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Abstract Limited data exist on viral hepatitis among migrant populations. This study investigated the prevalence of current hepatitis B virus (HBV) infection and lifetime hepatitis C virus (HCV) infection among Qatar's migrant craft and manual workers (CMWs), constituting 60% of the country's population. Sera collected during a nationwide COVID-19 population-based cross-sectional survey on CMWs between July 26 and September 9, 2020, underwent testing for HBsAg and HCV antibodies. Reactive samples underwent confirmatory testing, and logistic regression analyses were employed to explore associations with HBV and HCV infections. Among 2528 specimens tested for HBV infection, 15 were reactive, with 8 subsequently confirmed positive. Three samples lacked sufficient sera for confirmatory testing but were included in the analysis through multiple imputations. Prevalence of current HBV infection was 0.4% (95% CI 0.2–0.7%). Educational attainment and occupation were significantly associated with current HBV infection. For HCV infection, out of 2607 specimens tested, 46 were reactive, and 23 were subsequently confirmed positive. Prevalence of lifetime HCV infection was 0.8% (95% CI 0.5–1.2%). Egyptians exhibited the highest prevalence at 6.5% (95% CI 3.1–13.1%), followed by Pakistanis at 3.1% (95% CI 1.1–8.0%). Nationality, geographic location, and occupation were significantly associated with lifetime HCV infection. HBV infection is relatively low among CMWs, while HCV infection falls within the intermediate range, both compared to global and regional levels.

Background: This study aimed to examine the transmission dynamics of Neisseria gonorrhoeae (NG) in heterosexual sex work networks (HSWNs) and the impact of variation in sexual behavior and interventions on NG epidemiology. Methods: The study employed an individual-based mathematical model to simulate NG transmission dynamics in sexual networks involving female sex workers (FSWs) and their clients, primarily focusing on the Middle East and North Africa region. A deterministic model was also used to describe NG transmission from clients to their spouses. Results: NG epidemiology in HSWNs displays two distinct patterns. In the common low-partner-number HSWNs, a significant proportion of NG incidence occurs among FSWs, with NG prevalence 13 times higher among FSWs than clients, and three times higher among clients than their spouses. Interventions substantially reduce incidence. Increasing condom use from 10 % to 50 % lowers NG prevalence among FSWs, clients, and their spouses from 12.2 % to 6.4 %, 1.2 % to 0.5 %, and 0.4 % to 0.2 %, respectively. Increasing symptomatic treatment coverage among FSWs from 0 % to 100 % decreases prevalence from 10.6 % to 4.5 %, 0.8 % to 0.4 %, and 0.3 % to 0.1 %, respectively. Increasing asymptomatic treatment coverage among FSWs from 0 % to 50 % decreases prevalence from 8.2 % to 0.4 %, 0.6 % to 0.1 %, and 0.2 % to 0.0 %, respectively, with very low prevalence when coverage exceeds 50 %. In high-partner-number HSWNs, prevalence among FSWs saturates at a high level, and the vast majority of incidence occurs among clients and their spouses, with a limited impact of incremental increases in interventions. Conclusion: NG epidemiology in HSWNs is typically a ''fragile epidemiology'' that is responsive to a range of interventions even if the interventions are incremental, partially efficacious, and only applied to FSWs.

BackgroundThere is a need for statistical methodologies that scrutinize civilian casualties in conflicts, evaluating the degree to which the conduct of war affects civilians and breaches the laws of war. Employing an epidemiological method, this study introduced, developed, and applied a novel approach for investigating mortality of civilians versus combatants in conflicts.MethodsA deterministic mathematical model, structured by age and sex, was developed to describe the process of conflict-related deaths among both combatants and civilians. The model was calibrated using demographic and conflict-related data from different Israel-Gaza conflicts. To quantify the extent of the impact on civilians and determine whether they are the primary focus of a conflict, a statistical metric, the index of killing civilians, along with associated criteria, was devised.ResultsThe model-estimated proportion of deaths in Gaza categorized as combatants was 62.1% (95% uncertainty interval (UI): 57.6–66.2%), 51.1% (95% UI: 47.1–54.9%), and 12.7% (95% UI: 9.7–15.4%) in the 2008–2009, 2014, and 2023 Israel-Gaza conflicts, respectively. The index of killing civilians was 0.61 (95% UI: 0.51–0.74), 0.96 (95% UI: 0.82–1.12), and 7.01 (95% UI: 5.50–9.29) in the 2008–2009, 2014, and 2023 conflicts, respectively. These index values indicate strong evidence for civilians being an object of war in the 2008–2009 and 2014 conflicts, but combatants were still identified as the primary focus of the conflict. In the 2023 conflict, there is robust evidence for civilians being an object of war, with civilians identified as the primary focus of the conflict.ConclusionFindings imply a progressive shift in Israel’s rules of engagement over time, with a trend towards higher acceptance of casualties among civilians. The 2023 conflict stands apart from preceding Israel-Gaza conflicts, with civilians identified as the primary focus of the conflict.

Objectives: We assessed short-, medium-, and long-term all-cause mortality risks after a primary SARS-CoV-2 infection. Methods: A national, matched, retrospective cohort study was conducted in Qatar to assess risk of all-cause mortality in the national SARS-CoV-2 primary infection cohort compared with the national infection-naïve cohort. Associations were estimated using Cox proportional-hazards regression models. Analyses were stratified by vaccination status and clinical vulnerability status. Results: Among unvaccinated persons, within 90 days after primary infection, the adjusted hazard ratio (aHR) comparing mortality incidence in the primary-infection cohort with the infection-naïve cohort was 1.19 (95% confidence interval 1.02-1.39). aHR was 1.34 (1.11-1.63) in persons more clinically vulnerable to severe COVID-19 and 0.94 (0.72-1.24) in those less clinically vulnerable. Beyond 90 days after primary infection, aHR was 0.50 (0.37-0.68); aHR was 0.41 (0.28-0.58) at 3-7 months and 0.76 (0.46-1.26) at ≥8 months. The aHR was 0.37 (0.25-0.54) in more clinically vulnerable persons and 0.77 (0.48-1.24) in less clinically vulnerable persons. Among vaccinated persons, mortality incidence was comparable in the primary-infection versus infection-naïve cohorts, regardless of clinical vulnerability status. Conclusions: COVID-19 mortality was primarily driven by an accelerated onset of death among individuals who were already vulnerable to all-cause mortality, but vaccination prevented these accelerated deaths.

Abstract Background Limited data exists on herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) infections in migrant populations. This study investigated HSV-1 and HSV-2 seroprevalences and associations among craft and manual workers (CMWs) in Qatar who constitute 60% of Qatar’s population. Methods A national population-based cross-sectional seroprevalence survey was conducted on the CMW population, all men, between July 26 and September 9, 2020. 2,612 sera were tested for anti-HSV-1 IgG antibodies using HerpeSelect 1 ELISA IgG kits and for anti-HSV-2 IgG antibodies using HerpeSelect 2 ELISA IgG kits (Focus Diagnostics, USA). Univariable and multivariable logistic regression analyses were conducted to identify associations with HSV-1 and HSV-2 infections. Results Serological testing identified 2,171 sera as positive, 403 as negative, and 38 as equivocal for HSV-1 antibodies, and 300 sera as positive, 2,250 as negative, and 62 as equivocal for HSV-2 antibodies. HSV-1 and HSV-2 seroprevalences among CMWs were estimated at 84.2% (95% CI 82.8–85.6%) and 11.4% (95% CI 10.1–12.6%), respectively. HSV-1 infection was associated with nationality, educational attainment, and occupation. HSV-2 infection was associated with age, nationality, and educational attainment. Conclusions Over 80% of CMWs are infected with HSV-1 and over 10% are infected with HSV-2. The findings highlight the need for sexual health programs to tackle sexually transmitted infections among the CMW population.

IntroductionReinfections are increasingly becoming a feature in the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, accurately defining reinfection poses methodological challenges. Conventionally, reinfection is defined as a positive test occurring at least 90 days after a previous infection diagnosis. Yet, this extended time window may lead to an underestimation of reinfection occurrences. This study investigated the prospect of adopting an alternative, shorter time window for defining reinfection.MethodsA longitudinal study was conducted to assess the incidence of reinfections in the total population of Qatar, from February 28, 2020 to November 20, 2023. The assessment considered a range of time windows for defining reinfection, spanning from 1 day to 180 days. Subgroup analyses comparing first versus repeat reinfections and a sensitivity analysis, focusing exclusively on individuals who underwent frequent testing, were performed.ResultsThe relationship between the number of reinfections in the population and the duration of the time window used to define reinfection revealed two distinct dynamical domains. Within the initial 15 days post-infection diagnosis, almost all positive tests for SARS-CoV-2 were attributed to the original infection. However, surpassing the 30-day post-infection threshold, nearly all positive tests were attributed to reinfections. A 40-day time window emerged as a sufficiently conservative definition for reinfection. By setting the time window at 40 days, the estimated number of reinfections in the population increased from 84,565 to 88,384, compared to the 90-day time window. The maximum observed reinfections were 6 and 4 for the 40-day and 90-day time windows, respectively. The 40-day time window was appropriate for defining reinfection, irrespective of whether it was the first, second, third, or fourth occurrence. The sensitivity analysis, confined to high testers exclusively, replicated similar patterns and results.DiscussionA 40-day time window is optimal for defining reinfection, providing an informed alternative to the conventional 90-day time window. Reinfections are prevalent, with some individuals experiencing multiple instances since the onset of the pandemic.

Background: The rapid growth of Qatar in the last two decades has attracted a large influx of immigrant craft and manual workers (CMWs) seeking employment in jobs associated with food handling, domestic service, and construction. Nearly 60 % of Qatar's population are expatriates CMWs, including many from hyperendemic countries for HEV. Thus, estimating the seroprevalence of HEV in Qatar and understanding its epidemiology is essential for public health efforts to control HEV transmission in Qatar. Methods: Blood samples from 2670 CMWs were collected between 2020 and 2021. All samples were tested for HEV-IgG antibodies. Positive HEV-IgG samples were tested for HEV-IgM antibodies, and those positives were also tested for viral antigens using an HEV-Ag ELISA kit and HEV-RNA by RT-PCR to confirm current HEV infections. Results: The seroprevalence of HEV-IgG was 27.3 % (729/2670; 95 % CI: 25.6–29.0). Of those HEV-IgG positive, 8.23 % (60/729; 95 % CI: 6.30–10.5) were HEV-IgM positive. Of the IgM-positive samples, 2 were HEV-RNA positive (3.39 %; 95 % CI: 0.40–11.7), and 1 was HEV-Ag positive (1.69 %; 95 % CI: 0.04–9.09). In addition, HEV-IgG seroprevalence was associated with age and nationality, with the highest seroprevalence in participants from Egypt (IgG 60.0 %; IgM 5.56 %), Pakistan (IgG 59.0 %; IgM 2.24 %), Nepal (IgG 29.3 %; IgM 2.70 %), Bangladesh (IgG 27.8 %; IgM 2.45 %), and India (IgG 23.9 %; IgM 2.43 %). Conclusion: In this study, we showed that the seroprevalence of HEV among CMWs was slightly higher than what was previously reported among the urban population in Qatar (2013–2016).

Background: Some studies have reported that influenza vaccination is associated with lower risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and/or coronavirus disease 2019 (COVID-19) morbidity and mortality. This study aims to estimate effectiveness of influenza vaccination, using Abbott’s quadrivalent Influvac Tetra vaccine, against SARS-CoV-2 infection and against severe COVID-19. Methods: This matched, test-negative, case-control study was implemented on a population of 30,774 healthcare workers (HCWs) in Qatar during the 2020 annual influenza vaccination campaign, September 17, 2020-December 31, 2020, before introduction of COVID-19 vaccination. Results: Of 30,774 HCWs, 576 with PCR-positive tests and 10,033 with exclusively PCR-negative tests were eligible for inclusion in the study. Matching by sex, age, nationality, reason for PCR testing, and PCR test date yielded 518 cases matched to 2058 controls. Median duration between influenza vaccination and the PCR test was 43 days (IQR, 29–62). Estimated effectiveness of influenza vaccination against SARS-CoV-2 infection> 14 days after receiving the vaccine was 29.7% (95% CI: 5.5–47.7%). Estimated effectiveness of influenza vaccination against severe, critical, or fatal COVID-19 was 88.9% (95% CI: 4.1–98.7%). Sensitivity analyses confirmed the main analysis results. Conclusions: Recent influenza vaccination is associated with a significant reduction in the risk of SARS-CoV-2 infection and COVID-19 severity.

Summary: Background: Protection against SARS-CoV-2 symptomatic infection and severe COVID-19 of previous infection, mRNA two-dose vaccination, mRNA three-dose vaccination, and hybrid immunity of previous infection and vaccination were investigated in Qatar for the Alpha, Beta, and Delta variants. Methods: Six national, matched, test-negative, case-control studies were conducted between January 18 and December 18, 2021 on a sample of 239,120 PCR-positive tests and 6,103,365 PCR-negative tests. Findings: Effectiveness of previous infection against Alpha, Beta, and Delta reinfection was 89.5% (95% CI: 85.5–92.3%), 87.9% (95% CI: 85.4–89.9%), and 90.0% (95% CI: 86.7–92.5%), respectively. Effectiveness of two-dose BNT162b2 vaccination against Alpha, Beta, and Delta infection was 90.5% (95% CI, 83.9–94.4%), 80.5% (95% CI: 79.0–82.0%), and 58.1% (95% CI: 54.6–61.3%), respectively. Effectiveness of three-dose BNT162b2 vaccination against Delta infection was 91.7% (95% CI: 87.1–94.7%). Effectiveness of hybrid immunity of previous infection and two-dose BNT162b2 vaccination was 97.4% (95% CI: 95.4–98.5%) against Beta infection and 94.5% (95% CI: 92.8–95.8%) against Delta infection. Effectiveness of previous infection and three-dose BNT162b2 vaccination was 98.1% (95% CI: 85.7–99.7%) against Delta infection. All five forms of immunity had >90% protection against severe, critical, or fatal COVID-19 regardless of variant. Similar effectiveness estimates were observed for mRNA-1273. A mathematical model accurately predicted hybrid immunity protection by assuming that the individual effects of previous infection and vaccination acted independently. Interpretation: Hybrid immunity, offering the strongest protection, was mathematically predicted by assuming that the immunities obtained from previous infection and vaccination act independently, without synergy or redundancy. Funding: The Biomedical Research Program and the Biostatistics, Epidemiology, and the Biomathematics Research Core, both at Weill Cornell Medicine-Qatar, Ministry of Public Health, Hamad Medical Corporation, Sidra Medicine, Qatar Genome Programme, Qatar University Biomedical Research Center, and Qatar University Internal Grant ID QUCG-CAS-23/24-114.

Summary: Background: Waning of natural infection protection and vaccine protection highlight the need to evaluate changes in population immunity over time. Population immunity of previous SARS-CoV-2 infection or of COVID-19 vaccination are defined, respectively, as the overall protection against reinfection or against breakthrough infection at a given point in time in a given population. Methods: We estimated these population immunities in Qatar's population between July 1, 2020 and November 30, 2022, to discern generic features of the epidemiology of SARS-CoV-2. Effectiveness of previous infection, mRNA primary-series vaccination, and mRNA booster (third-dose) vaccination in preventing infection were estimated, month by month, using matched, test-negative, case–control studies. Findings: Previous-infection effectiveness against reinfection was strong before emergence of Omicron, but declined with time after a wave and rebounded after a new wave. Effectiveness dropped after Omicron emergence from 88.3% (95% CI: 84.8–91.0%) in November 2021 to 51.0% (95% CI: 48.3–53.6%) in December 2021. Primary-series effectiveness against infection was 84.0% (95% CI: 83.0–85.0%) in April 2021, soon after introduction of vaccination, before waning gradually to 52.7% (95% CI: 46.5–58.2%) by November 2021. Effectiveness declined linearly by ∼1 percentage point every 5 days. After Omicron emergence, effectiveness dropped from 52.7% (95% CI: 46.5–58.2%) in November 2021 to negligible levels in December 2021. Booster effectiveness dropped after Omicron emergence from 83.0% (95% CI: 65.6–91.6%) in November 2021 to 32.9% (95% CI: 26.7–38.5%) in December 2021, and continued to decline thereafter. Effectiveness of previous infection and vaccination against severe, critical, or fatal COVID-19 were generally >80% throughout the study duration. Interpretation: High population immunity against infection may not be sustained beyond a year, but population immunity against severe COVID-19 is durable with slow waning even after Omicron emergence. Funding: The Biomedical Research Program and the Biostatistics, Epidemiology, and the Biomathematics Research Core, both at Weill Cornell Medicine-Qatar, Ministry of Public Health, Hamad Medical Corporation, Sidra Medicine, Qatar Genome Programme, Qatar University Biomedical Research Center, and Qatar University Internal Grant ID QUCG-CAS-23/24-114.

BackgroundDirect-acting antivirals opened an opportunity for eliminating hepatitis C virus (HCV) infection in the Middle East and North Africa (MENA), the region most affected by HCV infection. Impact of HCV treatment as prevention (HCV-TasP) was investigated in 19 MENA countries.MethodsAn age-structured mathematical model was used to assess program impact using epidemiologic and programming measures. The model was fitted to a database of systematically gathered HCV antibody prevalence data. Two main scenarios were investigated for the treatment roll-out to achieve (i) 80% reduction in HCV incidence by 2030, and (ii) incidence rate

The level of immunity induced by infection with different SARS-CoV-2 Omicron sub-lineages against infection with other sub-lineages is not known. Here, the authors use data from Qatar and show that infection with BA.1 induces strong protection against infection with BA.2, and vice versa, for several weeks.

The SARS-CoV-2 Omicron variant has subvariants with divergent properties but relative vaccine effectiveness has not been characterized. Here, the authors show that mRNA vaccine effectiveness is similar for the subvariants BA.1 and BA.2, with a decline three months after the second dose and increase after the booster.

SARS-CoV-2 breakthrough infections in vaccinated individuals and reinfections in those with prior infection are a public health concern. Here, the authors show that viral loads of vaccine breakthrough infections and reinfections are generally lower than primary infections of unvaccinated individuals, potentially indicating lower infectiousness.

Background Economic losses due to herpes simplex infections in low- and middle-income countries (LMICs) are unknown. We estimated economic and quality-of-life losses due to genital herpes in 2019, in 90 LMICs, and from 2020 to 2030 in 45 countries in the World Health Organization (WHO) Africa. We additionally estimated economic losses due to human immunodeficiency virus (HIV) attributable to herpes simplex virus type 2 (HSV-2) infections. Methods and findings We estimated genital herpes-related spending on treatment, wage losses due to absenteeism, and reductions in quality of life, for individuals aged 15 to 49 years, living with genital herpes. Had HSV-2 had contributed to the transmission of HIV, we estimated the share of antiretroviral treatment costs and HIV-related wage losses in 2019 that can be attributed to incident and prevalent HSV-2 infections in 2018. For the former, we used estimates of HSV-2 incidence and prevalence from the global burden of disease (GBD) study. For the latter, we calculated population attributable fractions (PAFs), using the classic (Levin’s) epidemiological formula for polytomous exposures, with relative risks (RRs) reported in literature. To extend estimates from 2020 to 2030, we modeled the transmission of HSV-2 in 45 African countries using a deterministic compartmental mathematical model, structured by age, sex, and sexual activity, which was fitted to seroprevalence gathered from a systematic review and meta-regression analysis. In the 90 LMICs, genital herpes contributed to US$813.5 million in treatment and productivity losses in 2019 (range: US$674.4 to US$952.2 million). Given observed care-seeking and absenteeism, losses are in the range of US$29.0 billion (US$25.6 billion to US$34.5 billion). Quality-of-life losses in the amount of 61.7 million quality-adjusted life years (QALYs) are also possible (50.4 million to 74.2 million). The mean annual cost of treatment and wage losses per infection is US$183.00 (95% CI: US$153.60 to US$212.55); the mean annual cost of quality-of-life losses is US$343.27 (95% CI: 272.41 to 414.14). If HSV-2 has fueled the transmission of HIV, then seroprevalent HSV-2 cases in 2018 can account for 33.2% of the incident HIV infections in 2019, with an associated antiretroviral therapy (ART) cost of US$186.3 million (range: US$163.6 to US$209.5 million) and 28.6% of HIV-related wage losses (US$21.9 million; range: US$19.2 to US$27.4 million). In the WHO Africa region, the 3.9 million seroprevalent genital herpes cases from 2020 to 2030 contributed to US$700.2 million in treatment and productivity losses. Additionally, quality-of-life losses in the range of 88 million to 871 million QALYs are also possible. If HSV-2 has contributed to the transmission of HIV, then in 2020, the PAF of HIV due to prevalent HSV-2 will be 32.8% (95% CI: 26.7% to 29.9%) and due to incident infections will be 4.2% (95% CI: 2.6% to 3.4%). The PAF due to prevalent infections will decline to 31.0% by 2030 and incident infections to 3.6%. Though we have accounted for the uncertainty in the epidemiological and economic parameter values via the sensitivity analysis, our estimates still undervalue losses due to limiting to the 15- to 49-year-old population. Conclusions Economic losses due to genital herpes in LMICs can be large, especially when considering the lifelong nature of the disease. Quality-of-life losses outweigh spending on treatment and reductions in productivity. If HSV-2 has contributed to the spread of HIV in LMICs, then nearly one third of antiretroviral costs and HIV-related wage losses can be attributed to HSV-2. Given the magnitude of the combined losses, a vaccine against HSV-2 must be a global priority. In a modelling study, Dr Sachin Silva and colleagues estimate the economic burden of genital herpes and HIV attributable to herpes simplex virus type-2 infections in 90 low and middle income countries. Author summary Why was this study done? ▪ Economic losses due to herpes simplex virus type 2 (HSV-2) infections in low- and middle-income countries (LMICs) are unknown. ▪ Quality-of-life losses due to genital herpes in LMICs are also unknown, both in terms of their magnitude and their economic value. ▪ If HSV-2 has indeed fueled the spread of human immunodeficiency virus (HIV), as has been conjectured, then the share of HIV-related spending in LMICs that are attributable to HSV-2 infections are also unknown. What did the researchers do and find? ▪ We estimated direct and indirect economic losses and quality-of-life losses due to genital herpes in individuals between the aged of 15 to 49 living in 90 LMICs in 2019. ▪ We also estimated these costs in 45 countries in the World Health Organization (WHO) Africa region from 2020 to 2030, by constructing a mathematical model of HSV-2 dynamics to predict HSV-2 incidence and prevalence. ▪ We supplemented the 2019 estimates with the share of HIV-related spending in 2019 attributable HSV-2 infections in 2018. ▪ For the 90 LMICs, we found that treatment costs and productivity losses in 2019 are in the range of US$674.4 and US$952.2 million. ▪ Quality-of-life losses are in the range of 50.4 million to 74.2 million quality-adjusted life years (QALYs). ▪ Additionally, seroprevalent HSV-2 cases in 2019 can account for 33.2% of antiretroviral therapy (ART) costs for incident HIV cases and 28.6% of HIV-related wage. What do these findings mean? ▪ Economic losses due to genital herpes can be substantial, especially when considering the lifelong nature of the disease. ▪ The quality-of-life losses due to genital herpes outweigh spending on treatment and reduced productivity (on the order of US$212 billion). ▪ If HSV-2 has indeed contributed to the transmission of HIV, then nearly one third of antiretroviral costs and HIV-related wage losses add to these costs. ▪ Given the magnitude of the above losses in LMICs, a vaccine against HSV-2 should be a global priority.

Abstract The SARS-CoV-2 pandemic resulted in considerable morbidity and mortality as well as severe economic and societal disruptions. Despite scientific progress, true infection severity, factoring both diagnosed and undiagnosed infections, remains poorly understood. This study aimed to estimate SARS-CoV-2 age-stratified and overall morbidity and mortality rates based on analysis of extensive epidemiological data for the pervasive epidemic in Qatar, a country where

In 2021, Qatar experienced considerable incidence of SARS-CoV-2 infection that was dominated sequentially by the Alpha, Beta, and Delta variants. Using the cycle threshold (Ct) value of an RT-qPCR-positive test to proxy the inverse of infectiousness, we investigated infectiousness of SARS-CoV-2 infections by variant, age, sex, vaccination status, prior infection status, and reason for testing in a random sample of 18,355 RT-qPCR-genotyped infections. Regression analyses were conducted to estimate associations with the Ct value of RT-qPCR-positive tests. Compared to Beta infections, Alpha and Delta infections demonstrated 2.56 higher Ct cycles (95% CI: 2.35-2.78), and 4.92 fewer cycles (95% CI: 4.67- 5.16), respectively. The Ct value declined gradually with age and was especially high for children

We investigated what proportion of the population acquired severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whether the herd immunity threshold has been reached in 10 communities in Qatar. The study included 4,970 participants during June 21–September 9, 2020. Antibodies against SARS-CoV-2 were detected by using an electrochemiluminescence immunoassay. Seropositivity ranged from 54.9% (95% CI 50.2%–59.4%) to 83.8% (95% CI 79.1%–87.7%) across communities and showed a pooled mean of 66.1% (95% CI 61.5%–70.6%). A range of other epidemiologic measures indicated that active infection is rare, with limited if any sustainable infection transmission for clusters to occur. Only 5 infections were ever severe and 1 was critical in these young communities; infection severity rate of 0.2% (95% CI 0.1%–0.4%). Specific communities in Qatar have or nearly reached herd immunity for SARS-CoV-2 infection: 65%–70% of the population has been infected.

Abstract The overarching objective of this study was to provide the descriptive epidemiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Qatar by addressing specific research questions through a series of national epidemiologic studies. Sources of data were the centralized and standardized national databases for SARS-CoV-2 infection. By July 10, 2020, 397,577 individuals had been tested for SARS-CoV-2 using polymerase-chain-reaction (PCR), of whom 110,986 were positive, a positivity cumulative rate of 27.9% (95% CI 27.8–28.1%). As of July 5, case severity rate, based on World Health Organization (WHO) severity classification, was 3.4% and case fatality rate was 1.4 per 1,000 persons. Age was by far the strongest predictor of severe, critical, or fatal infection. PCR positivity of nasopharyngeal/oropharyngeal swabs in a national community survey (May 6–7) including 1,307 participants was 14.9% (95% CI 11.5–19.0%); 58.5% of those testing positive were asymptomatic. Across 448 ad-hoc testing campaigns in workplaces and residential areas including 26,715 individuals, pooled mean PCR positivity was 15.6% (95% CI 13.7–17.7%). SARS-CoV-2 antibody prevalence was 24.0% (95% CI 23.3–24.6%) in 32,970 residual clinical blood specimens. Antibody prevalence was only 47.3% (95% CI 46.2–48.5%) in those who had at least one PCR positive result, but 91.3% (95% CI 89.5–92.9%) among those who were PCR positive > 3 weeks before serology testing. Qatar has experienced a large SARS-CoV-2 epidemic that is rapidly declining, apparently due to growing immunity levels in the population.

Different COVID-19 treatment candidates are under development, and some are becoming available including two promising drugs from Merck and Pfizer. This study provides conceptual frameworks for the effects of three types of treatments, both therapeutic and prophylactic, and to investigate their population-level impact, to inform drug development, licensure, decision-making, and implementation. Different drug efficacies were assessed using an age-structured mathematical model describing SARS-CoV-2 transmission and disease progression, with application to the United States as an illustrative example. Severe and critical infection treatment reduces progression to COVID-19 severe and critical disease and death with small number of treatments needed to avert one disease or death. Post-exposure prophylaxis treatment had a large impact on flattening the epidemic curve, with large reductions in infection, disease, and death, but the impact was strongly age dependent. Pre-exposure prophylaxis treatment had the best impact and effectiveness, with immense reductions in infection, disease, and death, driven by the robust control of infection transmission. Effectiveness of both pre-exposure and post-exposure prophylaxis treatments was disproportionally larger when a larger segment of the population was targeted than a specific age group. Additional downstream potential effects of treatment, beyond the primary outcome, enhance the population-level impact of both treatments. COVID-19 treatments are an important modality in controlling SARS-CoV-2 disease burden. Different types of treatment act synergistically for a larger impact, for these treatments and vaccination.

We aimed to estimate, albeit crudely and provisionally, national, regional, and global proportions of respective populations that have been infected with SARS-CoV-2 in the first year after the introduction of this virus into human circulation, and to assess infection morbidity and mortality rates, factoring both documented and undocumented infections. The estimates were generated by applying mathematical models to 159 countries and territories. The percentage of the world's population that has been infected as of 31 December 2020 was estimated at 12.56% (95% CI: 11.17–14.05%). It was lowest in the Western Pacific Region at 0.66% (95% CI: 0.59–0.75%) and highest in the Americas at 41.92% (95% CI: 37.95–46.09%). The global infection fatality rate was 10.73 (95% CI: 10.21–11.29) per 10,000 infections. Globally per 1000 infections, the infection acute-care bed hospitalization rate was 19.22 (95% CI: 18.73–19.51), the infection ICU bed hospitalization rate was 4.14 (95% CI: 4.10–4.18). If left unchecked with no vaccination and no other public health interventions, and assuming circulation of only wild-type variants and no variants of concern, the pandemic would eventually cause 8.18 million deaths (95% CI: 7.30–9.18), 163.67 million acute-care hospitalizations (95% CI: 148.12–179.51), and 33.01 million ICU hospitalizations (95% CI: 30.52–35.70), by the time the herd immunity threshold is reached at 60–70% infection exposure. The global population remained far below the herd immunity threshold by end of 2020. Global epidemiology reveals immense regional variation in infection exposure and morbidity and mortality rates.

Abstract Background Herpes simplex virus type 1 (HSV-1) is a prevalent lifelong infection that appears to be undergoing an epidemiologic transition in the United States (US). Using an analytical approach, this study aimed to characterize HSV-1 transitioning epidemiology and estimate its epidemiologic indicators, past, present, and future. Methods An age-structured mathematical model was developed to describe HSV-1 transmission through oral and sexual modes of transmission. The model was fitted to the National Health and Nutrition Examination Surveys, 1976–2016 data series. Results HSV-1 seroprevalence was projected to decline from 61.5% in 1970 to 54.8% in 2018, 48.5% in 2050, and 42.0% in 2100. In 30% for those aged 0–19 years, but 60. Meanwhile, the number of new infections per year (oral and genital) was persistent at 2,762,000 in 1970, 2,941,000 in 2018, 2,933,000 in 2050, and 2,960,000 in 2100. Of this total, genital acquisitions contributed 252,000 infections in 1970, 410,000 in 2018, 478,000 in 2050, and 440,000 in 2100—a quarter of which are symptomatic with clinical manifestations. For those aged 15–49 years, nearly 25% of incident infections are genital. Most genital acquisitions (> 85%) were due to oral-to-genital transmission through oral sex, as opposed to genital-to-genital transmission through sexual intercourse. Conclusion HSV-1 epidemiology is undergoing a remarkable transition in the US, with less exposure in childhood and more in adulthood, and less oral but more genital acquisition. HSV-1 will persist as a widely prevalent infection, with ever-increasing genital disease burden.

Background: Reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. SARS-CoV-2 reinfections were assessed in a cohort of antibody-positive persons in Qatar. Methods: All SARS-CoV-2 antibody-positive persons from April 16 to December 31, 2020 with a PCR-positive swab ≥14 days after the first-positive antibody test were investigated for evidence of reinfection. Viral genome sequencing was conducted for paired viral specimens to confirm reinfection. Incidence of reinfection was compared to incidence of infection in the complement cohort of those who were antibody-negative. Findings: Among 43,044 antibody-positive persons who were followed for a median of 16.3 weeks (range: 0–34.6), 314 individuals (0.7%) had at least one PCR positive swab ≥14 days after the first-positive antibody test. Of these individuals, 129 (41.1%) had supporting epidemiological evidence for reinfection. Reinfection was next investigated using viral genome sequencing. Applying the viral-genome-sequencing confirmation rate, the incidence rate of reinfection was estimated at 0.66 per 10,000 person-weeks (95% CI: 0.56–0.78). Incidence rate of reinfection versus month of follow-up did not show any evidence of waning of immunity for over seven months of follow-up. Meanwhile, in the complement cohort of 149,923 antibody-negative persons followed for a median of 17.0 weeks (range: 0–45.6), incidence rate of infection was estimated at 13.69 per 10,000 person-weeks (95% CI: 13.22–14.14). Efficacy of natural infection against reinfection was estimated at 95.2% (95% CI: 94.1–96.0%). Reinfections were less severe than primary infections. Only one reinfection was severe, two were moderate, and none were critical or fatal. Most reinfections (66.7%) were diagnosed incidentally through random or routine testing, or through contact tracing. Interpretation: Reinfection is rare in the young and international population of Qatar. Natural infection appears to elicit strong protection against reinfection with an efficacy ~95% for at least seven months. Funding: Biomedical Research Program, the Biostatistics, Epidemiology, and Biomathematics Research Core, and the Genomics Core, all at Weill Cornell Medicine-Qatar, the Ministry of Public Health, Hamad Medical Corporation, and the Qatar Genome Programme.

A novel coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China. This study aims to characterize key attributes of SARS-CoV-2 epidemiology as the infection emerged in China. An age-stratified mathematical model was constructed to describe transmission dynamics and estimate age-specific differences in biological susceptibility to infection, age-assortativeness in transmission mixing, and transition in rate of infectious contacts (and reproduction number R0) following introduction of mass interventions. The model estimated the infectious contact rate in early epidemic at 0.59 contacts/day (95% uncertainty interval-UI = 0.48–0.71). Relative to those 60–69 years, susceptibility was 0.06 in those ≤19 years, 0.34 in 20–29 years, 0.57 in 30–39 years, 0.69 in 40–49 years, 0.79 in 50–59 years, 0.94 in 70–79 years, and 0.88 in ≥80 years. Assortativeness in transmission mixing by age was limited at 0.004 (95% UI = 0.002–0.008). R0 rapidly declined from 2.1 (95% UI = 1.8–2.4) to 0.06 (95% UI = 0.05–0.07) following interventions' onset. Age appears to be a principal factor in explaining the transmission patterns in China. The biological susceptibility to infection seems limited among children but high among those >50 years. There was no evidence for differential contact mixing by age.

Objectives: Hepatitis C virus (HCV) clearance rate (fclearance) is defined as the proportion of infected persons who will spontaneously clear their infection after acute infection. We aimed to estimate fclearance using a novel approach that avoids limitations in existing estimates, and to clarify the link between fclearance and HCV viremic rate—the latter being the proportion of RNA positivity among those antibody positive. Methods: A mathematical model was developed to describe HCV transmission. fclearance was estimated by fitting the model to probability-based and nationally representative population-based data for Egypt (Egypt 2008 and Egypt 2015) and USA (NHANES A and NHANES B). Uncertainty and sensitivity analyses were conducted. Results: fclearance was estimated at 39.9% (95% uncertainty interval (UI): 34.3%–46.4%) and 33.5% (95% UI: 29.2%–38.3%) for Egypt 2008 and Egypt 2015 data, respectively; and at 29.6% (23.0%–37.1%) and 39.9% (31.2%–51.0%) for NHANES A and NHANES B data, respectively. fclearance was found related to HCV viremic rate through (approximately) the formula fclearance = 1.16 (1 − HCV viremic rate). HCV viremic rate was higher with higher risk of HCV exposure. Robustness of results was demonstrated in uncertainty and sensitivity analyses. Conclusion: One-third of HCV-infected persons clear their infection spontaneously, higher than earlier estimates—the immune-system capacity to clear HCV infection may have been underestimated. Keywords: Clearance rate, Viremic rate, Mathematical model, Infectious disease transmission, Epidemiology

Introduction: HIV epidemics in hard-to-reach high-risk subpopulations are often discovered years after epidemic emergence in settings with poor surveillance infrastructure. Using hypothesis-generation modeling, we aimed to investigate and demonstrate the concept of using routine HIV testing data to identify and characterize hidden epidemics in high-risk subpopulations. We also compared this approach to surveillance based on AIDS case notifications. Methods: A deterministic mathematical model was developed to simulate an emerging HIV epidemic in a high-risk subpopulation. A stochastic Monte Carlo simulation was implemented on the total population to simulate the sampling process of generating routine HIV testing data. Epidemiological measures were estimated on the simulated epidemic and on the generated testing sample. Sensitivity analyses were conducted on the results. Results: In the simulated epidemic, HIV prevalence saturated at 32% in the high-risk subpopulation and at 0.33% in the total population. The epidemic started its emerging-epidemic phase 28 years after infection introduction, and saturated 67 years after infection introduction. In the simulated HIV testing sample, a significant time trend in prevalence was identified, and the generated metrics of epidemic emergence and saturation were similar to those of the simulated epidemic. The epidemic was identified 4.0 (95% CI 3.4–4.6) years after epidemic emergence using routine HIV testing, but 29.7 (95% CI 15.8–52.1) years after emergence using AIDS case notifications. In the sensitivity analyses, none of the sampling biases affected the conclusion of an emerging epidemic, but some affected the estimated epidemic growth rate. Conclusions: Routine HIV testing data provides a tool to identify and characterize hidden and emerging epidemics in high-risk subpopulations. This approach can be specially useful in resource-limited settings, and can be applied alone, or along with other complementary data, to provide a meaningful characterization of emerging but hidden epidemics. Keywords: HIV, High-risk subpopulation, Surveillance, Mathematical modeling, Monte Carlo simulations, Epidemiology, Sexually transmitted infection

This study forecasts Coronavirus Disease 2019 (COVID-19) vaccination impact in two countries at different epidemic phases, the United States (US) and China. We assessed the impact of both a vaccine that prevents infection (VES of 95%) and a vaccine that prevents only disease (VEP of 95%) through mathematical modeling. For VES of 95% and gradual easing of restrictions, vaccination in the US reduced the peak incidence of infection, disease, and death by >55% and cumulative incidence by >32% and in China by >77% and >65%, respectively. Nearly three vaccinations were needed to avert one infection in the US, but only one was needed in China. For VEP of 95%, vaccination benefits were half those for VES of 95%. In both countries, impact of vaccination was substantially enhanced with rapid scale-up, vaccine coverage >50%, and slower or no easing of restrictions, particularly in the US. COVID-19 vaccination can flatten, delay, and/or prevent future epidemic waves. However, vaccine impact is destined to be heterogeneous across countries because of an underlying “epidemiologic inequity” that reduces benefits for countries already at high incidence, such as the US. Despite 95% efficacy, actual vaccine impact could be meager in such countries if vaccine scale-up is slow, acceptance is poor, or restrictions are eased prematurely.

This study aims to inform SARS-CoV-2 vaccine development/licensure/decision-making/implementation, using mathematical modeling, by determining key preferred vaccine product characteristics and associated population-level impacts of a vaccine eliciting long-term protection. A prophylactic vaccine with efficacy against acquisition (VES) ≥70% can eliminate the infection. A vaccine with VES VES of 50%, the number of vaccinated persons needed to avert one infection is 2.4, and the number is 25.5 to avert one severe disease case, 33.2 to avert one critical disease case, and 65.1 to avert one death. The probability of a major outbreak is zero at VES ≥70% regardless of the number of virus introductions. However, an increase in social contact rate among those vaccinated (behavior compensation) can undermine vaccine impact. In addition to the reduction in infection acquisition, developers should assess the natural history and disease progression outcomes when evaluating vaccine impact.

This study aims to inform herpes simplex virus type 2 (HSV-2) vaccine development, licensure, and implementation by delineating the population-level impact of vaccination. Mathematical models were constructed to describe the transmission dynamics in presence of prophylactic or therapeutic vaccines assuming 50% efficacy, with application to the United States. Catch-up prophylactic vaccination will reduce, by 2050, annual number of new infections by 58%, incidence rate by 60%, seroprevalence by 21%, and avert yearly as much as 350,000 infections. Number of vaccinations needed to avert one infection was only 50 by 2050, 34 by prioritizing those aged 15–19 years, 4 by prioritizing the highest sexual risk group, 43 by prioritizing women, and 47 by prioritizing men. Therapeutic vaccination of infected adults with symptomatic disease will reduce, by 2050, annual number of new infections by 12%, incidence rate by 13%, seroprevalence by 4%, and avert yearly as much as 76,000 infections. Number of vaccinations needed to avert one infection was eight by 2050, two by prioritizing those aged 15–19 years, three by prioritizing the highest sexual risk group, seven by prioritizing men, and ten by prioritizing women. HSV-2 vaccination offers an impactful and cost-effective intervention to prevent genital herpes medical and psychosexual disease burden.