Examining operational efficiency with prudent risks of Covid-19: a contextual DEA analysis with an undesirable intermediate measure.

In the wake of the losses of human lives and disruption to the world economy caused by the spread of the COVID-19 pandemic, it has become imperative to assess the effectiveness of containment strategies adopted by countries. The success of any containment strategy of achieving low mortality and high recovery rate depends on the efficient utilization of available but limited resources, such as number of hospital beds and healthcare workers. While the spreading pattern of the pandemic has been researched heavily, there is limited research that comprehensively focuses on the efficient utilization of available resources to achieve the desired aims of low mortality and high recovery. In order to close this research gap, we employ a two-stage network data envelopment analysis (DEA) to identify the inefficiency in the process and resolve the resource constraints by considering medical and non-medical (administrative) interventions as two serial stages. The number of infected people is treated as the intermediate product, which is an undesirable output of the first stage and subsequently enters the second stage as an input. This network DEA model successfully addresses the conflict between the two stages over the handling of infected people and assesses the vulnerabilities of the countries against the transmission rates of the disease in the respective countries. Thus, the objective of this study is to develop a well-coordinated plan for different government agencies to jointly mitigate the risk under constrained resources. The findings reveal that almost 60 % of the Organization for Economic Cooperation and Development (OECD) countries have used their resources suboptimally and are producing, on average, almost half the amount of the maximum possible outputs. As a sizeable amount of inefficiency can be explained by varying economic and demographic factors, such as health expenditure and the proportion of the aged population, the efficiency evaluation has been revisited with adjustments for unfavorable externalities. The analysis and its implications can help policymakers formulate optimal resource plans and identify potential areas for improvement.

Examining operational efficiency with prudent risks of Covid-19: a contextual DEA analysis with an undesirable intermediate measure

In the wake of the losses of human lives and disruption to the world economy caused by the spread of the COVID-19 pandemic, it has become imperative to assess the effectiveness of containment strategies adopted by countries. The success of any containment strategy of achieving low mortality and high recovery rate depends on the efficient utilization of available but limited resources, such as number of hospital beds and healthcare workers. While the spreading pattern of the pandemic has been researched heavily, there is limited research that comprehensively focuses on the efficient utilization of available resources to achieve the desired aims of low mortality and high recovery. In order to close this research gap, we employ a two-stage network data envelopment analysis (DEA) to identify the inefficiency in the process and resolve the resource constraints by considering medical and non-medical (administrative) interventions as two serial stages. The number of infected people is treated as the intermediate product, which is an undesirable output of the first stage and subsequently enters the second stage as an input. This network DEA model successfully addresses the conflict between the two stages over the handling of infected people and assesses the vulnerabilities of the countries against the transmission rates of the disease in the respective countries. Thus, the objective of this study is to develop a well-coordinated plan for different government agencies to jointly mitigate the risk under constrained resources. The findings reveal that almost

Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series.

BACKGROUND: There is increasing concern that persistent infection of SARS-CoV-2 within immunocompromised hosts could serve as a reservoir for mutation accumulation and subsequent emergence of novel strains with the potential to evade immune responses. METHODS: We describe three patients with acute lymphoblastic leukemia who were persistently positive for SARS-CoV-2 by real-time polymerase chain reaction. Viral viability from longitudinally-collected specimens was assessed. Whole-genome sequencing and serological studies were performed to measure viral evolution and evidence of immune escape. FINDINGS: We found compelling evidence of ongoing replication and infectivity for up to 162 days from initial positive by subgenomic RNA, single-stranded RNA, and viral culture analysis. Our results reveal a broad spectrum of infectivity, host immune responses, and accumulation of mutations, some with the potential for immune escape. INTERPRETATION: Our results highlight the potential need to reassess infection control precautions in the management and care of immunocompromised patients. Routine surveillance of mutations and evaluation of their potential impact on viral transmission and immune escape should be considered.

High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19.

BACKGROUND: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children. METHODS: Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity. RESULTS: Higher viral load was detected in symptomatic patients (P = .0007) and in children <5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California. CONCLUSIONS: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test.

Nucleic acid amplification tests (NAATs) are the primary means of identifying acute infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accurate and fast test results may permit more efficient use of protective and isolation resources and allow rapid therapeutic interventions. We evaluated the analytical and clinical performance characteristics of the Xpert Xpress SARS-CoV-2 (Xpert) test, a rapid, automated molecular test for SARS-CoV-2. Analytical sensitivity and specificity/interference were assessed with infectious SARS-CoV-2; other infectious coronavirus species, including SARS-CoV; and 85 nasopharyngeal swab specimens positive for other respiratory viruses, including endemic human coronaviruses (hCoVs). Clinical performance was assessed using 483 remnant upper- and lower-respiratory-tract specimens previously analyzed by standard-of-care (SOC) NAATs. The limit of detection of the Xpert test was 0.01 PFU/ml. Other hCoVs, including Middle East respiratory syndrome coronavirus, were not detected by the Xpert test. SARS-CoV, a closely related species in the subgenus Sarbecovirus, was detected by a broad-range target (E) but was distinguished from SARS-CoV-2 (SARS-CoV-2-specific N2 target). Compared to SOC NAATs, the positive agreement of the Xpert test was 219/220 (99.5%), and the negative agreement was 250/261 (95.8%). A third tie-breaker NAAT resolved all but three of the discordant results in favor the Xpert test. The Xpert test provided sensitive and accurate detection of SARS-CoV-2 in a variety of upper- and lower-respiratory-tract specimens. The high sensitivity and short time to results of approximately 45 min may impact patient management.