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False Negative Mitigation in Group Testing for COVID-19 Screening.

ABSTRACT: After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

SUBMITTER: Alizad-Rahvar AR

PROVIDER: S-EPMC8170512 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Objectives: With the worldwide spread of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), various antibody detection kits have been developed to test for SARS-CoV-2- specific IgG, IgM, and total antibody. However, the use of different testing methods under various heat-inactivation conditions might affect the COVID-19 detection results. Methods: Seven different antibody detection kits produced by four manufacturers for detection of SARS-CoV-2 IgG, IgM, and total antibody were tested at Wuhan Huoshenshan Hospital, China. Most of the kits used the indirect immunity, capture, and double-antigen sandwich methods. The effects of various heat-inactivation conditions on SARS-CoV-2-specific IgG, IgM, and total antibody detection were analyzed for the different test methods. Results: Using the indirect immunity method, values for SARS-CoV-2 IgG antibody significantly increased and those for IgM antibody decreased with increasing temperature of heat-inactivation using indirect immunity method. However, values for SARS-CoV-2 IgM and total antibody showed no change when the capture and double-antigen sandwich methods were used. The changes in IgG and IgM antibody values with the indirect immunity method indicated that heat-inactivation could affect COVID-19 detection results obtained using this method. In particular, 18 (22.2%) SARS-CoV-2 IgM positive samples were detected as negative with heat-inactivation at 65°C for 30 min, and one (25%) IgG negative sample was detected as positive after heat-inactivation at 56°C for 60 min and 60°C for 30 min. Conclusions: Heat-inactivation could increase SARS-CoV-2 IgG antibody values, and decrease IgM antibody values, causing potential false-positive or false-negative results for COVID-19 antibody detection using the indirect immunity method. Thus, before conducting antibody testing, the testing platforms should be evaluated in accordance with the relevant requirements to ensure accurate COVID-19 detection results.

Project description:A variety of mitigation strategies have been employed against the Covid-19 pandemic. Social distancing is still one of the main methods to reduce spread, but it entails a high toll on personal freedom and economic life. Alternative mitigation strategies that do not come with the same problems but are effective at preventing disease spread are therefore needed. Repetitive mass-testing using PCR assays for viral RNA has been suggested, but as a stand-alone strategy this would be prohibitively resource intensive. Here, we suggest a strategy that aims at targeting the limited resources available for viral RNA testing to subgroups that are more likely than the average population to yield a positive test result. Importantly, these pre-selected subgroups include symptom-free people. By testing everyone in these subgroups, in addition to symptomatic cases, large fractions of pre- and asymptomatic people can be identified, which is only possible by testing-based mitigation. We call this strategy smart testing (ST). In principle, pre-selected subgroups can be found in different ways, but for the purpose of this study we analyze a pre-selection procedure based on cheap and fast virus antigen tests. We quantify the potential reduction of the epidemic reproduction number by such a two-stage ST strategy. In addition to a scenario where such a strategy is available to the whole population, we analyze local applications, e.g. in a country, company, or school, where the tested subgroups are also in exchange with the untested population. Our results suggest that a two-stage ST strategy can be effective to curb pandemic spread, at costs that are clearly outweighed by the economic benefit. It is technically and logistically feasible to employ such a strategy, and our model predicts that it is even effective when applied only within local groups. We therefore recommend adding two-stage ST to the portfolio of available mitigation strategies, which allow easing social distancing measures without compromising public health.

Project description:ImportanceBlack and Latinx communities have been disproportionately affected by the COVID-19 pandemic, yet little work has sought to understand their perspectives.ObjectiveTo explore the experiences of Black and Latinx communities during the pandemic to better understand their perspectives on COVID-19 mitigation behaviors (eg, mask wearing), testing, and vaccines.Design, setting, and participantsIn this community-engaged qualitative study conducted with 18 community-based organizations and 4 health care organizations between November 19, 2020, and February 5, 2021, in New Jersey counties severely affected by the pandemic, group and individual interviews were used to purposively sample 111 Black and Latinx individuals. A total of 13 group interviews were organized by race/ethnicity and language: 4 English-speaking groups with Black participants (n = 34), 3 Spanish-speaking groups with Latinx participants (n = 24), and 4 English-speaking groups with Black and Latinx participants (n = 36). To understand the views of health care workers from these communities, 2 additional groups (n = 9) were convened and supplemented with individual interviews.Main outcomes and measuresDescription of Black and Latinx participants' experiences during the COVID-19 pandemic and their perspectives on mitigation behaviors, testing, and vaccines.ResultsThe study included 111 participants (87 women [78.4%]; median age, 43 years [range, 18-93 years]). Participants described the devastating effects of the pandemic on themselves, loved ones, and their community. Their experiences were marked by fear, illness, loss, and separation. These experiences motivated intense information seeking, mitigation behaviors, and testing. Nevertheless, vaccine skepticism was high across all groups. Participants did not trust the vaccine development process and wanted clearer information. Black participants expressed that they did not want to be subjects of experiments.Conclusions and relevanceThe remaining unknowns about new vaccines need to be acknowledged and described for Black and Latinx communities to make informed decisions. Ultimately, scientists and public officials need to work transparently to address unanswered questions and work collaboratively with trusted community leaders and health professionals to foster partnered approaches, rather than focusing on marketing campaigns, to eliminate vaccine skepticism.

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False Negative Mitigation in Group Testing for COVID-19 Screening.

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