Charting the challenges behind the testing of COVID-19 in developing countries: Nepal as a case study

Symptoms of depression among outpatients with suspected COVID-19 in metropolitan Local Government Areas of Kaduna State, Nigeria

BACKGROUND

The novel SARS-CoV-2 virus that causes Coronavirus disease (COVID-19) has redefined global health and response to Acute Respiratory Infection (ARI). The outbreak of a cluster of influenza-like illnesses in Wuhan, China, has morphed into a pandemic in the last quarter of 2019, stretching from South East Asia to Europe, The Americas, Africa, and the Australian subcontinent. We evaluated the prevalence of depression among outpatients diagnosed with ARI.

MATERIALS AND METHODS

We utilized a cross-sectional, observational design and investigated the prevalence of symptoms of depression among outpatients with ARI and described the characteristics of outpatients with ARI in Kaduna State.

RESULTS

The prevalence of symptoms of depression was 19.6% for respondents with symptoms of ARI and 14.4% for those without symptoms of ARI. On no risk of depression, we had a higher proportion of the respondents without symptoms of ARI (86%) than those with symptoms of depression (80%) (M = 318.4, SD = 29.62 case, and M = 344.0, SD = 14.2 control, r = 0.88, CI = 13.5 to 6.5, P = 0.000952). Likewise, in the category with mild risk of depression, respondents without symptoms of ARI were fewer (10%) than those with symptoms of depression (15%) (M = 58.4, SD = 26.0 case, and M = 42.1, SD = 12.7 control, r = 0.86, CI = 11.8 to 5.8, P = 0.0136. There was no significant difference between respondents with symptoms of ARI and without symptoms of ARI in the categories of moderate (M = 13.6, SD = 5.1 case, and M = 11.6, SD = 4.6 control, r = 0.87, CI = 2.3 to 2.1, P = 0.178) and high (M = 5.6, SD = 2.5 case, and M = 4.4, SD = 3.2 control, r = 0.61, CI = 1.2 to 1.5, P = 0.174) risk of depression.

CONCLUSION

Symptoms of depression were commoner among respondents who presented with symptoms of Acute Respiratory Infection (ARI) at the Outpatient Department (OPD). However, further explanatory research is needed to establish causality.

Self-Diagnosis of SARS-CoV-2 from Saliva Samples at Home: Isothermal Amplification Enabled by Do-It-Yourself Portable Incubators and Laminated Poly-ethyl Sulfonate Membranes

COVID-19 made explicit the need for rethinking the way in which we conduct testing for epidemic emergencies. During the COVID-19 pandemic, the dependence on centralized lab facilities and resource-intensive methodologies (e.g., RT-qPCR methods) greatly limited the deployment of widespread testing efforts in many developed and underdeveloped countries. Here, we illustrate the development of a simple and portable diagnostic kit that enables self-diagnosis of COVID-19 at home from saliva samples. We describe the development of a do-it-yourself (DIY) incubator for Eppendorf tubes that can be used to conduct SARS-CoV-2 detection with competitive sensitivity and selectivity from saliva at home. In a proof-of-concept experiment, we assembled Eppendorf-tube incubators at our home shop, prepared a single-tube mix of reagents and LAMP primers in our lab, and deployed these COVID-19 detection kits using urban delivery systems (i.e., Rappifavor or Uber) to more than 15 different locations in Monterrey, México. This straightforward strategy enabled rapid and cost-effective at-home molecular diagnostics of SARS-CoV-2 from real saliva samples with a high sensitivity (100%) and high selectivity (87%).

Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021

There has been raging discussion and debate around the quality of COVID death data in South Asia. According to WHO, of the 5.5 million reported COVID-19 deaths from 2020-2021, 0.57 million (10%) were contributed by five low and middle income countries (LMIC) countries in the Global South: India, Pakistan, Bangladesh, Sri Lanka and Nepal. However, a number of excess death estimates show that the actual death toll from COVID-19 is significantly higher than the reported number of deaths. For example, the IHME and WHO both project around 14.9 million total deaths, of which 4.5-5.5 million were attributed to these five countries in 2020-2021. We focus our gaze on the COVID-19 performance of these five countries where 23.5% of the world population lives in 2020 and 2021, via a counterfactual lens and ask, to what extent the mortality of one LMIC would have been affected if it adopted the pandemic policies of another, similar country? We use a Bayesian semi-mechanistic model developed by Mishra et al. (2021) to compare both the reported and estimated total death tolls by permuting the time-varying reproduction number (Rt) across these countries over a similar time period. Our analysis shows that, in the first half of 2021, mortality in India in terms of reported deaths could have been reduced to 96 and 102 deaths per million compared to actual 170 reported deaths per million had it adopted the policies of Nepal and Pakistan respectively. In terms of total deaths, India could have averted 481 and 466 deaths per million had it adopted the policies of Bangladesh and Pakistan. On the other hand, India had a lower number of reported COVID-19 deaths per million (48 deaths per million) and a lower estimated total deaths per million (80 deaths per million) in the second half of 2021, and LMICs other than Pakistan would have lower reported mortality had they followed India's strategy. The gap between the reported and estimated total deaths highlights the varying level and extent of under-reporting of deaths across the subcontinent, and that model estimates are contingent on accuracy of the death data. Our analysis shows the importance of timely public health intervention and vaccines for lowering mortality and the need for better coverage infrastructure for the death registration system in LMICs.

The impact of community nucleic acid testing on infection in residential compounds during a city-wide lockdown

The question of whether community nucleic acid testing contributes to an increase in infections within residential compounds has not been definitively answered. Shanghai, one of the largest cities in China, conducted city-wide community testing during its lockdown from late March to May 2022. This situation provided a unique opportunity to examine the effect of community testing on infection rates, as the lockdown largely eliminated confounding factors such as citizen mobility. In our study, based on a survey of 208 residential compounds in Shanghai and the daily infection data during the lockdown period, we found a significant correlation between community testing and infection risk in these compounds. However, after addressing potential issues of reverse causality and sampling bias, we found no significant causal link between community testing and infection risk. Furthermore, we discovered that increased awareness of mask-wearing correlated with a decrease in infections within the residential compounds during community testing. This suggests that the perceived correlation between community testing and infection risk may be confounded by residents' adherence to mask-wearing practices. Our findings emphasize the need for public health decision-makers to reinforce the importance of mask-wearing during community testing, as a means to prevent infections among citizens.

Development of an instrument-free and low-cost ELISA dot-blot test to detect antibodies against SARS-CoV-2

Most laboratory tests to detect the presence of anti-SARS-CoV-2 antibodies use enzyme-linked immunosorbent assays (ELISA) or chemiluminescence immunoassays (CLIA); however, equipment for these immunoassays is unavailable in many areas of low- and middle-income countries. Rapid lateral flow immunoassay (LFIA) tests are an equipment-free option, but their high price may make them less suitable for conducting seroprevalence surveys. Here, we describe a simple dual antigen ELISA dot-blot test to detect anti-SARS-CoV-2 IgG antibodies with high sensitivity (94-98%) and specificity (92-100%), compared to commercially available ELISA and CLIA options. Additionally, this ELISA dot-blot test can be completed in one hour using minimal laboratory equipment. Importantly, this immunoassay is significantly more affordable than most LFIA tests available on the global market. The dot-blot strips may be stored for up to 7 days under freezing conditions. This ELISA dot-blot test is a cost-effective option for conducting seroprevalence screenings in areas lacking ELISA or CLIA facilities, compared to LFIA tests.

Lessons learnt from the first wave of COVID-19 in Damascus, Syria: a multicentre retrospective cohort study

OBJECTIVES

The decade-long Syrian war led to fragile health infrastructures lacking in personal and physical resources. The public health of the Syrian population was, therefore, vulnerable to the COVID-19 pandemic, which devastated even well-resourced healthcare systems. Nevertheless, the officially reported incidence and fatality rates were significantly lower than the forecasted numbers.

DESIGN

A retrospective cohort study.

SETTING

The four main responding hospitals in Damascus, which received most of the cases during the first pandemic wave in Syria (i.e., June-August 2020).

PARTICIPANTS

One thousand one hundred eighty-four patients who were managed as inpatient COVID-19 cases.

PRIMARY AND SECONDARY OUTCOME MEASURES

The records of hospitalised patients were screened for clinical history, vital signs, diagnosis modality, major interventions and status at discharge.

RESULTS

The diagnostic and therapeutic preparedness for COVID-19 was significantly heterogeneous among the different centres and depleted rapidly after the arrival of the first wave. Only 32% of the patients were diagnosed based on positive reverse transcription-PCR tests. Five hundred twenty-six patients had an indication for intensive care unit admission, but only 82% of them received it. Two hundred fifty-seven patients needed mechanical ventilation, but ventilators were not available to 14% of them, all of whom died. Overall mortality during hospitalisation reached 46% and no significant difference was found in fatality between those who received and did not receive these care options.

CONCLUSIONS

The Syrian healthcare system expressed minor resilience in facing the COVID-19 pandemic, as its assets vanished swiftly with a limited number of cases. This forced physicians to reserve resources (e.g., ventilators) for the most severe cases, which led to poor outcomes of in-hospital management and limited the admission capacity for milder cases. The overwhelmed system additionally suffered from constrained coordination, suboptimal allocation of the accessible resources and a severe inability to informatively report on the catastrophic pandemic course in Syria.

The viral picture of well-being: Biggest concerns, losses, and unintended gifts of COVID-19 in the Philippines

The COVID-19 pandemic revealed more than anticipated about global human functioning and resiliency. This Philippines-based study replicated a recent U.S. COVID analysis on psychological well-being (PWB). Factors examined herein were grouped into categories for analysis: 1) predictors of PWB, 2) areas of greatest stress or worry (biggest concerns), 3) perceived or real losses across SES, and 4) identified "unintended gifts" across PWB. Participants (n = 1345) were volunteers who responded to an online survey from August to September 2021, peak of the Delta variant. Three general groups of predictors (biological, psychological, and socio-economic) contributed to PWB. A regression model containing a total of 11 variables was significant, F(11, 1092) = 116.02, p < .00, explaining 53.9% of the variance. The model indicated PWB was significantly predicted by physical health, age, spirituality, emotional loneliness, social loneliness, sense of agency, and income. The strongest predictors of PWB were a sense of agency, social loneliness, and spirituality. Qualitative data analysis was conducted examining biggest concerns, losses due to COVID, and unintended gifts. Top ranking participant concerns were the health of family and friends, personal wellness, and governmental inefficiency/lack of concern. Losses compared to pre-COVID life were analyzed by SES group, with the most frequent responses being missing face-to-face interactions and the freedom to go/do what they please. Low SES groups were most likely to endorse missing everyday routine and experiencing changes in housing conditions due to the pandemic. Unintended gifts of COVID explored by PWB, high PWB individuals significantly appreciated intentional time with family and friends, deepening their spiritual lives, the ability to work from home, less pollution, and more time for physical exercise. Low PWB individuals reported nothing gained, except more time playing video games and watching TV. Those with higher PWB identified more unintended gifts of COVID and coped more actively.

Global COVID-19 Policy Engagement With Scientific Research Information: Altmetric Data Study

BACKGROUND

Previous studies on COVID-19 scholarly articles have primarily focused on bibliometric characteristics, neglecting the identification of institutional actors that cite recent scientific contributions related to COVID-19 in the policy domain, and their locations.

OBJECTIVE

The purpose of this study was to assess the online citation network and knowledge structure of COVID-19 research across policy domains over 2 years from January 2020 to January 2022, with a particular emphasis on geographical frequency. Two research questions were addressed. The first question was related to who has been the most active in policy engagement with science and research information sharing during the COVID-19 pandemic, particularly in terms of countries and organization types. The second question was related to whether there are significant differences in the types of coronavirus research shared among countries and continents.

METHODS

The Altmetric database was used to collect policy report citations of scientific articles for 3 topic terms (COVID-19, COVID-19 vaccine, and COVID-19 variants). Altmetric provides the URLs of policy agencies that have cited COVID-19 research. The scientific articles used for Altmetric citations are extracted from journals indexed by PubMed. The numbers of COVID-19, COVID-19 vaccine, and COVID-19 variant research outputs between January 1, 2020, and January 31, 2022, were 216,787, 16,748, and 2777, respectively. The study examined the frequency of citations based on policy institutional domains, such as intergovernmental organizations, national and domestic governmental organizations, and nongovernmental organizations (think tanks and academic institutions).

RESULTS

The World Health Organization (WHO) stood out as the most notable institution citing COVID-19-related research outputs. The WHO actively sought and disseminated information regarding the COVID-19 pandemic. The COVID-19 vaccine citation network exhibited the most extensive connections in terms of degree centrality, 2-local eigenvector centrality, and eigenvector centrality among the 3 key terms. The Netherlands, the United States, the United Kingdom, and Australia were the countries that sought and shared the most information on COVID-19 vaccines, likely due to their high numbers of COVID-19 cases. Developing nations, although gaining quicker access to COVID-19 vaccine information, appeared to be relatively isolated from the enriched COVID-19 pandemic content in the global network.

CONCLUSIONS

The global scientific network ecology during the COVID-19 pandemic revealed distinct types of links primarily centered around the WHO. Western countries demonstrated effective networking practices in constructing these networks. The prominent position of the key term "COVID-19 vaccine" demonstrates that nation-states align with global authority regardless of their national contexts. In summary, the citation networking practices of policy agencies have the potential to uncover the global knowledge distribution structure as a proxy for the networking strategy employed during a pandemic.

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

Sniffer dogs performance is stable over time in detecting COVID-19 positive samples and agrees with the rapid antigen test in the field

Rapid antigen diagnostic (RAD) tests have been developed for the identification of the SARS-CoV-2 infection. However, they require nasopharyngeal or nasal swab, which is invasive, uncomfortable, and aerosolising. The use of saliva test was also proposed but has not yet been validated. Trained dogs may efficiently smell the presence of SARS-CoV-2 in biological samples of infected people, but further validation is needed both in laboratory and in field. The present study aimed to (1) assess and validate the stability over a specific time period of COVID-19 detection in humans' armpit sweat by trained dogs thanks to a double-blind laboratory test-retest design, and (2) assess this ability when sniffing people directly. Dogs were not trained to discriminate against other infections. For all dogs (n. 3), the laboratory test on 360 samples yielded 93% sensitivity and 99% specificity, an 88% agreement with the Rt-PCR, and a moderate to strong test-retest correlation. When sniffing people directly (n. 97), dogs' (n. 5) overall sensitivity (89%) and specificity (95%) were significantly above chance level. An almost perfect agreement with RAD results was found (kappa 0.83, SE 0.05, p = 0.001). Therefore, sniffer dogs met appropriate criteria (e.g., repeatability) and WHO's target product profiles for COVID-19 diagnostics and produced very promising results in laboratory and field settings, respectively. These findings support the idea that biodetection dogs could help reduce the spread of the virus in high-risk environments, including airports, schools, and public transport.

A comparison of SARS-CoV-2 rapid antigen testing with realtime RT-PCR among symptomatic and asymptomatic individuals

BACKGROUND

Identification of SARS-CoV-2 positive patients with rapid and cost-effective test methods is the key for isolating infected individuals, interrupting the transmission chain, and thus, containment of the CoVID-19 disease. In this regard, Rapid Antigen Test (RAT) plays an important role at point of care testing but the low sensitivity attributing towards escape of positive cases is reported as a major disadvantage of RAT which led us to evaluate a RAT kit among symptomatic and asymptomatic individuals suspected of CoVID-19.

METHODS

We analyzed 329 parallel nasopharyngeal swabs for RAT (Zydus Cadila, India) at the point of collection in a hospital-based facility and RealTime RT-PCR in the laboratory. The performance parameters were analyzed by evaluating the specificity, sensitivity, Negative Predictive Value (NPV), Positive Predictive Value (PPV), and Kappa coefficient.

RESULTS

The sensitivity and specificity were found to be 75.17% and 98.89% respectively. Positive Predictive value was 98.25% and the negative predictive value was 82.79%. The accuracy between the two techniques was found to be 88.14% with a kappa coefficient of 0.756 (SE: 0.036 and CI at 95%: 0.686 to 0.826) with a good strength of agreement (0.61-0.80) between the two testing techniques. Among the false-negative cases, 22 (59.5%) were asymptomatic having the Cycle Threshold (Ct) range 27 to 32.9 including 12 cases with a history of close contact with the known positive cases (i.e. household contact). The remaining 15 cases (40.5%) were symptomatic having low to moderate Ct values.

CONCLUSION

It is observed from the results that the false negative result for symptomatic individuals is a matter of concern as it was noted in 4 cases of our study subjects who required hospitalisation later. Also the positives among asymptomatic contacts are important from epidemiological point of view for isolation and curtailing the infection from spreading in a community. These results support the fact that RAT showing sensitivity below 80% can be used for mass screening purposes with provision for additional testing in case of false negative with symptomatic individuals. Also false-negative results should be interpreted cautiously considering the epidemiological link as well as the clinical condition of the patients.

BioBlocksLab: A portable DIY Bio Lab using BioBlocks language

Standard molecular biology laboratories are usually made with complex, sophisticated, and expensive equipment. Unfortunately, most of these labs are not affordable for everyone. In this paper, we show how we built a portable bio lab BioBlocksLab, made of four modules: a centrifuge, a thermocycler, electrophoresis, and an incubator. We also propose a new version of a blockly programming language to describe experimental lab protocols, called BioBlocks 2.0, which is based on the Microsoft MakeCode platform from the open-source project Microsoft Programming Experience Toolkit (PXT). We run BioBlocks programs of real lab protocols to control different hardware modules with biological reagents and get positive results. We offer an easy, affordable, and open-source way for everyone to do experiments with Do-It-Yourself (DIY) portable bio-labs.

COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.

COVID-19 self-testing in Nigeria: Stakeholders' opinions and perspectives on its value for case detection

BACKGROUND

COVID-19 testing coverage is limited in Nigeria. Access to rapid SARS-CoV-2 antigen-detection self-testing kits may help improve the detection of asymptomatic and mildly symptomatic cases and increase the country's low rate of SARS-CoV-2 testing. Before implementing self-testing in Nigeria, assessing the population's perceptions regarding this approach is imperative. In mid-2021, an exploratory cross-sectional qualitative research was conducted to investigate stakeholders' values and preferences for SARS-CoV-2 self-testing in Nigeria.

METHODS

In-person and online semi-structured interviews and focus group discussions with healthcare workers, representatives of civil society, and potential implementors of self-testing delivery programs were used to explore values and perceptions around access to conventional provider-initiated COVID-19 testing. Topics included the public's values in relation to SARS-CoV-2 self-testing, the safe and effective use of SARS-CoV-2 self-testing, and likely actions upon receiving a positive SARS-CoV-2 self-test result. A thematic analysis approach was applied.

RESULTS

The 58 informants (29 female) reported that Nigeria has limited availability of conventional provider-delivered SARS-CoV-2 testing. While just a few informants were familiar with SARS-CoV-2 self-testing, they generally supported using self-testing as an approach that they felt could assist with early case detection and improve access to testing. Concerns relating to the use of self-testing mainly related to the ability of low-literate individuals to use and interpret the self-tests, the affordability of self-tests, equity of access, and the availability of healthcare system support for those who self-test positive.

CONCLUSION

Although the Nigerian public perceive multiple benefits associated with access to SARS-CoV-2 self-testing, the perceived inefficiency of the national health service delivery system may limit the access of users of the kits to psychosocial and clinical support. Nevertheless, in Nigeria, where COVID-19 vaccine coverage is low and the risk of further waves of COVID-19 is high, self-testing may assist in the prompt detection of cases and contribute to halting the spread of the virus.

Real-Time fast PCR amplification using designated and conventional real time thermal cycler systems: COVID-19 perspective

The study aimed to shorten multiplex RT-PCR run time for detection of SARS CoV-2 N1 and N2 sequences and human RNase P (RP) sequence as internal mRNA control using conventional and designated real time thermal cycler systems. Optimization of Fast PCR protocol using plasmid-based N1 and N2 positive control and synthetic version of human RP was done on Applied Biosystems (ABI) QuantStudioTM5 (conventional), ABI 7500 Fast Dx (designated), and CFX96 Touch Real Time Detection System, Bio-Rad (conventional). Finally, a performance evaluation of Fast PCR was performed in terms of sensitivity, specificity, and precision. For a 40-cycle PCR with optimized Fast PCR protocols on QuantStudioTM5, ABI 7500 Fast Dx, and CFX96 Touch (conventional), standard/regular versus Fast PCR run times (min) were 84 vs. 49, 96 vs. 48, and 103 vs. 61, thereby saving 35, 48, and 43 min, respectively. For each thermal cycler, Standard and Fast PCR generated identical shapes of fluorescence curves, Ct values, and (3) R2 (0.95 to 0.99) for 5 10-log dilution panels of each positive control. The fast PCR approach generated results with 100% sensitivity and specificity. Median test comparisons between standard PCR and Fast PCR Cts of COVID-19 samples did not produce significance (p>0.5), suggesting that Fast PCR and Standard PCR were comparable. Also, the median and mean of each target had closely-related values, further suggesting that the two approaches were comparable. That is, there is an equivalency between Conventional and Fast PCR instruments for detection of COVID-19.

Modeling the impact of the COVID‐19 outbreak on environment, health sector and energy market

The global outbreak of COVID‐19 disease had a significant impact on the entire globe. Such a notable public health event can be seen as a “black swan” that brings unpredictable and unusual forces into the economic context and that it could typically lead to a chain of adverse reactions and market disruptions. Hence, the purpose of this study is to examine how COVID‐19 affects the environment, health, and the oil and energy markets. To achieve this objective, we used daily data for several measures that refer to the environment, health, and oil and energy, for the first wave of the COVID‐19 pandemic (December 31, 2019–May 22, 2020). The variable integration mix led to the approach of the ARDL model, and the Granger causality test was also employed. These empirical techniques allowed us to examine the cointegration between variables and causal relationships. The econometric results of the ARDL models exhibited that the global new cases and new deaths of COVID‐19 have short and long‐term effects on the environment, the health sector, the oil, and energy measures. However, no significant causal connection was found between the pandemic and the environment, the health sector, or the oil and energy industry, according to the Granger causality test. The uniqueness of current approach consists in the investigation of pandemic impact on the health, environment, oil, and energy sector by applying the ARDL model that permits the analysis of cointegration both in the long run and in the short term. This study provides important insights for investors and policy makers.

A Descriptive Comparison of Mass Testing During the COVID-19 Pandemic in Montreal, Paris, Bamako, and Recife

Objective: The aim of this descriptive article was to compare mass testing for SARS-CoV-2 during the first wave of the COVID-19 pandemic in Montreal, Canada; Bamako, Mali; Paris, France; and Recife, Brazil.

Methods: Data was collected through interviews with key informants involved in the testing response and a review of the grey literature. The TIDieR-PHP checklist was then used to provide the basis of the intervention descriptions and to compare the data between cities.

Results: Descriptive comparisons revealed that the type of test, the testing process, and materials used were similar between the cities during the first wave of the pandemic. In addition, all cities experienced similar material and personnel resource shortages, directly affecting testing accessibility and capacity. The main differences were related to testing capacity and implementation timelines, which were dependent on the state of the health care systems, governance, and access to resources.

Conclusion: Results of this study highlight the similarities and differences in testing between the cities and demonstrate the importance of comprehensive intervention descriptions to highlight lessons learned, increase knowledge sharing, and inform policy decisions.

Hundreds-Dollar-Level Multiplex Integrated RT-qPCR Quantitative System for Field Detection

The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.

Evaluation of the effectiveness of surveillance policies to control the COVID-19 pandemic in São Paulo, Brazil

BACKGROUND

Surveillance efforts are essential to pandemic control, especially where the state is the primary health provider, such as Brazil. When public health testing guidelines limit molecular tests, there are reductions in detection efforts aimed at early recognition, isolation, and treatment of those infected with the virus. This study evaluates the effectiveness of surveillance policies to control the COVID-19 pandemic in São Paulo.

METHODS

We conducted an interrupted time series analysis with a segmented regression model to analyze if changes in the state's guidelines improved RT-PCR testing outcomes in Brazil's most affluent and largest state, São Paulo. Anonymized daily data on the RT-PCR tests conducted in public laboratories belonging to the state-wide network from March 1, 2020 to June 5, 2021 were extracted from the Sao Paulo State open-source database, while the data on the genomic sequences were obtained from GISAID. We then aggregated these data for the 17 regional health departments in the state to evaluate regional-level outcomes.

RESULTS

The public health system restricted RT-PCR testing to hospitalized cases in the first months. Testing was expanded to permit symptomatic testing of non-hospitalized persons only in July 2020, but a statistically significant increase in surveillance efforts was not observed. Case definition was expanded to allow case confirmation based on clinical, laboratory and image data criteria other than an RT-PCR test without increasing the testing effort for asymptomatic suspicious cases in September 2020. There was an increase in the mean volume of testing in each RHD, but the test positivity rate increased due to insufficient testing expansion. Results also show an uneven improvement in testing outcomes following these changes across the state's regional health departments.

CONCLUSIONS

Evidence suggests that lower RT-PCR testing and genomic surveillance efforts are associated with areas characterized by a higher population concentration and a greater population reliance on the public health system. Our results highlight the need to structure health surveillance and information systems for disease control and prevention in emergency settings considering local demographics and vulnerabilities. In high prevalence settings, efforts at identifying and including vulnerable populations in routine and enhanced surveillance programs during COVID-19 must be significantly improved.

Point-of-care system for rapid real-time detection of SARS-CoV-2 virus based on commercially available Arduino platforms

The COVID-19 pandemic emphasized the importance of rapid, portable, and on-site testing technologies necessary for resource-limited settings for effective testing and screening to reduce spreading of the infection. Realizing this, we developed a fluorescence-based point-of-care (fPOC) detection system with real-time reverse transcriptase loop-mediated isothermal amplification for rapid and quantitative detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The system is built based on the Arduino platform compatible with commercially available open-source hardware–software and off-the-shelf electronic components. The fPOC system comprises of three main components: 1) an instrument with integrated heaters, 2) optical detection components, and 3) an injection-molded polymeric cartridge. The system was tested and experimentally proved to be able to use for fast detection of the SARS-CoV-2 virus in real-time in less than 30 min. Preliminary results of testing the performance of the fPOC revealed that the fPOC could detect the SARS-CoV-2 virus at a limit of detection (LOD_50%) at two to three copies/microliter (15.36 copies/reaction), which was comparable to reactions run on a standard commercial thermocycler. The performance of the fPOC was evaluated with 12 SARS-CoV-2 clinical throat swab samples that included seven positive and five negative samples, as confirmed by reverse transcription–polymerase chain reaction. The fPOC showed 100% agreement with the commercial thermocycler. This simple design of the fPOC system demonstrates the potential to greatly enhance the practical applicability to develop a totally integrated point-of-care system for rapid on-site screening of the SARS-CoV-2 virus in the management of the pandemic.

Association between the Human Development Index and Confirmed COVID-19 Cases by Country

It is important to understand the ultimate control of COVID-19 in all countries around the world in relation to the characteristics of developed countries, LDCs, and the variety of transmission characteristics of COVID-19. Therefore, this study aimed to identify factors associated with confirmed cases of COVID-19 with a focus on the Human Development Index (HDI). The units of analysis used for the current study were countries, and dataset were aggregated from multiple sources. This study used COVID-19 data from Our World in Data, the Global Health Security Index, and the WORLD BANK. A total of 171 countries were included in the analysis. A multi-variable linear regression with a hierarchical framework was employed to investigate whether the HDI is associated with confirmed COVID-19 cases after controlling for the demographic and healthcare system characteristics of the study countries. For Model 2, which controlled for demographic and healthcare system characteristics, HDI (β = 0.46, p < 0.001, 95% CI = 2.64−10.87) and the number of physicians per 1000 people (β = 0.34, p < 0.01, 95% CI = 0.21−0.75) had significant associations with the total number of confirmed COVID-19 cases per million people. Countries with a high HDI level are able to conduct higher per capita testing, resulting in higher numbers of confirmed cases than in countries with lower HDI levels. This study has shown evidence that could be used by governments and international organizations to identify national characteristics and provide the international cooperation necessary to develop effective prevention and intervention methods to deal with the global pandemic.

Lessons for improved COVID-19 surveillance from the scale-up of malaria testing strategies

Effective control of infectious diseases is facilitated by informed decisions that require accurate and timely diagnosis of disease. For malaria, improved access to malaria diagnostics has revolutionized malaria control and elimination programmes. However, for COVID-19, diagnosis currently remains largely centralized and puts many low- and middle-income countries (LMICs) at a disadvantage. Malaria and COVID-19 are infectious diseases that share overlapping symptoms. While the strategic responses to disease control for malaria and COVID-19 are dependent on the disease ecologies of each disease, the fundamental need for accurate and timely testing remains paramount to inform accurate responses. This review highlights how the roll-out of rapid diagnostic tests has been fundamental in the fight against malaria, primarily within the Asia Pacific and along the Greater Mekong Subregion. By learning from the successful elements of malaria control programmes, it is clear that improving access to point-of-care testing strategies for COVID-19 will provide a suitable framework for COVID-19 diagnosis in not only the Asia Pacific, but all malarious countries. In malaria-endemic countries, an integrated approach to point-of-care testing for COVID-19 and malaria would provide bi-directional benefits for COVID-19 and malaria control, particularly due to their paralleled likeness of symptoms, infection control strategies and at-risk individuals. This is especially important, as previous disease pandemics have disrupted malaria control infrastructure, resulting in malaria re-emergence and halting elimination progress. Understanding and combining strategies may help to both limit disruptions to malaria control and support COVID-19 control.

Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe

INTRODUCTION

Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated.

AREAS COVERED

A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type.

EXPERT OPINION

Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.

A Rotatable Paper Device Integrating Reverse Transcription Loop-Mediated Isothermal Amplification and a Food Dye for Colorimetric Detection of Infectious Pathogens

In this study, we developed a rotatable paper device integrating loop-mediated isothermal amplification (RT-LAMP) and a novel naked-eye readout of the RT-LAMP results using a food additive, carmoisine, for infectious pathogen detection. Hydroxyl radicals created from the reaction between CuSO₄ and H₂O₂ were used to decolor carmoisine, which is originally red. The decolorization of carmoisine can be interrupted in the presence of DNA amplicons produced by the RT-LAMP reaction due to how DNA competitively reacts with the hydroxyl radicals to maintain the red color of the solution. In the absence of the target DNA, carmoisine is decolored, owing to its reaction with hydroxyl radicals; thus, positive and negative samples can be easily differentiated based on the color change of the solution. A rotatable paper device was fabricated to integrate the RT-LAMP reaction with carmoisine-based colorimetric detection. The rotatable paper device was successfully used to detect SARS-CoV-2 and SARS-CoV within 70 min using the naked eye. Enterococcus faecium spiked in milk was detected using the rotatable paper device. The detection limits for the SARS-CoV-2 and SARS-CoV targets were both 10³ copies/µL. The rotatable paper device provides a portable and low-cost tool for detecting infectious pathogens in a resource-limited environment.

Nanomaterials for virus sensing and tracking

The effect of the on-going COVID-19 pandemic on global healthcare systems has underlined the importance of timely and cost-effective point-of-care diagnosis of viruses. The need for ultrasensitive easy-to-use platforms has culminated in an increased interest for rapid response equipment-free alternatives to conventional diagnostic methods such as polymerase chain reaction, western-blot assay, etc. Furthermore, the poor stability and the bleaching behavior of several contemporary fluorescent reporters is a major obstacle in understanding the mechanism of viral infection thus retarding drug screening and development. Owing to their extraordinary surface-to-volume ratio as well as their quantum confinement and charge transfer properties, nanomaterials are desirable additives to sensing and imaging systems to amplify their signal response as well as temporal resolution. Their large surface area promotes biomolecular integration as well as efficacious signal transduction. Due to their hole mobility, photostability, resistance to photobleaching, and intense brightness, nanomaterials have a considerable edge over organic dyes for single virus tracking. This paper reviews the state-of-the-art of combining carbon-allotrope, inorganic and organic-based nanomaterials with virus sensing and tracking methods, starting with the impact of human pathogenic viruses on the society. We address how different nanomaterials can be used in various virus sensing platforms (e.g. lab-on-a-chip, paper, and smartphone-based point-of-care systems) as well as in virus tracking applications. We discuss the enormous potential for the use of nanomaterials as simple, versatile, and affordable tools for detecting and tracing viruses infectious to humans, animals, plants as well as bacteria. We present latest examples in this direction by emphasizing major advantages and limitations.

Associations between COVID-19 testing status, non-communicable diseases and HIV status among residents of sub-Saharan Africa during the first wave of the pandemic

BACKGROUND

This study determined if non-communicable disease status, HIV status, COVID-19 status and co-habiting were associated with COVID-19 test status in sub-Saharan Africa.

METHODS

Data of 5945 respondents age 18-years-old and above from 31 countries in sub-Saharan Africa collected through an online survey conducted between June and December 2020, were extracted. The dependent variable was COVID-19 status (testing positive for COVID-19 and having symptoms of COVID-19 but not getting tested). The independent variables were non-communicable disease status (hypertension, diabetes, cancer, heart conditions, respiratory conditions, depression), HIV positive status, COVID-19 status (knowing a close friend who tested positive for COVID-19 and someone who died from COVID-19) and co-habiting (yes/no). Two binary logistic regression models developed to determine associations between the dependent and independent variables were adjusted for age, sex, employment, sub region and educational status.

RESULTS

Having a close friend who tested positive for COVID-19 (AOR:6.747), knowing someone who died from COVID-19 infection (AOR:1.732), and living with other people (AOR:1.512) were significantly associated with higher odds of testing positive for COVID-19 infection, while living with HIV was associated with significantly lower odds of testing positive for COVID-19 infection (AOR:0.284). Also, respondents with respiratory conditions (AOR:2.487), self-reported depression (AOR:1.901), those who had a close friend who tested positive for COVID-19 infection (AOR:2.562) and who knew someone who died from COVID-19 infection (AOR:1.811) had significantly higher odds of having symptoms of COVID-19 infection but not getting tested.

CONCLUSION

Non-communicable diseases seem not to increase the risk for COVID-19 positive test while cohabiting seems to reduce this risk. The likelihood that those who know someone who tested positive to or who died from COVID-19 not getting tested when symptomatic suggests there is poor contact tracing in the region. People with respiratory conditions and depression need support to get tested for COVID-19.

Respiratory viral co-infections in patients with COVID-19 and associated outcomes: A systematic review and meta-analysis

The aim of this systematic review and meta-analysis was to critically assess the published literature related to community-acquired viral co-infections and COVID-19 and to evaluate the prevalence, most identified co-pathogens, and relevant risk factors. Furthermore, we aimed to examine the clinical features and outcomes of co-infected compared to mono-infected COVID-19 patients. We systematically searched PubMed, Web of Science, Embase, Scopus, and The Cochrane Library for studies published from 1 November 2019 to 13 August 2021. We included patients of all ages and any COVID-19 severity who were screened for respiratory viral co-infection within 48 h of COVID-19 diagnosis. The main outcome was the proportion of patients with a respiratory viral co-infection. The systematic review was registered to PROSPERO (CRD42021272235). Out of 6053 initially retrieved studies, 59 studies with a total of 16,643 SARS-CoV-2 positive patients were included. The global pooled prevalence was 5.01% (95% CI 3.34%-7.27%; I²  = 95%) based on a random-effects model, with Influenza Viruses (1.54%) and Enteroviruses (1.32%) being the most prevalent pathogens. Subgroup analyses showed that co-infection was significantly higher in paediatric (9.39%) than adult (3.51%) patients (p-value = 0.02). Furthermore, co-infected patients were more likely to be dyspnoeic and the odds of fatality (OR = 1.66) were increased. Although a relatively low proportion of COVID-19 patients have a respiratory viral co-infection, our findings show that multiplex viral panel testing may be advisable in patients with compatible symptoms. Indeed, respiratory virus co-infections may be associated with adverse clinical outcomes and therefore have therapeutic and prognostic implications.

A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data

The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative framework based on excess mortality data to reconstruct SARS-CoV-2 transmission dynamics and assess the level of underreporting in infections and deaths. Using weekly all-cause mortality data from Iran, we are able to show a strong agreement between our attack rate estimates and seroprevalence measurements in each province and find significant heterogeneity in the level of exposure across the country with 11 provinces reaching near 100% attack rates. Despite having a young population, our analysis reveals that incorporating limited access to medical services in our model, coupled with undercounting of COVID-19-related deaths, leads to estimates of infection fatality rate in most provinces of Iran that are comparable to high-income countries.

Combining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country

Diagnostics for COVID-19 detection are limited in many settings. Syndromic surveillance is often the only means to identify cases but lacks specificity. Rapid antigen testing is inexpensive and easy-to-deploy but can lack sensitivity. We examine how combining these approaches can improve surveillance for guiding interventions in low-income communities in Dhaka, Bangladesh. Rapid-antigen-testing with PCR validation was performed on 1172 symptomatically-identified individuals in their homes. Statistical models were fitted to predict PCR-status using rapid-antigen-test results, syndromic data, and their combination. Under contrasting epidemiological scenarios, the models’ predictive and classification performance was evaluated. Models combining rapid-antigen-testing and syndromic data yielded equal-to-better performance to rapid-antigen-test-only models across all scenarios with their best performance in the epidemic growth scenario. These results show that drawing on complementary strengths across rapid diagnostics, improves COVID-19 detection, and reduces false-positive and -negative diagnoses to match local requirements; improvements achievable without additional expense, or changes for patients or practitioners.

Rapid antigen tests and syndromic surveillance for identification of COVID-19 cases are limited by low sensitivity and specificity, respectively. Here, the authors use data from Bangladesh and show that combining the two methods improves diagnostic accuracy in a range of epidemiological scenarios.

Dogs Detecting COVID-19 From Sweat and Saliva of Positive People: A Field Experience in Mexico

Context

Molecular tests are useful in detecting COVID-19, but they are expensive in developing countries. COVID-19-sniffing dogs are an alternative due to their reported sensitivity (&gt;80%) and specificity (&gt;90%). However, most of the published evidence is experimental, and there is a need to determine the performance of the dogs in field conditions. Hence, we aimed to test the sensitivity and specificity of COVID-19-sniffing dogs in the field.

Methods

We trained four dogs with sweat and three dogs with saliva of COVID-19-positive patients, respectively, for 4.5 months. The samples were obtained from a health center in Hermosillo, Sonora, with the restriction to spend 5 min per patient. We calculated sensitivity, specificity, and their 95% confidence intervals (CI).

Results

Two sweat-sniffing dogs reached 76 and 80% sensitivity, with the 95% CI not overlapping the random value of 50%, and 75 and 88% specificity, with the 95% CI not overlapping the 50% value. The 95% CI of the sensitivity and specificity of the other two sweat dogs overlapped the 50% value. Two saliva-sniffing dogs had 70 and 78% sensitivity, and the 95% CI of their sensitivity and specificity did not overlap the 50% value. The 95% CI of the third dog's sensitivity and specificity overlapped the 50% value.

Conclusion

Four of the six dogs were able to detect positive samples of patients with COVID-19, with sensitivity and specificity values significantly different from random in the field. We considered the performance of the dogs promising because it is reasonable to expect that with gauze exposed for a longer time to sweat and saliva of people with COVID-19, their detection capacity would improve. The target is to reach the sensitivity range requested by the World Health Organization for the performance of an antigen test (≥80% sensitivity, ≥97% specificity). If so, dogs could become important allies for the control of the COVID-19 pandemic, especially in developing countries.

Diagnostic Accuracy of Right Bronchial Infiltration on Chest X-rays in Diagnosing COVID-19 Patients in the Early Stage of the Disease

Purpose

SARS-CoV-2 has been a diagnostic challenge for healthcare setups worldwide since 2019 due to its proximity to a myriad of pathological processes. Although reverse transcription - polymerase chain reaction (RT-PCR) and high-resolution computed tomography (HRCT) have helped in the diagnosis of the disease, they are not as widely available as chest X-rays. This study aims to investigate the diagnostic accuracy of right bronchial infiltration in chest X-ray in diagnosing COVID-19.

Material and methods

This was a validation study conducted in a single center in Riyadh, Saudi Arabia. A total of 114 patients were enrolled according to the selection criteria of the study. Consent was waived off on the condition of confidentiality maintenance as per the ethical review board. X-rays of suspected patients were viewed and analyzed by two blinded consultant radiologists. Patients were followed for their RT-PCR reports. Data were entered and analyzed in SPSS Statistics v.23.0 (IBM Corp., Armonk, USA).

Results

Among the 114 patients, the mean age was 46.2±17.3 years and 85 (74.6%) were males. The total number of COVID-19-positive patients were 82 (71.9%) while the patients presenting with right bronchial infiltration (RBI) were 94 (82.5%). RBI was significantly associated with the presence and absence of COVID-19 on PCR (p<0.001) and the presence of comorbidities (p<0.001). The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the sign were 84.04%, 85.00%, 96.34%, 53.12%, and 84.21%, respectively.

Conclusions

RBI can be used as a diagnostic sign in X-rays for early identification of COVID-19 positive patients. This feature can be used in the triage of patients. This would decrease the spread of disease by providing early time to intervene to isolate patients.

Truncating fined-tuned vision-based models to lightweight deployable diagnostic tools for SARS-CoV-2 infected chest X-rays and CT-scans

In such a brief period, the recent coronavirus (COVID-19) already infected large populations worldwide. Diagnosing an infected individual requires a Real-Time Polymerase Chain Reaction (RT-PCR) test, which can become expensive and limited in most developing countries, making them rely on alternatives like Chest X-Rays (CXR) or Computerized Tomography (CT) scans. However, results from these imaging approaches radiated confusion for medical experts due to their similarities with other diseases like pneumonia. Other solutions based on Deep Convolutional Neural Network (DCNN) recently improved and automated the diagnosis of COVID-19 from CXRs and CT scans. However, upon examination, most proposed studies focused primarily on accuracy rather than deployment and reproduction, which may cause them to become difficult to reproduce and implement in locations with inadequate computing resources. Therefore, instead of focusing only on accuracy, this work investigated the effects of parameter reduction through a proposed truncation method and analyzed its effects. Various DCNNs had their architectures truncated, which retained only their initial core block, reducing their parameter sizes to <1 M. Once trained and validated, findings have shown that a DCNN with robust layer aggregations like the InceptionResNetV2 had less vulnerability to the adverse effects of the proposed truncation. The results also showed that from its full-length size of 55 M with 98.67% accuracy, the proposed truncation reduced its parameters to only 441 K and still attained an accuracy of 97.41%, outperforming other studies based on its size to performance ratio.

SPEEDS: A portable serological testing platform for rapid electrochemical detection of SARS-CoV-2 antibodies

The COVID-19 pandemic has resulted in a worldwide health crisis. Rapid diagnosis, new therapeutics and effective vaccines will all be required to stop the spread of COVID-19. Quantitative evaluation of serum antibody levels against the SARS-CoV-2 virus provides a means of monitoring a patient's immune response to a natural viral infection or vaccination, as well as evidence of a prior infection. In this paper, a portable and low-cost electrochemical immunosensor is developed for the rapid and accurate quantification of SARS-CoV-2 serum antibodies. The immunosensor is capable of quantifying the concentrations of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies against the SARS-CoV-2 spike protein in human serum. For IgG and IgM, it provides measurements in the range of 10.1 ng/mL − 60 μg/mL and 1.64 ng/mL − 50 μg/mL, respectively, both with an assay time of 13 min. We also developed device stabilization and storage strategies to achieve stable performance of the immunosensor over 24-week storage at room temperature. We evaluated the performance of the immunosensor using COVID-19 patient serum samples collected at different time points after symptom onset. The rapid and sensitive detection of IgG and IgM provided by our immunosensor fulfills the need of rapid COVID-19 serological testing for both point-of-care diagnosis and population immunity screening.

COVID-19 worries, concerns and mitigation behaviours: A snapshot of Nepal during the first wave

OBJECTIVES

To understand COVID-19 worries and how they influence COVID-19 mitigation behaviours, especially in communities prior to case surges, in Nepal.

METHODS

Data related to COVID-19 impacts on life disruptions were collected from households in the Chitwan Valley Family Study, a 25-year community panel study, during February-April 2021. COVID-19 worry was measured by the extent of respondent concern for themselves or household members getting COVID-19 in the prior 2 weeks. 11 items examined COVID-19 mitigation behaviours. Logistic regression models assessed associations between socio-demographic characteristics and COVID-19 worry and then the influence of worry on any mitigation behaviour and behaviour type adjusting for age, education, sex, ethnicity and COVID-19 exposure, accounting for neighbourhood clustering.

RESULTS

Of 2,678 households with a responding adult, ages 18-88, 394 (14.7%) reported moderate-to-extreme COVID-19 worry and 1,214 (45.3%) engaged in three or more mitigation behaviours. Prevalence of mitigation behaviours was higher among those with COVID-19 worry (e.g. avoided crowds: 62.7% versus 40.5% in those with minimal worry). Respondents self-reporting COVID-19 had higher odds of worry (adjusted odds ratio [aOR]: 2.73, 95% confidence interval [CI]: 1.13, 6.57). Odds of any mitigation behaviour were higher among those with COVID-19 worry compared to those with minimal worry (aOR: 6.19, 95% CI = 1.88, 20.35).

CONCLUSIONS

COVID-19 mitigation behaviours were more common in people with COVID-19 worry. To address current and potential future waves of the pandemic, public health efforts should include informational campaigns about mitigation behaviours particularly for those unconcerned with COVID-19 risks.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Acceptability and Willingness of UAE Residents to Use OTC Vending Machines to Deliver Self-Testing Kits for COVID-19 and the Implications

PURPOSE

Self-testing kits for SARS-CoV-2 appear effective, practical, safe and reliable as well as helping patients with mild-to-moderate symptoms to be successfully managed at home without going to hospital. As a result, ease pressures on hospitals. OTC vending machines offer the potential for SARS-CoV-2 self-testing kits alongside making available OTC treatments to alleviate the symptoms of COVID-19. As a result, providing confidentiality alongside ease of use in case people do not want their status broad casted. Consequently, there was a need to assess the acceptability and willingness regarding the availability of OTC vending machines to dispense self-testing kits for SARS-CoV-2 among UAE residents to provide future direction.

PATIENTS AND METHODS

A cross-sectional survey using a designed questionnaire was based on previous research and expert input and pilot tested. All items in the final questionnaire were seen as acceptable with a satisfactory content validity. A purposive sampling strategy was used in the principal study by primarily sending a link to the questionnaire to UAE universities via Facebook and WhatsApp.

RESULTS

A total of 876 respondents participated in the study and completed the whole questionnaire. Most participants were female (63%), Arabic origin (42%) and holding a bachelor's degree (84.5%). There was high acceptability and willingness to use self-testing kits (87.2%), with 88.6% of respondents believing OTC vending machines would be beneficial for patients with actual or suspected SARS-CoV-2. Gender, nationality, educational level, employment status, having relatives infected with SARS-CoV-2 and being vaccinated were significantly associated with attitudes towards the self-testing kits. Recognised barriers include their potential costs, ease of access and help for those who cannot read the instructions.

CONCLUSION

Overall, there was high acceptability and willingness to use OTC vending machines to deliver self-testing kits for SARS-CoV-2 among the surveyed participants. Key barriers will need to be addressed to enhance their use.

Development of a Biosensor Based on Angiotensin-Converting Enzyme II for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Human Saliva

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus responsible for COVID-19. Infection in humans requires angiotensin-converting enzyme II (hACE2) as the point of entry for SARS-CoV-2. PCR testing is generally definitive but expensive, although it is highly sensitive and accurate. Biosensor-based monitoring could be a low-cost, accurate, and non-invasive approach to improve testing capacity. We develop a capacitive hACE2 biosensor for intact SARS-CoV-2 detection in saliva. Laser-induced graphene (LIG) electrodes were modified with platinum nanoparticles. The quality control of LIG electrodes was performed using cyclic voltammetry. Truncated hACE2 was used as a biorecognition element and attached to the electrode surface by streptavidin-biotin coupling. Biolayer interferometry was used for qualitative interaction screening of hACE2 with UV-attenuated virions. Electrochemical impedance spectroscopy (EIS) was used for signal transduction. Truncated hACE2 binds wild-type SARS-CoV-2 and its variants with greater avidity than human coronavirus (common cold virus). The limit of detection (LoD) is estimated to be 2,960 copies/ml. The detection process usually takes less than 30 min. The strength of these features makes the hACE2 biosensor a potentially low-cost approach for screening SARS-CoV-2 in non-clinical settings with high demand for rapid testing (for example, schools and airports).

Intra- and Extra-Hospital Dissemination of IMP-22-Producing Klebsiella pneumoniae in Northern Portugal: The Breach of the Hospital Frontier Toward the Community

The emergence of infections (and colonization) with Enterobacteriaceae-producing carbapenemases is a threatening public health problem. In the last decades, we watched an isolated case becoming a brutal outbreak, a sporadic description becoming an endemic problem. The present study aims to highlight the dissemination of IMP-22-producing Klebsiella pneumoniae in the North of Portugal, through the phenotypic and genotypic characterization of isolates collected from hospitalized patients (n=5) and out-patients of the emergency ward of the same acute care hospital (n=2), and isolates responsible for the intestinal colonization of residents in a Long-Term Care Facility (n=4). Pulsed-field gel electrophoresis (PFGE) results, associated with conjugation experiments pointed to a pattern of both vertical and horizontal dissemination. Overall, and complementing other studies that give relevance to IMP-22-producing K. pneumoniae in the clinical settings, here we show for the first time the public health threatening breach of the hospital frontier of this resistance threat, toward the community.

Twelve lateral flow immunoassays (LFAs) to detect SARS-CoV-2 antibodies

BACKGROUND

There are an abundance of commercially available lateral flow assays (LFAs) that detect antibodies to SARS-CoV-2. Whilst these are usually evaluated by the manufacturer, externally performed diagnostic accuracy studies to assess performance are essential. Herein we present an evaluation of 12 LFAs.

METHODS

Sera from 100 SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) positive participants were recruited through the FASTER study. A total of 105 pre-pandemic sera from participants with other infections were included as negative samples.

RESULTS

At presentation sensitivity against RT-PCR ranged from 37.4 to 79% for IgM/IgG, 30.3-74% for IgG, and 21.2-67% for IgM. Sensitivity for IgM/IgG improved ≥ 21 days post symptom onset for 10/12 tests. Specificity ranged from 74.3 to 99.1% for IgM/IgG, 82.9-100% for IgG, and 75.2-98% for IgM. Compared to the EuroImmun IgG enzyme-linked immunosorbent assay (ELISA), sensitivity and specificity ranged from 44.6 to 95.4% and 85.4-100%, respectively.

CONCLUSION

There are many LFAs available with varied sensitivity and specificity. Understanding the diagnostic accuracy of these tests will be vital as we come to rely more on the antibody status of a person moving forward, and as such manufacturer-independent evaluations are crucial.

An Analysis of Health Science Students' Preparedness and Perception of Interactive Virtual Laboratory Simulation

The achievement of learning goals via laboratory practical depends on both extrinsic and intrinsic factors. They could be limited by laboratory time, incurred cost, safety, self-efficacy, inadequate prior preparation by learners, and different learning styles. Hence, virtual laboratory simulation (vLAB) may be an appropriate e-learning tool to overcome these restrictions. In this study, student's perception of the usefulness of vLAB was determined by using deoxyribonucleic acid (DNA) gel electrophoresis and polymerase chain reaction (PCR) as case examples. The perception of Year 2 and 3 health science undergraduate students' (N = 87) was studied using a questionnaire consisting of 12 items, rated on a 5-point Likert-scale. The attainment of learning outcomes was assessed using pre-and post-tests containing multiple-choice questions (MCQs). In addition, student's experience and learning from the vLAB were further explored using qualitative analysis. Although there was no significant difference between the mean scores of the pre-and post-tests, results showed that all participants perceived vLAB well, with a median score of 4 (Agree) for all items in the questionnaire. It provides a meaningful learning experience and an authentic environment where students feel safe to practice what they have learnt in lectures. Moreover, vLAB facilitates individualised learning and enhances self-efficacy among students. In conclusion, vLAB prepares students for physical laboratory sessions by activating the prehension dimension of Kolb's learning cycle, therefore complementing and strengthening the attainments of health sciences laboratory learning goals and outcomes.

Assessing Values and Preferences Toward SARS-CoV-2 Self-testing Among the General Population and Their Representatives, Health Care Personnel, and Decision-Makers: Protocol for a Multicountry Mixed Methods Study

Background

Accessible, safe, and client-centered SARS-CoV-2 testing services are an effective way to halt its transmission. Testing enables infected individuals to isolate or quarantine to prevent further transmission. In countries with limited health systems and laboratory capacity, it can be challenging to provide accessible and safe screening for COVID-19. Self-testing provides a convenient, private, and safe testing option; however, it also raises important concerns about lack of counseling and ensuring timely reporting of self-test results to national surveillance systems. Investigating community members’ views and perceptions regarding SARS-CoV-2 self-testing is crucial to inform the most effective and safe strategies for implementing said testing.

Objective

We aimed to determine whether SARS-CoV-2 self-testing was useful to diagnose and prevent the spread of SARS-CoV-2 for populations in low-resource settings and under which circumstances it would be acceptable.

Methods

This multisite, mixed methods, observational study will be conducted in 9 countries—Brazil, India, Indonesia, Kenya, Malawi, Nigeria, Peru, the Philippines, and South Africa—and will consists of 2 components: cross-sectional surveys and interviews (semistructured and group) among 4 respondent groupings: the general population, general population representatives, health care workers, and decision-makers. General population and health care worker survey responses will be analyzed separately from each other, using bivariate and multivariate inferential analysis and descriptive statistics. Semistructured interviews and group interviews will be audiorecorded, transcribed, and coded for thematic comparative analysis.

Results

As of November 19, 2021, participant enrollment is ongoing; 4364 participants have been enrolled in the general population survey, and 2233 participants have been enrolled in the health care workers survey. In the qualitative inquiry, 298 participants have been enrolled. We plan to complete data collection by December 31, 2021 and publish results in 2022 via publications, presentations at conferences, and dissemination events specifically targeted at local decision-makers, civil society, and patient groups.

Conclusions

The views and perceptions of local populations are crucial in the discussion of the safest strategies for implementing SARS-CoV-2 self-testing. We intend to identify sociocultural specificities that may hinder or accelerate the widespread utilization of SARS-CoV-2 self-testing.

International Registered Report Identifier (IRRID)

DERR1-10.2196/33088

Connecting Crises: Young People in Nepal Reflecting on Life Course Transitions and Trajectories during Times of Uncertainty

During certain crises, displacement of populations seeking safe refuge elsewhere can occur without the certainty of a return, if at all. Children and young people in such contexts often face the additional challenge of restrictions or disregard towards engaging their agency in migration decision-making processes. Through 60 in-depth interviews with 30 trans-Himalayan participants (ages of 16–23) and multi-sited ethnography throughout Nepal, this paper investigates multiple experiences of crises experienced by young people and the effects on their life course trajectories. From focusing on the Civil War in 1996–2006, the 2015 earthquake, and most recently the COVID-19 pandemic, this paper proposes that initial displacements from the Civil War, when connected with other crises later on in a participant’s life course, better prepared them to deal with crises and enabled them to create a landscape of resilience. Furthermore, a landscape of resilience that connects past and present life course experiences during crises prepared some participants for helping their larger communities alleviate certain crises-related tension. Overall, this paper extends analysis on an under-researched group of young migrants by connecting crises that shaped their (im)mobility and life trajectories, rather than approaching crises as singular, isolated experiences.

Computational Method-Based Optimization of Carbon Nanotube Thin-Film Immunosensor for Rapid Detection of SARS-CoV-2 Virus

The recent global spread of COVID‐19 stresses the importance of developing diagnostic testing that is rapid and does not require specialized laboratories. In this regard, nanomaterial thin‐film‐based immunosensors fabricated via solution processing are promising, potentially due to their mass manufacturability, on‐site detection, and high sensitivity that enable direct detection of virus without the need for molecular amplification. However, thus far, thin‐film‐based biosensors have been fabricated without properly analyzing how the thin‐film properties are correlated with the biosensor performance, limiting the understanding of property−performance relationships and the optimization process. Herein, the correlations between various thin‐film properties and the sensitivity of carbon nanotube thin‐film‐based immunosensors are systematically analyzed, through which optimal sensitivity is attained. Sensitivities toward SARS‐CoV‐2 nucleocapsid protein in buffer solution and in the lysed virus are 0.024 [fg/mL]⁻¹ and 0.048 [copies/mL]⁻¹, respectively, which are sufficient for diagnosing patients in the early stages of COVID‐19. The technique, therefore, can potentially elucidate complex relationships between properties and performance of biosensors, thereby enabling systematic optimization to further advance the applicability of biosensors for accurate and rapid point‐of‐care (POC) diagnosis.

Considerations for resuming global surgery outreach programs during and after the coronavirus disease 2019 (COVID-19) pandemic

BACKGROUND

The coronavirus disease 2019 pandemic has disrupted the delivery of safe surgical care worldwide. One specific aspect of global surgical care that has been severely limited is the ability for physicians and trainees to participate in global surgical outreach programs in low- and middle-income countries.

METHODS

A narrative review of the literature regarding global surgical outreach programs during the coronavirus disease 2019 pandemic was performed. Factors that must be considered in the reinstatement of global surgical outreach programs were identified, and suggestions to address them were provided based on the available literature and the experiences of the senior authors.

RESULTS

As global surgical outreach programs were canceled at the start of the pandemic, many academic surgeons turned to digital solutions to continue to engage with low- and middle-income country partners. With the advent of coronavirus disease 2019 vaccines and improved access to testing and treatment worldwide, the recommencement of global surgical outreach programs may begin to be considered. Important considerations before initiation include vaccine and testing availability for visiting providers, local staff, and patients, local hospital capacity, staff and equipment shortages, and the characteristics of the patient population and visiting providers. Region- and country-specific factors, including local infection rates and concomitant health crises, must also be taken into account. Expansion of digital collaborative efforts may further deepen international connections and promote sustainable models of care.

CONCLUSION

With careful consideration, global surgical outreach programs may begin to be safely restarted in the near future. The current article evaluates individual factors that must be considered to safely restart global surgical outreach programs as the coronavirus disease 2019 pandemic is better controlled.

Antigen-based Rapid Diagnostic Testing or Alternatives for Diagnosis of Symptomatic COVID-19: A Simulation-based Net Benefit Analysis

BACKGROUND

SARS-CoV-2 antigen-detection rapid diagnostic tests can diagnose COVID-19 rapidly and at low cost, but lower sensitivity compared with reverse-transcriptase polymerase chain reaction (PCR) has limited clinical adoption.

METHODS

We compared antigen testing, PCR testing, and clinical judgment alone for diagnosing symptomatic COVID-19 in an outpatient setting (10% COVID-19 prevalence among the patients tested, 3-day PCR turnaround) and a hospital setting (40% prevalence, 24-hour PCR turnaround). We simulated transmission from cases and contacts, and relationships between time, viral burden, transmission, and case detection. We compared diagnostic approaches using a measure of net benefit that incorporated both clinical and public health benefits and harms of the intervention.

RESULTS

In the outpatient setting, we estimated that using antigen testing instead of PCR to test 200 individuals could be equivalent to preventing all symptomatic transmission from one person with COVID-19 (one "transmission-equivalent"). In a hospital, net benefit analysis favored PCR and testing 25 patients with PCR instead of antigen testing achieved one transmission-equivalent of benefit. In both settings, antigen testing was preferable to PCR if PCR turnaround time exceeded 2 days. Both tests provided greater net benefit than management based on clinical judgment alone unless intervention carried minimal harm and was provided equally regardless of diagnostic approach.

CONCLUSIONS

For diagnosis of symptomatic COVID-19, we estimated that the speed of diagnosis with antigen testing is likely to outweigh its lower accuracy compared with PCR, wherever PCR turnaround time is 2 days or longer. This advantage may be even greater if antigen tests are also less expensive.

Early Detection of COVID-19 Waves From Cases in a Neighboring Country With an Open Border

Border closure or travel restriction is a critical issue as closing the border early can badly affect the economy of the country, whereas substantial delay can put human lives at stake. While many papers discuss closing the border early in the pandemic, the question of when to close the border has not been addressed well. We have tried to estimate a date of closing the border by taking the reference of a neighboring country with a high correlation in Covid-19 incidence. Here we have used non-linear methods to probe the landscape of correlation between temporal COVID-19 incidences and deaths. We have tested our method on two neighboring countries, Nepal and India, with open borders, where closing the borders are among the top priorities to reduce the spread and spill-out of variants. We have selected these countries as they have close connectivity and intertwined socio-economic network with thousands of people crossing the border every day. We found the distance correlation for COVID-19 incidence between these countries to be statistically significant (p < 0.001) and there is a lag of 6 days for maximum correlation. In addition, we analyzed the correlation for each wave and found the distance correlation for the first phase is 0.8145 (p < 0.001) with a lag of 2 days, and the distance correlation for the second wave is 0.9685 (p < 0.001) without any lag. This study can be a critical planning tool for policymakers and public health practitioners to make an informed decision on border closure in the early days as it is critically associated with the legal and diplomatic agreements and regulations between two countries.

Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Portable and Label-Free Quantitative Loop-Mediated Isothermal Amplification (LF-qLamp) for Reliable COVID-19 Diagnostics in Three Minutes of Reaction Time: Arduino-Based Detection System Assisted by a pH Microelectrode

Loop-mediated isothermal amplification (LAMP) has been recently studied as an alternative method for cost-effective diagnostics in the context of the current COVID-19 pandemic. Recent reports document that LAMP-based diagnostic methods have a comparable sensitivity and specificity to that of RT-qPCR. We report the use of a portable Arduino-based LAMP-based amplification system assisted by pH microelectrodes for the accurate and reliable diagnosis of SARS-CoV-2 during the first 3 min of the amplification reaction. We show that this simple system enables a straightforward discrimination between samples containing or not containing artificial SARS-CoV-2 genetic material in the range of 10 to 10,000 copies per 50 µL of reaction mix. We also spiked saliva samples with SARS-CoV-2 synthetic material and corroborated that the LAMP reaction can be successfully monitored in real time using microelectrodes in saliva samples as well. These results may have profound implications for the design of real-time and portable quantitative systems for the reliable detection of viral pathogens including SARS-CoV-2.

SARS-CoV-2 and approaches for a testing and diagnostic strategy

The COVID-19 pandemic has led to an unprecedented global health challenge, creating sudden, massive demands for diagnostic testing, treatment, therapies, and vaccines. In particular, the development of diagnostic assays for SARS-CoV-2 has been pursued as they are needed for quarantine, disease surveillance, and patient treatment. One of the major lessons the pandemic highlighted was the need for fast, cheap, scalable and reliable diagnostic methods, such as paper-based assays. Furthermore, it has previously been suggested that paper-based tests may be more suitable for settings with lower resource availability and may help alleviate some supply chain challenges which arose during the COVID-19 pandemic. Therefore, we explore how such devices may fit in a comprehensive diagnostic strategy and how some of the challenges to the technology, e.g. low sensitivity, may be addressed. We discuss the properties of the SARS-CoV-2 virus itself, the COVID-19 disease pathway, and the immune response. We then describe the different diagnostic strategies that have been pursued, focusing on molecular strategies for viral genetic material, antigen tests, and serological assays, and innovations for improving the diagnostic sensitivity and capabilities. Finally, we discuss pressing issues for the future, and what needs to be addressed for the ongoing pandemic and future outbreaks.