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There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario. Despite the consensus that mass vaccination against SARS-CoV-2 will ultimately end the pandemic, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. Here, the authors investigate relaxation scenarios using an age-structured transmission model that has been fitted to data for Portugal.

The coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every country in the world since it first emerged in China in December 2019. Many countries have implemented social distancing as a measure to \"flatten the curve\" of the ongoing epidemics. Evaluation of the impact of government-imposed social distancing and of other measures to control further spread of COVID-19 is urgent, especially because of the large societal and economic impact of the former. The aim of this study was to compare the individual and combined effectiveness of self-imposed prevention measures and of short-term government-imposed social distancing in mitigating, delaying, or preventing a COVID-19 epidemic. We developed a deterministic compartmental transmission model of SARS-CoV-2 in a population stratified by disease status (susceptible, exposed, infectious with mild or severe disease, diagnosed, and recovered) and disease awareness status (aware and unaware) due to the spread of COVID-19. Self-imposed measures were assumed to be taken by disease-aware individuals and included handwashing, mask-wearing, and social distancing. Government-imposed social distancing reduced the contact rate of individuals irrespective of their disease or awareness status. The model was parameterized using current best estimates of key epidemiological parameters from COVID-19 clinical studies. The model outcomes included the peak number of diagnoses, attack rate, and time until the peak number of diagnoses. For fast awareness spread in the population, self-imposed measures can significantly reduce the attack rate and diminish and postpone the peak number of diagnoses. We estimate that a large epidemic can be prevented if the efficacy of these measures exceeds 50%. For slow awareness spread, self-imposed measures reduce the peak number of diagnoses and attack rate but do not affect the timing of the peak. Early implementation of short-term government-imposed social distancing alone is estimated to delay (by at most 7 months for a 3-month intervention) but not to reduce the peak. The delay can be even longer and the height of the peak can be additionally reduced if this intervention is combined with self-imposed measures that are continued after government-imposed social distancing has been lifted. Our analyses are limited in that they do not account for stochasticity, demographics, heterogeneities in contact patterns or mixing, spatial effects, imperfect isolation of individuals with severe disease, and reinfection with COVID-19. Our results suggest that information dissemination about COVID-19, which causes individual adoption of handwashing, mask-wearing, and social distancing, can be an effective strategy to mitigate and delay the epidemic. Early initiated short-term government-imposed social distancing can buy time for healthcare systems to prepare for an increasing COVID-19 burden. We stress the importance of disease awareness in controlling the ongoing epidemic and recommend that, in addition to policies on social distancing, governments and public health institutions mobilize people to adopt self-imposed measures with proven efficacy in order to successfully tackle COVID-19.

To escape immune recognition in previously infected hosts, viruses evolve genetically in immunologically important regions. The host's immune system responds by generating new memory cells recognizing the mutated viral strains. Despite recent advances in data collection and analysis, it remains conceptually unclear how epidemiology, immune response, and evolutionary factors interact to produce the observed speed of evolution and the incidence of infection. Here we establish a general and simple relationship between long-term cross-immunity, genetic diversity, speed of evolution, and incidence. We develop an analytic method fusing the standard epidemiological susceptible-infected-recovered approach and the modern virus evolution theory. The model includes the factors of strain selection due to immune memory cells, random genetic drift, and clonal interference effects. We predict that the distribution of recovered individuals in memory serotypes creates a moving fitness landscape for the circulating strains which drives antigenic escape. The fitness slope (effective selection coefficient) is proportional to the reproductive number in the absence of immunity R0 and inversely proportional to the cross-immunity distance a, defined as the genetic distance of a virus strain from a previously infecting strain conferring 50% decrease in infection probability. Analysis predicts that the evolution rate increases linearly with the fitness slope and logarithmically with the genomic mutation rate and the host population size. Fitting our analytic model to data obtained for influenza A H3N2 and H1N1, we predict the annual infection incidence within a previously estimated range, (4-7)%, and the antigenic mutation rate of Ub = (5 - 8) ⋅ 10(-4) per transmission event per genome. Our prediction of the cross-immunity distance of a = (14 - 15) aminoacid substitutions agrees with independent data for equine influenza.

The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures at different time points during the COVID-19 pandemic in the Netherlands. Our analyses suggest that the impact of measures reducing school-based contacts depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce the effective reproduction number ( R e ) with non-school-based measures are exhausted or undesired and R e is still close to 1, the additional benefit of school-based measures may be considerable, particularly among older school children. As two examples, we demonstrate that keeping schools closed after the summer holidays in 2020, in the absence of other measures, would not have prevented the second pandemic wave in autumn 2020 but closing schools in November 2020 could have reduced R e below 1, with unchanged non-school-based contacts. The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. Here, the authors use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures during the COVID-19 pandemic in the Netherlands.

Once the first SARS-CoV-2 vaccine became available, mass vaccination was the main pillar of the public health response to the COVID-19 pandemic. It was very effective in reducing hospitalizations and deaths. Here, we discuss the possibility that mass vaccination might accelerate SARS-CoV-2 evolution in antibody-binding regions compared to natural infection at the population level. Using the evidence of strong genetic variation in antibody-binding regions and taking advantage of the similarity between the envelope proteins of SARS-CoV-2 and influenza, we assume that immune selection pressure acting on these regions of the two viruses is similar. We discuss the consequences of this assumption for SARS-CoV-2 evolution in light of mathematical models developed previously for influenza. We further outline the implications of this phenomenon, if our assumptions are confirmed, for the future design of SARS-CoV-2 vaccination strategies. Rouzine and Rozhnova discuss the potential consequences of vaccination on the antigenic evolution of the SARS-CoV-2 virus. The authors outline the possibility of its acceleration by mass vaccination and considerations for future vaccination strategies.

[This corrects the article DOI: 10.1371/journal.ppat.1007291.].[This corrects the article DOI: 10.1371/journal.ppat.1007291.].

HIV risk perception plays a crucial role in the uptake of preventive strategies. We investigated how risk perception and its determinants changed between 1999 and 2018 in an open, prospective cohort of 1323 HIV-negative men who have sex with men (MSM). Risk perception, defined as the perceived likelihood of acquiring HIV in the past 6 months, changed over time: being relatively lower in 2008–2011, higher in 2012–2016, and again lower in 2017–2018. Irrespective of calendar year, condomless anal intercourse (AI) with casual partners and high numbers of partners were associated with higher risk perception. In 2017–2018, condomless receptive AI with a partner living with HIV was no longer associated with risk perception, while PrEP use and condomless AI with a steady partner were associated with lower risk perception. We showed that risk perception has fluctuated among MSM in the past 20 years. The Undetectable equals Untransmittable statement and PrEP coincided with lower perceived risk.

The number of new HIV infections among men who have sex with men (MSM) in the Netherlands has been decreasing, but additional efforts are required to bring it further down. This study aims to assess the impact of increased diagnosis of early HIV infection combined with immediate antiretroviral treatment (ART) initiation on reducing HIV transmission among MSM. We developed an agent-based model calibrated to HIV surveillance and sexual behavior data for MSM in the Netherlands in 2017-2022. Starting in 2023, we simulated a 10-year intervention that accelerates HIV diagnosis during the first 3 or 6 months after HIV acquisition across five levels of increased diagnosis rates (2, 4, 8, 16, and 32-fold), followed by immediate ART initiation. The upper limit of the intervention’s impact over 10 years is projected to result in the cumulative 298 (95-th QI: 162–451) HIV infections averted. A 32-fold increase in the diagnosis rate within 3 months after HIV acquisition (corresponding to 100% of all new HIV infections diagnosed within 3 months of acquisition) results in 269 (95-th QI: 147–400) infections averted, approaching closely maximum impact. By extending the scope of the intervention to individuals who acquired HIV infection within the previous 6 months, a smaller 8-fold increase in the diagnosis rate (corresponding to 97% of new HIV infections diagnosed within 6 months of acquisition) approaches closely the maximum impact of the intervention by averting 256 (95-th QI: 122–411) HIV infections. Our sensitivity analyses showed that, in an epidemiological context similar to the modern-day the Netherlands, immediate initiation of ART accompanying accelerated diagnosis of individuals with early HIV infection does not significantly affect HIV transmission dynamics. Accelerating early HIV diagnosis through increased awareness, screening, and testing can further reduce transmission among MSM. Meeting this goal necessitates a stakeholder needs assessment.

The development of an HIV cure is a global health priority, with the target product profile (TPP) for an HIV cure guiding research efforts. Using a mathematical model calibrated to data from men who have sex with men (MSM) in the Netherlands, we assessed whether an effective cure could help end the HIV epidemic. Following the TPP, we evaluated two scenarios: (i) HIV remission, where the virus is suppressed in an individual without ongoing antiretroviral therapy (ART) but may rebound, and (ii) HIV eradication, which aims to completely remove the virus from the individual. Here, we show that sustained HIV remission (without rebound) or HIV eradication could reduce new HIV infections compared to a scenario without a cure. In contrast, transient HIV remission with a risk of rebound could increase new infections if rebounds are not closely monitored, potentially undermining HIV control efforts. Our findings emphasize the critical role of cure characteristics in maximizing cure benefits for public health and highlight the need to align HIV cure research with public health objectives to end the HIV epidemic. Development of an HIV cure is a global health priority and the target product profile for a cure has been set. Here, the authors use mathematical modelling to assess the potential impacts of cures with different characteristics on HIV transmission dynamics using data from the Netherlands.

Household studies provide an efficient means to study transmission of infectious diseases, enabling estimation of susceptibility and infectivity by person-type. A main inclusion criterion in such studies is usually the presence of an infected person. This precludes estimation of the hazards of pathogen introduction into the household. Here we estimate age- and time-dependent household introduction hazards together with within household transmission rates using data from a prospective household-based study in the Netherlands. A total of 307 households containing 1,209 persons were included from August 2020 until March 2021. Follow-up of households took place between August 2020 and August 2021 with maximal follow-up per household mostly limited to 161 days. Almost 1 out of 5 households (59/307) had evidence of an introduction of SARS-CoV-2. We estimate introduction hazards and within-household transmission rates in our study population with penalized splines and stochastic epidemic models, respectively. The estimated hazard of introduction of SARS-CoV-2 in the households was lower for children (0-12 years) than for adults (relative hazard: 0.62; 95%CrI: 0.34-1.0). Estimated introduction hazards peaked in mid October 2020, mid December 2020, and mid April 2021, preceding peaks in hospital admissions by 1-2 weeks. Best fitting transmission models included increased infectivity of children relative to adults and adolescents, such that the estimated child-to-child transmission probability (0.62; 95%CrI: 0.40-0.81) was considerably higher than the adult-to-adult transmission probability (0.12; 95%CrI: 0.057-0.19). Scenario analyses indicate that vaccination of adults can strongly reduce household infection attack rates and that adding adolescent vaccination offers limited added benefit.