AMR Surveillance Network (EARS-Net), was collated for the period 2017-19. Adapting the methodology of the European Centres for Disease Control Burden of Communicable Diseases in Europe (BCoDE), we modelled the PHB of five types of antibiotic-resistant infection (invasive and non-invasive), and 7 pathogens which associated with AMR, using the Burden of Healthcare-Acquire Infection (BHAI) R package. Postcodes were used to assign patients' resident health board, as well as their relative socio-economic deprivation, using the Welsh Index of Multiple Deprivation (WIMD). Results Preliminary results (median estimation with 95% confidence interval (CI)) were calculated for: number of infections with AMRnumber of deaths attributable to AMRnumber of DALYs attributable to AMR Estimates were stratified by age; sex; HB; relative deprivation; and pathogen and infection type. Conclusions This is the first study of its kind to study the relationship between AMR incidence and relative deprivation. It offers a clear picture of the epidemiology of AMR within Wales to support public health action. Key messages Infections from AMR bacteria represent a major PHB in Wales, and the modelling PHB of AMR by socioeconomic group and local area can inform effective public health action. The results of this study are valuable for guiding public health action to address AMR at the national and international level.

scholarly journals Know Thine Enemy: Viral Genome Sequencing in Outbreaks

2020 ◽  
pp. 34-37
Author(s):  
Katherine Colvin
Keyword(s):  
Public Health ◽  
Vaccine Development ◽  
Treatment Options ◽  
Epidemiologic Study ◽  
Latency Period ◽  
Contact Tracing ◽  
Genomic Sequencing ◽  
Remote Communities ◽  
Public Health Response ◽  
Health Measures

CONTAINING a viral outbreak with public health measures firstly requires identification of the causative virus, followed by more detailed understanding of viral features. Genomic sequencing provides exhaustive insight into viral features that may help predict outbreak behaviours, assist in diagnosis and tracking, and shape treatment and vaccination strategies. When coupled with epidemiologic study of outbreak data, viral genomic sequencing can be used to direct public health measures and increase the speed of understanding compared to epidemiology alone. Community spread of cases can be used to guide mathematic models and contact tracing of viral outbreaks for public health response. However, epidemiologic data alone better suits responses to low-prevalence and less-widespread outbreaks. Where pathogens have a longer latency period or spread affects rural and remote communities, features of the virus itself must be considered in determining the response. Genotypic and phenotypic characteristics, identified using molecular biology tools, can clarify the type and strain of a virus responsible for an outbreak, and inform and improve case diagnosis, treatment options, and vaccine development, as well as improve tracing accuracy.1

scholarly journals Investigation and public health response to a COVID-19 outbreak in a rural resort community — Blaine County, Idaho, 2020

2021 ◽  
Author(s):  
Eileen M. Dunne ◽  
Tanis Maxwell ◽  
Christi Dawson-Skuza ◽  
Matthew Burns ◽  
Christopher Ball ◽  
...  
Keyword(s):  
Public Health ◽  
Rural Communities ◽  
Mitigation Strategies ◽  
Test Results ◽  
Public Health Response ◽  
Public Health Action ◽  
Central Public Health ◽  
South Central ◽  
Laboratory Test Results ◽  
Close Contacts

AbstractBlaine County, Idaho, a rural area with a renowned resort, experienced an outbreak of novel coronavirus disease (COVID-19). We undertook an epidemiologic investigation to describe the outbreak and guide public health action. Confirmed cases of COVID-19 were identified from reports of SARS-CoV-2-positive laboratory test results to South Central Public Health District.Information on symptoms, hospitalization, recent travel, healthcare worker status, and close contacts was obtained by medical record review and patient interviews. Viral sequence analysis was conducted on a subset of available specimens. During March 13–April 10, 2020, a total of 451 COVID-19 cases occurred among Blaine County residents (1,959 cases per 100,000 population). An additional 37 cases occurred in out-of-state residents. Among the 451 COVID-19 patients, the median age was 51 years (Interquartile range [IQR]: 37–63), 52 (11.5%) were hospitalized, and 5 (1.1%) died. The median duration between specimen collection and a positive laboratory result was 9 days (IQR: 4–10). Forty-four (9.8%) patients reported recent travel. Healthcare workers comprised 56 (12.4%) cases; 33 of whom worked at the only hospital in the county, leading to a 15-day disruption of hospital services. Of 562 close contacts monitored by public health authorities, 22 (3.9%) had laboratory-confirmed COVID-19 and an additional 29 (5.2%) experienced compatible symptoms. Sequencing results from 34 Idaho specimens supported epidemiologic findings indicating travel as a source of SARS-CoV-2, and identified multiple lineages among hospital workers. Community mitigation strategies included school and resort closure, stay-at-home orders, and restrictions on incoming travelers. COVID-19 outbreaks in rural communities can disrupt health services. Lack of local laboratory capacity led to long turnaround times for COVID-19 test results. Rural communities frequented by tourists should consider implementing restrictions on incoming travelers among other mitigation strategies to reduce COVID-19 transmission.

scholarly journals Investigation and public health response to a COVID-19 outbreak in a rural resort community—Blaine County, Idaho, 2020

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250322
Author(s):  
Eileen M. Dunne ◽  
Tanis Maxwell ◽  
Christina Dawson-Skuza ◽  
Matthew Burns ◽  
Christopher Ball ◽  
...  
Keyword(s):  
Public Health ◽  
Rural Communities ◽  
Mitigation Strategies ◽  
Test Results ◽  
Public Health Response ◽  
Public Health Action ◽  
Illness Onset ◽  
South Central ◽  
Laboratory Test Results ◽  
Close Contacts

Blaine County, Idaho, a rural area with a renowned resort, experienced a COVID-19 outbreak early in the pandemic. We undertook an epidemiologic investigation to describe the outbreak and guide public health action. Confirmed cases of COVID-19 were identified from reports of SARS-CoV-2-positive laboratory test results to South Central Public Health District. Information on symptoms, hospitalization, recent travel, healthcare worker status, and close contacts was obtained by medical record review and patient interviews. Viral sequence analysis was conducted on a subset of available specimens. During March 13–April 10, 2020, a total of 451 COVID-19 cases among Blaine County residents (1,959 cases per 100,000 population) were reported, with earliest illness onset March 1. The median patient age was 51 years (interquartile range [IQR]: 37–63), 52 (11.5%) were hospitalized, and 5 (1.1%) died. The median duration between specimen collection and a positive laboratory result was 9 days (IQR: 4–10). Forty-four (9.8%) patients reported recent travel and an additional 37 cases occurred in out-of-state residents. Healthcare workers comprised 56 (12.4%) cases; 33 of whom worked at the only hospital in the county, leading to a 15-day disruption of hospital services. Among 562 close contacts monitored by public health authorities, laboratory-confirmed COVID-19 or compatible symptoms were identified in 51 (9.1%). Sequencing results from 34 specimens supported epidemiologic findings indicating travel as a source of SARS-CoV-2, and identified multiple lineages among hospital workers. Community mitigation strategies included school and resort closure, stay-at-home orders, and restrictions on incoming travelers. COVID-19 outbreaks in rural communities can disrupt health services. Lack of local laboratory capacity led to long turnaround times for COVID-19 test results. Rural communities frequented by tourists face unique challenges during the COVID-19 pandemic. Implementing restrictions on incoming travelers and other mitigation strategies helped reduce COVID-19 transmission early in the pandemic.

scholarly journals Wastewater-based Epidemiology for Averting COVID-19 Outbreaks on The University of Arizona Campus

2020 ◽  
Author(s):  
Walter W. Betancourt ◽  
Bradley W. Schmitz ◽  
Gabriel K. Innes ◽  
Kristen M. Pogreba Brown ◽  
Sarah M. Prasek ◽  
...  
Keyword(s):  
Public Health ◽  
Disease Transmission ◽  
Population Level ◽  
Nasopharyngeal Swab ◽  
Clinical Testing ◽  
Surveillance Strategy ◽  
Public Health Action ◽  
University Of Arizona ◽  
Wastewater Samples ◽  
The University

AbstractThe University of Arizona utilized wastewater-based epidemiology paired with clinical testing as a surveillance strategy to monitor COVID-19 prevalence in a dormitory community. Positive SARS-CoV-2 RNA detection in wastewater led to prompt testing of all residents and the identification and isolation of three infected individuals which averted potential disease transmission.TextWastewater-based epidemiology (WBE) utilizes concentrations of SARS-CoV-2 in sewage to monitor population-level COVID-19 infections (1–3). Currently, WBE is a promising indicator to support public health decisions (3,4). In this case study, WBE was used to detect a COVID-19 outbreak in a student dormitory (henceforth Dorm A) at the University of Arizona (UArizona).The StudyUArizona incorporated wastewater surveillance as a potential early-warning tool for COVID-19 outbreaks on campus. Grab samples (1L) were collected from a sewer manhole specific to Dorm A, between August 18-31 to monitor SARS-CoV-2 RNA in wastewater. Upon positive detection of viral RNA in wastewater samples, clinical testing was conducted on every individual living in the dorm. UArizona performed two clinical testing modalities, antigen (1 hour turnaround) test via anterior nasal swab and RT-PCR (48-72 hour turnaround) via nasopharyngeal swab samples. Individuals were subject to clinical testing via two routes: Campus Health Services (CHS) if experiencing symptoms or Test All Test Smart (TATS) regardless of symptoms. Refer to Appendix for method details.Article Summary LineWastewater-based epidemiology with subsequent clinical testing identified individuals infected with COVID-19 living in a dormitory and further spread of disease was prevented with public health action.

scholarly journals COVID-19, Australia: Epidemiology Report 13: Reporting week ending 23:59 AEST 26 April 2020

2020 ◽  
Vol 44 ◽  
Author(s):  
Keyword(s):  
Public Health ◽  
Disease Transmission ◽  
Case Fatality ◽  
The United States ◽  
International Travel ◽  
World Health ◽  
Public Health Response ◽  
Public Health Action ◽  
Case Ascertainment ◽  
Overseas Travel

Confirmed cases in Australia notified up to 26 April 2020: notifications = 6,711; deaths = 77. The reduction in international travel and domestic movement, social distancing measures and public health action have likely slowed the spread of COVID-19 in Australia. Notifications in Australia remain predominantly among people with recent overseas travel, with some locally-acquired cases being detected. Most locally-acquired cases can be linked back to a confirmed case, with a small portion unable to be epidemiologically linked to another case. The ratio of overseas-acquired cases to locally-acquired cases varies by jurisdiction. The crude case fatality rate (CFR) in Australia remains low (1.1%) compared to the World Health Organization’s globally-reported rate (6.9%) and to other comparable high-income countries such as the United States of America (5.1%) and the United Kingdom (13.7%). The lower CFR in Australia is likely reflective of high case ascertainment including detection of mild cases. High case ascertainment and prompt identification of contacts enables an effective public health response and a reduction of disease transmission. Internationally, cases continue to increase. The rates of increase have started to slow in several regions, although it is too soon to tell whether this trend will be sustained. Interpretation of international epidemiology should be conducted with caution as it differs from country to country depending not only on the disease dynamics, but also on differences in case detection, testing and implemented public health measures.

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