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1.
Nat Genet ; 2023.
Article in English | PubMed | ID: covidwho-2185946

ABSTRACT

The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.

2.
PLoS Global Public Health ; 2(5), 2022.
Article in English | CAB Abstracts | ID: covidwho-1902604

ABSTRACT

Countries around the world have implemented restrictions on mobility, especially cross-border travel to reduce or prevent SARS-CoV-2 community transmission. Rapid antigen testing (Ag-RDT), with on-site administration and rapid turnaround time may provide a valuable screening measure to ease cross-border travel while minimizing risk of local transmission. To maximize impact, we developed an optimal Ag-RDT screening algorithm for cross-border entry. Using a previously developed mathematical model, we determined the daily number of imported COVID-19 cases that would generate no more than a relative 1% increase in cases over one month for different effective reproductive numbers (Rt) and COVID-19 prevalence within the recipient country. We then developed an algorithm - for differing levels of Rt, arrivals per day, mode of travel, and SARS-CoV-2 prevalence amongst travelers - to determine the minimum proportion of people that would need Ag-RDT testing at border crossings to ensure no greater than the relative 1% community spread increase. When daily international arrivals and/or COVID-19 prevalence amongst arrivals increases, the proportion of arrivals required to test using Ag-RDT increases. At very high numbers of international arrivals/COVID-19 prevalence, Ag-RDT testing is not sufficient to prevent increased community spread, especially when recipient country prevalence and Rt are low. In these cases, Ag-RDT screening would need to be supplemented with other measures to prevent an increase in community transmission. An efficient Ag-RDT algorithm for SARS-CoV-2 testing depends strongly on the epidemic status within the recipient country, volume of travel, proportion of land and air arrivals, test sensitivity, and COVID-19 prevalence among travelers.

3.
PLoS Global Public Health ; 2(4), 2022.
Article in English | CAB Abstracts | ID: covidwho-1854950

ABSTRACT

With the Covid-19 pandemic and the introduction of the WHO's Essential Diagnostics List (EDL), increasing global attention is focused on the crucial role of diagnostics in achieving universal health coverage. To create national EDLs and to aid health system planning, it is vital to understand the most common conditions with which people present at primary care health facilities. We undertook a systematic review of the most common reasons for primary care visits in low- and middle-income countries. Six databases were searched for articles published between January 2009 and December 2019, with the search updated on MEDLINE to January 2021. Data on the most common patient reasons for encounter (RFEs) and provider diagnoses were collected. 17 of 22,279 screened articles were included. Most studies used unvalidated diagnostic classification systems or presented provider diagnosis data grouped by organ system, rather than presenting specific diagnoses. No studies included data from low-income countries. Only four studies (from Brazil, India, Nigeria and South Africa) using the ICPC-2 classification system contained RFE and provider diagnosis data and could be pooled. The top five RFEs from the four studies were headache, fever, back or low back symptom, cough and pain general/multiple sites. The top five diagnoses were uncomplicated hypertension, upper respiratory tract infection, type 2 diabetes, malaria and health maintenance/prevention. No psychological symptoms were among the top 10 pooled RFEs. There was more variation in top diagnoses between studies than top RFEs, showing the importance of creating location-specific lists of essential diagnostics for primary care. Future studies should aim to sample primary care facilities from across their country of study and use ICPC-3 to report both patient RFEs and provider diagnoses.

4.
Topics in Antiviral Medicine ; 29(1):269, 2021.
Article in English | EMBASE | ID: covidwho-1250207

ABSTRACT

Background: The World Health Organization (WHO) has called for increased testing to help arrest the transmission of coronavirus disease 19 (COVID-19). Molecular testing (PCR) is the recommended method for the diagnosis of COVID-19. In low-resource settings (LRS) however, the availability and public health impact of these tests is constrained by availability of testing capacity, shortages of reagents/supplies, lack of skilled personnel, long turnaround times (TAT), and costs. Despite lower sensitivity, antigen detection rapid diagnostic tests (AgRDTs) could provide improved access at lower costs and quicker TAT. We evaluated the optimal use of AgRDTs to increase testing access within TAT and reduce the cost and the number of cases missed in LRS. Methods: We modeled estimated COVID-19 testing demand coverage based on current PCR capacity in three different epidemic phases across five African countries (Strategy 1). We then modelled five additional testing strategies that utilized a combination of PCR and AgRDT: 2)replacing current PCR coverage with AgRDT;3)saturating testing demand with AgRDT only;4)saturating testing demand first with PCR then the remainder with AgRDT;5)saturating testing demand with AgRDT and reflex testing with PCR for patients at risk of severe disease;6)constrained by budget of Scenario 1, using a mix of PCR and AgRDT. We estimated the total number of correct test results expected within a 48hr TAT, corresponding costs (assuming $12/PCR and $6/AgRDT), and the incremental cost-effectiveness ratios for each strategy and epidemic phase by country. Results: Across all countries and phase of epidemic, there was insufficient PCR capacity to meet the calculated required testing demand within a 48hr TAT (ranging from 0-20%) (Figure). In no instance was the base case strategy that was limited to current PCR capacity considered cost-effective (CE). Strategy 3, in which testing demand was saturated with AgRDT, was considered robustly CE in every epidemic phase ($4-$7 per additional person with a correct test result within 48hr TAT), and would require both a large increase in budget and wide AgRDT availability. Additional strategies on the CE frontier were country and epidemic-phase specific. Conclusion: Inclusion of AgRDT in testing strategies is CE and critical in increasing timely testing access in countries with low PCR capacity. Given the importance of timely results for epidemic control, future work should quantify the epidemic impact of saturating testing demand in LRS.

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