A meta-analysis of estimates of the AIDS incubation distribution

Is 14-Days a Sensible Quarantine Length for COVID-19? Examinations of Some Associated Issues with a Case Study of COVID-19 Incubation Times

To confine the spread of an infectious disease, setting a sensible quarantine time is crucial. To this end, it is imperative to well understand the distribution of incubation times of the disease. Regarding the ongoing COVID-19 pandemic, 14-days is commonly taken as a quarantine time to curb the virus spread in balancing the impacts of COVID-19 on diverse aspects of the society, including public health, economy, and humanity perspectives, etc. However, setting a sensible quarantine time is not trivial and it depends on various underlying factors. In this article, we take an angle of examining the distribution of the COVID-19 incubation time using likelihood-based methods. Our study is carried out on a dataset of 178 COVID-19 cases dated from January 20, 2020 to February 29, 2020, with the information of exposure periods and dates of symptom onset collected. To gain a good understanding of possible scenarios, we employ different models to describe incubation times of COVID-19. Our findings suggest that statistically, the 14-day quarantine time may not be long enough to control the probability of an early release of infected individuals to be small. While the size of the study data is not large enough to offer us a definitely acceptable quarantine time, and further in practice, the decision-makers may take account of other factors related to social and economic concerns to set up a practically acceptable quarantine time, our study demonstrates useful methods to determine a reasonable quarantine time from a statistical standpoint. Further, it reveals some associated complexity for fully understanding the COVID-19 incubation time distribution.

Trends in three decades of HIV/AIDS epidemic in Thailand by nonparametric backcalculation method

OBJECTIVES

To reconstruct the past HIV incidence and prevalence in Thailand from 1980 to 2008 and predict the country's AIDS incidence from 2009 to 2011.

METHODS

Nonparametric backcalculation was adopted utilizing 100 quarterly observed new AIDS counts excluding pediatric cases. The accuracy of data was enhanced through a series of data adjustments using the weight method to account for several surveillance reporting issues. The mixture of time-dependent distributions allowed the effects of age at seroconversion and antiretroviral therapy to be incorporated simultaneously. Sensitivity analyses were conducted to assess model variations that were subject to major uncertainties. Future AIDS incidence was projected for various predetermined HIV incidence patterns.

RESULTS

HIV incidence in Thailand reached its peak in 1992 with approximately 115,000 cases. A steep decline thereafter discontinued in 1997 and was followed by another strike of 42,000 cases in 1999. The second surge, which happened concurrently with the major economic crisis, brought on 60,000 new infections. As of December 2008, more than 1 million individuals had been infected and around 430,000 adults were living with HIV corresponding to a prevalence rate of 1.2%. The incidence rate had become less than 0.1% since 2002. The backcalculated estimates were dominated by postulated median AIDS progression time and adjustments to surveillance data.

CONCLUSION

Our analysis indicated that, thus far, the 1990s was the most severe era of HIV/AIDS epidemic in Thailand with two HIV incidence peaks. A drop in new infections led to a decrease in recent AIDS incidence, and this tendency is likely to remain unchanged until 2011, if not further.

Back-calculation and projection of the HIV/AIDS epidemic among homosexual/ bisexual men in three European countries: evalution of past projections and updates allowing for treatment effects

This study critically evaluates the quality of 1990 back-calculations and long-term projections of the HIV/AIDS epidemic for homosexual/bisexual men in France, the Federal Republic of Germany, and the UK. The projection captured the general pattern observed in all three countries although the observed AIDS incidence peaked 2-3 years later and declined faster than had been projected. Total AIDS incidences from 1989 to 2000 were overestimated by 38.5% in France, and underestimated by 23.9 and 17.5% in western Germany and the UK. Updated back-calculations and projections to 2020 use AIDS incidence data up to 2000. The procedure incorporates an asymmetric long-tailed cumulative HIV curve as well as the increase in the median incubation period brought about by new therapies introduced during the 1990s. The results suggest that: (i) The rapid decrease in cases during the late 1990s was caused by a median incubation period that increased from 10 years to 21-23 years by the late 1990s. (ii) An imminent bottoming out followed by a protracted increase in AIDS cases from 2000 to at least 2010 could be the consequence of a leveling off of the median incubation period. (iii) A low variant of the projections shows that at least 40,000 homosexual men could develop AIDS in the three countries after 2000.

Effectiveness of Antiretroviral Therapy after Protease Inhibitor Failure: An Analytic Overview

To examine effectiveness of subsequent antiretroviral therapy (ART), studies published during the period of 1 January 1997 through 31 May 2003 involving patients who had failed a protease inhibitor (PI)-containing regimen and were switched to another regimen were reviewed. Twelve studies describing 1197 patients were analyzed. A total of 38% of patients had human immunodeficiency virus (HIV) RNA levels of <500 copies/mL at 24 weeks. After adjustment for baseline HIV RNA level, the rate of virologic suppression ranged from 16% for patients switching drugs within previously failed classes to 54% for nonnucleoside reverse-transcriptase inhibitor (NNRTI)-naive patients switched to boosted PI- and NNRTI-containing regimens. ART regimens in patients who failed a PI-containing regimen provided virologic suppression only in a few patients. The best response was seen in NNRTI-naive patients receiving NNRTI- and boosted PI-containing regimens. New approaches are needed to achieve better suppression in pretreated HIV-infected patients.

Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss

RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.

Improved methods and assumptions for estimation of the HIV/AIDS epidemic and its impact: Recommendations of the UNAIDS Reference Group on Estimates, Modelling and Projections

UNAIDS and WHO produce biannual country-specific estimates of HIV/AIDS and its impact. These estimates are based on methods and assumptions that reflect the best understanding of HIV epidemiology and demography at the time. Where significant advances are made in epidemiological and demographic research, the methods and assumptions must evolve to match these advances. UNAIDS established an Epidemiology Reference Group in 1999 to advise them and other organisations on HIV epidemiology and methods for making estimates and projections of HIV/AIDS. During the meeting of the reference group in 2001, four priority areas were identified where methods and assumptions should be reviewed and perhaps modified: a) models of the HIV epidemic, b) survival of adults with HIV-1 in low and middle income countries, c) survival of children with HIV-1 in low and middle income countries, and d) methods to estimate numbers of AIDS orphans. Research and literature reviews were carried out by Reference Group members and invited specialists, prior to meetings held during 2001-2. Recommendations reflecting the consensus of the meeting participants on the four priority areas were determined at each meeting. These recommendations were followed in UNAIDS and WHO development of country-specific estimates of HIV/AIDS and its impact for end of 2001.

The continuing HIV epidemic among men who have sex with men

OBJECTIVES

This study characterized the AIDS epidemic among urban men who have sex with men (MSM).

METHODS

A probability sample of MSM was obtained in 1997 (n = 2881; 18 years and older) from New York, Los Angeles, Chicago, and San Francisco, and HIV status was determined through self-report and biological measures.

RESULTS

HIV prevalence was 17% (95% confidence interval = 15%, 19%) overall, with extremely high levels in African Americans (29%), MSM who used injection drugs (40%), "ultraheavy" noninjection drug users (32%), and less educated men (< high school, 37%). City-level HIV differences were non-significant once these other factors were controlled for. In comparing the present findings with historical data based on public records and modeling, HIV prevalence appears to have declined as a result of high mortality (69%) and stable, but high, incidence rates (1%-2%).

CONCLUSIONS

Although the findings suggest that HIV prevalence has declined significantly from the mid-1980s, current levels among urban MSM in the United States approximate those of sub-Saharan countries (e.g., 14%-25%) and are extremely high in many population subsegments. Despite years of progress, the AIDS epidemic continues unabated among subsegments of the MSM community.