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1.
Nat Med ; 2022 Feb 24.
Article in English | MEDLINE | ID: covidwho-1713204

ABSTRACT

Given global Coronavirus Disease 2019 (COVID-19) vaccine shortages and inequity of vaccine distributions, fractionation of vaccine doses might be an effective strategy for reducing public health and economic burden, notwithstanding the emergence of new variants of concern. In this study, we developed a multi-scale model incorporating population-level transmission and individual-level vaccination to estimate the costs of hospitalization and vaccination and the economic benefits of reducing COVID-19 deaths due to dose-fractionation strategies in India. We used large-scale survey data of the willingness to pay together with data of vaccine and hospital admission costs to build the model. We found that fractional doses of vaccines could be an economically viable vaccination strategy compared to alternatives of either full-dose vaccination or no vaccination. Dose-sparing strategies could save a large number of lives, even with the emergence of new variants with higher transmissibility.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-309733

ABSTRACT

Background: To mitigate the coronavirus pandemic that emerged in 2019 (COVID-19), countries worldwide have enacted unprecedented movement restrictions, social distancing measures, and face mask requirements. Until safe and efficacious vaccines or antiviral drugs become widely available, viral testing remains the primary mitigation measure for rapid identification and isolation of infected cases. Methods: We evaluate the economic tradeoffs of expanding and accelerating SARS-CoV-2 testing using a multi-scale model that incorporates SARS-CoV-2 transmission at the population level and daily viral load dynamics at the individual level. Findings: Assuming a willingness-to-pay of $100,000 per year of life lost (YLL) and a price of $5 per test, the strategy most likely to be cost-effective under a rapid transmission scenario (Re > 2) is daily testing followed by a one-week rather than two-week isolation period subsequent to test confirmation. Under lower transmission scenarios, weekly testing of the population is expected to be more cost effective. Expanded surveillance testing is expected to be cost effective if the price per test is less than $400 across all transmission rates considered. Interpretation: Extensive expansion of testing coupled with isolation of confirmed cases is essential for mitigating the COVID-19 pandemic. Further, resources recouped from shortened isolation duration could be cost-effectively allocated to more frequent testing.Funding Statement: US National Institutes of Health and US Centers for Disease Control and Prevention.Declaration of Interests: The authors declare no competing interests.Ethics Approval Statement: Not applicable.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-309732

ABSTRACT

Given constrained vaccine supplies globally, fractionation of vaccine doses may be an effective strategy for reducing disease and healthcare burdens, even with the emergence of COVID-19 variants. Using a multi-scale model that incorporates population-level transmission and individual-level vaccination, we estimate the costs associated with hospitalization, vaccine costs, and the economic benefit of reducing COVID-19 deaths associated with dose-fractionation strategies. Assuming a willingness-to-pay of US$10,517 per averted year of life lost (YLL) and a price of $12 per vaccine, under various transmission scenarios, with effective reproduction numbers ranging from 1.1 to 5.0 and with vaccine efficacy against transmission from 52% to 91%, the optimal vaccination strategy would always involve fractional doses of vaccines. Vaccine dose fractionation is a cost-effective strategy for mitigating the COVID-19 pandemic and could save a large number of lives, even after the emergence of variants with higher transmissibility.

4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-321678

ABSTRACT

The COVID-19 pandemic has resulted in more than 125 million infections and more than 2.7 million casualties. In this paper, we attempt to classify covid vs non-covid cough sounds using signal processing and deep learning methods. Air turbulence, the vibration of tissues, movement of fluid through airways, opening, and closure of glottis are some of the causes for the production of the acoustic sound signals during cough. Does the COVID-19 alter the acoustic characteristics of breath, cough, and speech sounds produced through the respiratory system? This is an open question waiting for answers. In this paper, we incorporated novel data augmentation methods for cough sound augmentation and multiple deep neural network architectures and methods along with handcrafted features. Our proposed system gives 14% absolute improvement in area under the curve (AUC). The proposed system is developed as part of Interspeech 2021 special sessions and challenges viz. diagnosing of COVID-19 using acoustics (DiCOVA). Our proposed method secured the 5th position on the leaderboard among 29 participants.

5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318637

ABSTRACT

The novel coronavirus disease (COVID-19) pandemic has resulted in over 200,000 cases in India. Thus far, India has implemented lockdown measures to curb disease transmission. However, commercial sex work in red-light areas (RLAs) has potential to lead to COVID-19 resurgence after lockdown. We developed a model of COVID-19 transmission in RLAs, evaluating the impact of extended RLA closure compared with RLA reopening on cases, hospitalizations, and mortality rates within the RLAs of five major Indian cities, within the cities, and across India. Closure lowered transmission at all scales. More than 90% of cumulative cases and deaths among RLA residents of Kolkata, Pune, and Nagpur could be averted by the time the epidemic would peak under a re-opening scenario. Across India, extended closure of RLAs would benefit the population at large, delaying the peak of COVID-19 cases by 8 to 23 days, and avert 32% to 60.2% of cumulative cases and 43% to 67.6% of cumulative deaths at the peak of the epidemic. Extended closure of RLAs until better prevention and treatment strategies are developed would benefit public health in India.

6.
Lancet Reg Health Am ; 8: 100182, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1620909

ABSTRACT

Background: As SARS-CoV-2 vaccines are administered worldwide, the COVID-19 pandemic continues to exact significant human and economic costs. Mass testing of unvaccinated individuals followed by isolation of positive cases can substantially mitigate risks and be tailored to local epidemiological conditions to ensure cost effectiveness. Methods: Using a multi-scale model that incorporates population-level SARS-CoV-2 transmission and individual-level viral load kinetics, we identify the optimal frequency of proactive SARS-CoV-2 testing, depending on the local transmission rate and proportion immunized. Findings: Assuming a willingness-to-pay of US$100,000 per averted year of life lost (YLL) and a price of $10 per test, the optimal strategy under a rapid transmission scenario (Re ∼ 2.5) is daily testing until one third of the population is immunized and then weekly testing until half the population is immunized, combined with a 10-day isolation period of positive cases and their households. Under a low transmission scenario (Re ∼ 1.2), the optimal sequence is weekly testing until the population reaches 10% partial immunity, followed by monthly testing until 20% partial immunity, and no testing thereafter. Interpretation: Mass proactive testing and case isolation is a cost effective strategy for mitigating the COVID-19 pandemic in the initial stages of the global SARS-CoV-2 vaccination campaign and in response to resurgences of vaccine-evasive variants. Funding: US National Institutes of Health, US Centers for Disease Control and Prevention, HK Innovation and Technology Commission, China National Natural Science Foundation, European Research Council, and EPSRC Impact Acceleration Grant.

7.
The Lancet regional health. Europe ; 2022.
Article in English | EuropePMC | ID: covidwho-1615425

ABSTRACT

Background Numerous countries have imposed strict travel restrictions during the COVID-19 pandemic, contributing to a large socioeconomic burden. The long quarantines that have been applied to contacts of cases may be excessive for travel policy. Methods We developed an approach to evaluate imminent countrywide COVID-19 infections after 0–14-day quarantine and testing. We identified the minimum travel quarantine duration such that the infection rate within the destination country did not increase compared to a travel ban, defining this minimum quarantine as “sufficient.” Findings We present a generalised analytical framework and a specific case study of the epidemic situation on November 21, 2021, for application to 26 European countries. For most origin-destination country pairs, a three-day or shorter quarantine with RT-PCR or antigen testing on exit suffices. Adaptation to the European Union traffic-light risk stratification provided a simplified policy tool. Our analytical approach provides guidance for travel policy during all phases of pandemic diseases. Interpretation For nearly half of origin-destination country pairs analysed, travel can be permitted in the absence of quarantine and testing. For the majority of pairs requiring controls, a short quarantine with testing could be as effective as a complete travel ban. The estimated travel quarantine durations are substantially shorter than those specified for traced contacts. Funding EasyJet (JPT and APG), the Elihu endowment (JPT), the Burnett and Stender families’ endowment (APG), the Notsew Orm Sands Foundation (JPT and APG), the National Institutes of Health (MCF), Canadian Institutes of Health Research (SMM) and Natural Sciences and Engineering Research Council of Canada EIDM-MfPH (SMM).

9.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-295884

ABSTRACT

Recent evidence suggests that some new SARS-CoV-2 variants with spike mutations, such as P.1 (Gamma) and B.1.617.2 (Delta), exhibit partial immune evasion to antibodies generated by natural infection or vaccination. By considering the Gamma and Delta variants in a multi-variant transmission dynamic model, we evaluated the dominance of these variants in the United States (US) despite mounting vaccination coverage and other circulating variants. Our results suggest that while the dominance of the Gamma variant is improbable, the Delta variant would become the most prevalent variant in the US, driving a surge in infections and hospitalizations. Our study highlights the urgency for accelerated vaccination and continued adherence to non-pharmaceutical measures until viral circulation is driven low.

12.
Cancer ; 127(18): 3466-3475, 2021 09 15.
Article in English | MEDLINE | ID: covidwho-1258048

ABSTRACT

BACKGROUND: The authors sought to study the risk factors associated with severe outcomes in hospitalized coronavirus disease 2019 (COVID-19) patients with cancer. METHODS: The authors queried the New York University Langone Medical Center's records for hospitalized patients who were polymerase chain reaction-positive for severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) and performed chart reviews on patients with cancer diagnoses to identify patients with active cancer and patients with a history of cancer. Descriptive statistics were calculated and multivariable logistic regression was used to determine associations between clinical, demographic, and laboratory characteristics with outcomes, including death and admission to the intensive care unit. RESULTS: A total of 4184 hospitalized SARS CoV-2+ patients, including 233 with active cancer, were identified. Patients with active cancer were more likely to die than those with a history of cancer and those without any cancer history (34.3% vs 27.6% vs 20%, respectively; P < .01). In multivariable regression among all patients, active cancer (odds ratio [OR], 1.89; CI, 1.34-2.67; P < .01), older age (OR, 1.06; CI, 1.05-1.06; P < .01), male sex (OR for female vs male, 0.70; CI, 0.58-0.84; P < .01), diabetes (OR, 1.26; CI, 1.04-1.53; P = .02), morbidly obese body mass index (OR, 1.87; CI, 1.24-2.81; P < .01), and elevated D-dimer (OR, 6.41 for value >2300; CI, 4.75-8.66; P < .01) were associated with increased mortality. Recent cancer-directed medical therapy was not associated with death in multivariable analysis. Among patients with active cancer, those with a hematologic malignancy had the highest mortality rate in comparison with other cancer types (47.83% vs 28.66%; P < .01). CONCLUSIONS: The authors found that patients with an active cancer diagnosis were more likely to die from COVID-19. Those with hematologic malignancies were at the highest risk of death. Patients receiving cancer-directed therapy within 3 months before hospitalization had no overall increased risk of death. LAY SUMMARY: Our investigators found that hospitalized patients with active cancer were more likely to die from coronavirus disease 2019 (COVID-19) than those with a history of cancer and those without any cancer history. Patients with hematologic cancers were the most likely among patients with cancer to die from COVID-19. Patients who received cancer therapy within 3 months before hospitalization did not have an increased risk of death.


Subject(s)
COVID-19/therapy , Neoplasms/complications , Adult , Aged , COVID-19/complications , COVID-19/virology , Case-Control Studies , Female , Humans , Male , Middle Aged , New York City , SARS-CoV-2/isolation & purification , Young Adult
13.
EClinicalMedicine ; 33: 100761, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1131250

ABSTRACT

BACKGROUND: Black populations in the United States are being disproportionately affected by the COVID-19 pandemic, but the increased mortality burden after accounting for health and other demographic characteristics is not well understood. We examined characteristics of individuals who died from COVID-19 in Michigan by race stratified by their age, sex and comorbidity prevalence to illustrate and understand this disparity in mortality risk. METHODS: We evaluate COVID-19 mortality in Michigan by demographic and health characteristics, using individual-level linked death certificate and surveillance data collected by the Michigan Department of Health and Human Services from March 16 to October 26, 2020. We identified differences in demographics and comorbidity prevalence across race among individuals who died from COVID-19 and calculated mortality rates by age, sex, race, and number of comorbidities. FINDINGS: Among the 6,065 COVID-19 related deaths in Michigan, Black individuals are experiencing 3·6 times the mortality rate of White individuals (p<0.001), with a mortality rate for Black individuals under 65 years without comorbidities that is 12·6 times that of their White counterparts (p<0.001). After accounting for age, race, sex, and number of comorbidities, we find that Black individuals in all strata are at higher risk of COVID-19 mortality than their White counterparts. INTERPRETATION: Our findings demonstrate that Black populations are disproportionately burdened by COVID-19 mortality, even after accounting for demographic and underlying health characteristics. We highlight how disparities across race, which result from systemic racism, are compounded in crises. FUNDING: ASP, AP and APG were funded by NSF Expeditions grant 1918784, NIH grant 1R01AI151176-01, NSF Rapid Response Research for COVID-19 grant RAPID-2027755, and the Notsew Orm Sands Foundation. MCF was supported by NIH grant K01AI141576.

15.
Lancet Public Health ; 6(3): e184-e191, 2021 03.
Article in English | MEDLINE | ID: covidwho-1065700

ABSTRACT

BACKGROUND: To mitigate the COVID-19 pandemic, countries worldwide have enacted unprecedented movement restrictions, physical distancing measures, and face mask requirements. Until safe and efficacious vaccines or antiviral drugs become widely available, viral testing remains the primary mitigation measure for rapid identification and isolation of infected individuals. We aimed to assess the economic trade-offs of expanding and accelerating testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across the USA in different transmission scenarios. METHODS: We used a multiscale model that incorporates SARS-CoV-2 transmission at the population level and daily viral load dynamics at the individual level to assess eight surveillance testing strategies that varied by testing frequency (from daily to monthly testing) and isolation period (1 or 2 weeks), compared with the status-quo strategy of symptom-based testing and isolation. For each testing strategy, we first estimated the costs (incorporating costs of diagnostic testing and admissions to hospital, and salary lost while in isolation) and years of life lost (YLLs) prevented under rapid and low transmission scenarios. We then assessed the testing strategies across a range of scenarios, each defined by effective reproduction number (Re), willingness to pay per YLL averted, and cost of a test, to estimate the probability that a particular strategy had the greatest net benefit. Additionally, for a range of transmission scenarios (Re from 1·1 to 3), we estimated a threshold test price at which the status-quo strategy outperforms all testing strategies considered. FINDINGS: Our modelling showed that daily testing combined with a 2-week isolation period was the most costly strategy considered, reflecting increased costs with greater test frequency and length of isolation period. Assuming a societal willingness to pay of US$100 000 per YLL averted and a price of $5 per test, the strategy most likely to be cost-effective under a rapid transmission scenario (Re of 2·2) is weekly testing followed by a 2-week isolation period subsequent to a positive test result. Under low transmission scenarios (Re of 1·2), monthly testing of the population followed by 1-week isolation rather than 2-week isolation is likely to be most cost-effective. Expanded surveillance testing is more likely to be cost-effective than the status-quo testing strategy if the price per test is less than $75 across all transmission rates considered. INTERPRETATION: Extensive expansion of SARS-CoV-2 testing programmes with more frequent and rapid tests across communities coupled with isolation of individuals with confirmed infection is essential for mitigating the COVID-19 pandemic. Furthermore, resources recouped from shortened isolation duration could be cost-effectively allocated to more frequent testing. FUNDING: US National Institutes of Health, US Centers for Disease Control and Prevention, and Love, Tito's.


Subject(s)
COVID-19 Testing/economics , COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Cost-Benefit Analysis , Humans , Models, Theoretical , United States/epidemiology
16.
Nat Commun ; 12(1): 356, 2021 01 07.
Article in English | MEDLINE | ID: covidwho-1015013

ABSTRACT

For COVID-19, it is vital to understand if quarantines shorter than 14 days can be equally effective with judiciously deployed testing. Here, we develop a mathematical model that quantifies the probability of post-quarantine transmission incorporating testing into travel quarantine, quarantine of traced contacts with an unknown time of infection, and quarantine of cases with a known time of exposure. We find that testing on exit (or entry and exit) can reduce the duration of a 14-day quarantine by 50%, while testing on entry shortens quarantine by at most one day. In a real-world test of our theory applied to offshore oil rig employees, 47 positives were obtained with testing on entry and exit to quarantine, of which 16 had tested negative at entry; preventing an expected nine offshore transmission events that each could have led to outbreaks. We show that appropriately timed testing can make shorter quarantines effective.


Subject(s)
COVID-19/diagnosis , Quarantine , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , Contact Tracing , Humans , Models, Theoretical , Probability , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Time Factors
17.
Proc Natl Acad Sci U S A ; 117(30): 17513-17515, 2020 07 28.
Article in English | MEDLINE | ID: covidwho-635447

ABSTRACT

Since the emergence of coronavirus disease 2019 (COVID-19), unprecedented movement restrictions and social distancing measures have been implemented worldwide. The socioeconomic repercussions have fueled calls to lift these measures. In the absence of population-wide restrictions, isolation of infected individuals is key to curtailing transmission. However, the effectiveness of symptom-based isolation in preventing a resurgence depends on the extent of presymptomatic and asymptomatic transmission. We evaluate the contribution of presymptomatic and asymptomatic transmission based on recent individual-level data regarding infectiousness prior to symptom onset and the asymptomatic proportion among all infections. We found that the majority of incidences may be attributable to silent transmission from a combination of the presymptomatic stage and asymptomatic infections. Consequently, even if all symptomatic cases are isolated, a vast outbreak may nonetheless unfold. We further quantified the effect of isolating silent infections in addition to symptomatic cases, finding that over one-third of silent infections must be isolated to suppress a future outbreak below 1% of the population. Our results indicate that symptom-based isolation must be supplemented by rapid contact tracing and testing that identifies asymptomatic and presymptomatic cases, in order to safely lift current restrictions and minimize the risk of resurgence.


Subject(s)
Asymptomatic Infections/epidemiology , Betacoronavirus/isolation & purification , Contact Tracing/statistics & numerical data , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Infection Control/methods , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Quarantine/statistics & numerical data , Adolescent , Adult , Aged , COVID-19 , Child , Child, Preschool , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , SARS-CoV-2 , Young Adult
20.
Proc Natl Acad Sci U S A ; 117(16): 9122-9126, 2020 04 21.
Article in English | MEDLINE | ID: covidwho-34058

ABSTRACT

In the wake of community coronavirus disease 2019 (COVID-19) transmission in the United States, there is a growing public health concern regarding the adequacy of resources to treat infected cases. Hospital beds, intensive care units (ICUs), and ventilators are vital for the treatment of patients with severe illness. To project the timing of the outbreak peak and the number of ICU beds required at peak, we simulated a COVID-19 outbreak parameterized with the US population demographics. In scenario analyses, we varied the delay from symptom onset to self-isolation, the proportion of symptomatic individuals practicing self-isolation, and the basic reproduction number R 0 Without self-isolation, when R 0 = 2.5, treatment of critically ill individuals at the outbreak peak would require 3.8 times more ICU beds than exist in the United States. Self-isolation by 20% of cases 24 h after symptom onset would delay and flatten the outbreak trajectory, reducing the number of ICU beds needed at the peak by 48.4% (interquartile range 46.4-50.3%), although still exceeding existing capacity. When R 0 = 2, twice as many ICU beds would be required at the peak of outbreak in the absence of self-isolation. In this scenario, the proportional impact of self-isolation within 24 h on reducing the peak number of ICU beds is substantially higher at 73.5% (interquartile range 71.4-75.3%). Our estimates underscore the inadequacy of critical care capacity to handle the burgeoning outbreak. Policies that encourage self-isolation, such as paid sick leave, may delay the epidemic peak, giving a window of time that could facilitate emergency mobilization to expand hospital capacity.


Subject(s)
Coronavirus Infections , Disease Outbreaks , Hospital Bed Capacity , Hospitals , Intensive Care Units , Pandemics , Patient Acceptance of Health Care , Pneumonia, Viral , Betacoronavirus , COVID-19 , Coronavirus Infections/epidemiology , Coronavirus Infections/therapy , Disease Outbreaks/statistics & numerical data , Forecasting , Hospitals/statistics & numerical data , Humans , Intensive Care Units/statistics & numerical data , Models, Theoretical , Patient Acceptance of Health Care/statistics & numerical data , Patient Isolation , Pneumonia, Viral/epidemiology , Pneumonia, Viral/therapy , SARS-CoV-2 , Time Factors , United States
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