Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.

For the COVID-19 pandemic, viral transmission has been documented in many historical and geographical contexts. Nevertheless, few studies have explicitly modeled the spatiotemporal flow based on genetic sequences, to develop mitigation strategies. Additionally, thousands of SARS-CoV-2 genomes have been sequenced with associated records, potentially providing a rich source for such spatiotemporal analysis, an unprecedented amount during a single outbreak. Here, in a case study of seven states, we model the first wave of the outbreak by determining regional connectivity from phylogenetic sequence information (i.e. "genetic connectivity"), in addition to traditional epidemiologic and demographic parameters. Our study shows nearly all of the initial outbreak can be traced to a few lineages, rather than disconnected outbreaks, indicative of a mostly continuous initial viral flow. While the geographic distance from hotspots is initially important in the modeling, genetic connectivity becomes increasingly significant later in the first wave. Moreover, our model predicts that isolated local strategies (e.g. relying on herd immunity) can negatively impact neighboring regions, suggesting more efficient mitigation is possible with unified, cross-border interventions. Finally, our results suggest that a few targeted interventions based on connectivity can have an effect similar to that of an overall lockdown. They also suggest that while successful lockdowns are very effective in mitigating an outbreak, less disciplined lockdowns quickly decrease in effectiveness. Our study provides a framework for combining phylodynamic and computational methods to identify targeted interventions.

Impact of tiered measures on social contact and mixing patterns of in Italy during the second wave of COVID-19.

BACKGROUND: Most countries around the world enforced non-pharmaceutical interventions against COVID-19. Italy was one of the first countries to be affected by the pandemic, imposing a hard lockdown, in the first epidemic wave. During the second wave, the country implemented progressively restrictive tiers at the regional level according to weekly epidemiological risk assessments. This paper quantifies the impact of these restrictions on contacts and on the reproduction number. METHODS: Representative (with respect to age, sex, and region of residence) longitudinal surveys of the Italian population were undertaken during the second epidemic wave. Epidemiologically relevant contact patterns were measured and compared with pre-pandemic levels and according to the level of interventions experienced by the participants. Contact matrices were used to quantify the reduction in the number of contacts by age group and contact setting. The reproduction number was estimated to evaluate the impact of restrictions on the spread of COVID-19. RESULTS: The comparison with the pre-pandemic baseline shows a significant decrease in the number of contacts, independently from the age group or contact settings. This decrease in the number of contacts significantly depends on the strictness of the non-pharmaceutical interventions. For all levels of strictness considered, the reduction in social mixing results in a reproduction number smaller than one. In particular, the impact of the restriction on the number of contacts decreases with the severity of the interventions. CONCLUSIONS: The progressive restriction tiers implemented in Italy reduced the reproduction number, with stricter interventions associated with higher reductions. Readily collected contact data can inform the implementation of mitigation measures at the national level in epidemic emergencies to come.

Pediatric asthma control during the COVID-19 pandemic.

BACKGROUND: The lockdown imposed by the COVID-19 pandemic resulted in a completely different style of life with possible effects on the attitude toward their disease in patients with chronic lung disease, such as asthma. The aim of our study was to investigate in asthmatic children the level of asthma control and the maintenance therapy used during the lockdown. METHODS: Among asthmatic children attending our clinic, we identified those who had been prescribed the same therapy in March-April 2019 and March-April 2020. The level of asthma control (GINA-score) and the maintenance therapy used during the lockdown (March-April 2020) were compared with those of March-April 2019. We separately analyzed a small group of children with severe asthma treated with Omalizumab during the lockdown. RESULTS: We enrolled 92 asthmatic children (67 males). Compared to 2019, in 2020 a higher proportion of children modified their maintenance therapy (38% vs. 15.2%, p < .001), with a significant increase in both the proportion of children who increased (p = .033) and in that of children who decreased their therapy (p = .026). The level of control resulted as significantly higher in 2020 (March p = .023; April p = .007). Also, the 13 children treated with Omalizumab showed a good level of control in 2020. CONCLUSIONS: In asthmatic children, the COVID-19 pandemic lockdown had a significant impact on their asthma control and on their attitude toward maintenance therapy.

Environmental and Mobility Strategies During Early COVID-19: Insights From an Empirical Study Focusing on Park Visitations in El Paso, TX.

OBJECTIVES: We explored the importance of environmental and mobility strategies during early COVID-19 by age and ethnicity and investigated predictors of park visitations considering the COVID-19 impacts. BACKGROUND: Parks are safe and accessible venues to stay active and reduce social isolation, which is especially important considering COVID-19 and the associated lockdowns. METHODS: We analyzed online survey data from 683 residents (collected July 2020) of El Paso, TX, and objective measures of neighborhood park characteristics. Chi-square tests and mixed-effects logistic regression analyses were performed to examine the environmental/mobility strategies, personal and environmental factors, and park visitations, considering the COVID-19 impacts. RESULTS: The percentage of those who visited (1+ times/week) parks or trails/paths in the neighborhood dropped from 41.7% to 19.5% since the start of COVID-19 (OR = 0.015, p < .001). Before COVID-19, middle-aged and older adults were less likely to visit parks than younger adults, while this difference became insignificant during early COVID-19. Hispanic adults were more likely to visit parks than non-Hispanics both before and during early COVID-19. Positive environmental predictors of park visitations included park availability in the neighborhood, proximity to the closest park, seeing people being physically active in the neighborhood, and neighborhood aesthetics. CONCLUSIONS: Proximately located parks, trails, and paths well integrated into residential communities, and high aesthetic quality of the neighborhood are the potential features of pandemic-resilient communities and should be considered an important national priority to maintain and promote the health and well-being of the population, especially during pandemics like COVID-19.

Comparative analysis of prevention and control measures toward COVID-19 epidemic between Shanghai and Beijing.

Purpose: By serving and providing a guide for other regional places, this study aims to advance and guide the epidemic prevention and control methods, and practices and strengthen people's ability to respond to COVID-19 and other future potential public health risks. Design/methodology/approach: A comparative analysis was conducted that the COVID-19 epidemic development trend and prevention and control effects both in Beijing and Shanghai. In fact, regarding the COVID-19 policy and strategic areas, the differences between governmental, social, and professional management were discussed and explored. To prevent and be ready for potential pandemics, experience and knowledge were used and summarized. Findings: The strong attack of the Omicron variant in early 2022 has posed challenges to epidemic prevention and control practices in many Chinese cities. Shanghai, which had achieved relatively good performance in the fight against the epidemic, has exposed limitations in its epidemic prevention and control system in the face of Omicron. In fact, the city of Beijing has undertaken prompt and severe lockdown measures and achieved rather good results in epidemic prevention and control because of learning from Shanghai's experience and lessons; adhering to the overall concept of "dynamic clearing," implementing precise prevention and monitoring, enhancing community control, and making emergency plans and preparations. All these actions and measures are still essential in the shift from pandemic response to pandemic control. Research limitations/implications: Different places have introduced different urgent policies to control the spread of the pandemic. Strategies to control COVID-19 have often been based on preliminary and limited data and have tended to be slow to evolve as new evidence emerges. Hence, the effects of these anti-epidemic policies need to be further tested.

COVID-19 epidemic phases and morbidity in different areas of Chinese mainland, 2020.

Background: In the early stage of COVID-19 epidemic, the Chinese mainland once effectively controlled the epidemic, but COVID-19 eventually spread faster and faster in the world. The purpose of this study is to clarify the differences in the epidemic data of COVID-19 in different areas and phases in Chinese mainland in 2020, and to analyze the possible factors affecting the occurrence and development of the epidemic. Methods: We divided the Chinese mainland into areas I, I and III, and divided the epidemic process into phases I to IV: limited cases, accelerated increase, decelerated increase and containment phases. We also combined phases II and III as outbreak phase. The epidemic data included the duration of different phases, the numbers of confirmed cases, asymptomatic infections, and the proportion of imported cases from abroad. Results: In area I, II and III, only area I has a Phase I, and the Phase II and III of area I are longer. In Phase IV, there is a 17-day case clearing period in area I, while that in area II and III are 2 and 0 days, respectively. In phase III or the whole outbreak phase, the average daily increase of confirmed cases in area I was higher than that in areas II and III (P = 0.009 and P = 0.001 in phase III; P = 0.034 and P = 0.002 in the whole outbreak phase), and the average daily in-hospital cases were most in area I and least in area III (P = 0.000, P = 0.000, and P = 0.000 in phase III; P = 0.000, P = 0.000, and P = 0.009 in the whole outbreak phase). The average number of daily in-hospital COVID-19 cases in phase III was more than that in phase II in each area (P = 0.000, P = 0.000, and P = 0.001). In phase IV, from March 18, 2020 to January 1, 2021, the increase of confirmed cases in area III was higher than areas I and II (both P = 0.000), and the imported cases from abroad in Chinese mainland accounted for more than 55-61%. From June 16 to July 2, 2020, the number of new asymptomatic infections in area III was higher than that in area II (P = 0.000), while there was zero in area I. From July 3, 2020 to January 1, 2021, the increased COVID-19 cases in area III were 3534, while only 14 and 0, respectively, in areas I and II. Conclusions: The worst epidemic areas in Chinese mainland before March 18, 2020 and after June 15, 2020 were area I and area III, respectively, and area III had become the main battlefield for Chinese mainland to fight against imported epidemic since March 18, 2020. In Wuhan, human COVID-19 infection might occur before December 8, 2019, while the outbreak might occur before January 16 or even 10, 2020. Insufficient understanding of COVID-19 hindered the implementation of early effective isolation measures, leading to COVID-19 outbreak in Wuhan, and strict isolation measures were effective in controlling the epidemic. The import of foreign COVID-19 cases has made it difficult to control the epidemic of area III. When humans are once again faced with potentially infectious new diseases, it is appropriate to first and foremost take strict quarantine measures as soon as possible, and mutual cooperation between regions should be explored to combat the epidemic.

Determinants of malaria infections among children in refugee settlements in Uganda during 2018-2019.

BACKGROUND: While 5% of 247 million global malaria cases are reported in Uganda, it is also a top refugee hosting country in Africa, with over 1.36 million refugees. Despite malaria being an emerging challenge for humanitarian response in refugee settlements, little is known about its risk factors. This study aimed to investigate the risk factors for malaria infections among children under 5 years of age in refugee settlements in Uganda. METHODS: We utilized data from Uganda's Malaria Indicator Survey which was conducted between December 2018 and February 2019 at the peak of malaria season. In this national survey, household level information was obtained using standardized questionnaires and a total of 7787 children under 5 years of age were tested for malaria using mainly the rapid diagnostic test. We focused on 675 malaria tested children under five in refugee settlements located in Yumbe, Arua, Adjumani, Moyo, Lamwo, Kiryadongo, Kyegegwa, Kamwenge and Isingiro districts. The extracted variables included prevalence of malaria, demographic, social-economic and environmental information. Multivariable logistic regression was used to identify and define the malaria associated risk factors. RESULTS: Overall, malaria prevalence in all refugee settlements across the nine hosting districts was 36.6%. Malaria infections were higher in refugee settlements located in Isingiro (98.7%), Kyegegwa (58.6%) and Arua (57.4%) districts. Several risk factors were significantly associated with acquisition of malaria including fetching water from open water sources [adjusted odds ratio (aOR) = 1.22, 95% CI: 0.08-0.59, P = 0.002], boreholes (aOR = 2.11, 95% CI: 0.91-4.89, P = 0.018) and water tanks (aOR = 4.47, 95% CI: 1.67-11.9, P = 0.002). Other factors included pit-latrines (aOR = 1.48, 95% CI: 1.03-2.13, P = 0.033), open defecation (aOR = 3.29, 95% CI: 1.54-7.05, P = 0.002), lack of insecticide treated bed nets (aOR = 1.15, 95% CI: 0.43-3.13, P = 0.003) and knowledge on the causes of malaria (aOR = 1.09, 95% CI: 0.79-1.51, P = 0.005). CONCLUSIONS: The persistence of the malaria infections were mainly due to open water sources, poor hygiene, and lack of preventive measures that enhanced mosquito survival and infection. Malaria elimination in refugee settlements requires an integrated control approach that combines environmental management with other complementary measures like insecticide treated bed nets, indoor residual spraying and awareness.

Mental Health Risks after Repeated Exposure to Multiple Stressful Events during Ongoing Social Unrest and Pandemic in Hong Kong: The Role of Rumination: Risques pour la santé mentale après une exposition répétée à de multiples événements stressants d'agitation sociale durable et de pandémie à Hong Kong: le rôle de la rumination.

OBJECTIVES: The co-occurrence of different classes of population-level stressors, such as social unrest and public health crises, is common in contemporary societies. Yet, few studies explored their combined mental health impact. The aim of this study was to examine the impact of repeated exposure to social unrest-related traumatic events (TEs), coronavirus disease 2019 (COVID-19) pandemic-related events (PEs), and stressful life events (SLEs) on post-traumatic stress disorder (PTSD) and depressive symptoms, and the potential mediating role of event-based rumination (rumination of TEs-related anger, injustice, guilt, and insecurity) between TEs and PTSD symptoms. METHODS: Community members in Hong Kong who had utilized a screening tool for PTSD and depressive symptoms were invited to complete a survey on exposure to stressful events and event-based rumination. RESULTS: A total of 10,110 individuals completed the survey. Hierarchical regression analysis showed that rumination, TEs, and SLEs were among the significant predictors for PTSD symptoms (all P < 0.001), accounting for 32% of the variance. For depression, rumination, SLEs, and PEs were among the significant predictors (all P < 0.001), explaining 24.9% of the variance. Two-way analysis of variance of different recent and prior TEs showed significant dose-effect relationships. The effect of recent TEs on PTSD symptoms was potentiated by prior TEs (P = 0.005). COVID-19 PEs and prior TEs additively contributed to PTSD symptoms, with no significant interaction (P = 0.94). Meanwhile, recent TEs were also potentiated by SLEs (P = 0.002). The effects of TEs on PTSD symptoms were mediated by rumination (ß = 0.38, standard error = 0.01, 95% confidence interval: 0.36 to 0.41), with 40.4% of the total effect explained. All 4 rumination subtypes were significant mediators. CONCLUSIONS: Prior and ongoing TEs, PEs, and SLEs cumulatively exacerbated PTSD and depressive symptoms. The role of event-based rumination and their interventions should be prioritized for future research.

Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland.

Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between 28 February and 20 March 2020. Estimates of the impact of these interventions on SARS-CoV-2 transmission are critical for decision making in this and future outbreaks. We here aim to assess the impact of these NPIs on disease transmission by estimating changes in the basic reproduction number (R0) at national and cantonal levels in relation to the timing of these NPIs. We estimated the time-varying R0 nationally and in eleven cantons by fitting a stochastic transmission model explicitly simulating within-hospital dynamics. We used individual-level data from more than 1000 hospitalised patients in Switzerland and public daily reports of hospitalisations and deaths. We estimated the national R0 to be 2.8 (95% confidence interval 2.1–3.8) at the beginning of the epidemic. Starting from around 7 March, we found a strong reduction in time-varying R0 with a 86% median decrease (95% quantile range [QR] 79–90%) to a value of 0.40 (95% QR 0.3–0.58) in the period of 29 March to 5 April. At the cantonal level, R0 decreased over the course of the epidemic between 53% and 92%. Reductions in time-varying R0 were synchronous with changes in mobility patterns as estimated through smartphone activity, which started before the official implementation of NPIs. We inferred that most of the reduction of transmission is attributable to behavioural changes as opposed to natural immunity, the latter accounting for only about 4% of the total reduction in effective transmission. As Switzerland considers relaxing some of the restrictions of social mixing, current estimates of time-varying R0 well below one are promising. However, as of 24 April 2020, at least 96% (95% QR 95.7–96.4%) of the Swiss population remains susceptible to SARS-CoV-2. These results warrant a cautious relaxation of social distance practices and close monitoring of changes in both the basic and effective reproduction numbers.

Comparative effectiveness of contact tracing interventions in the context of the COVID-19 pandemic: a systematic review.

Contact tracing is a non-pharmaceutical intervention (NPI) widely used in the control of the COVID-19 pandemic. Its effectiveness may depend on a number of factors including the proportion of contacts traced, delays in tracing, the mode of contact tracing (e.g. forward, backward or bidirectional contact training), the types of contacts who are traced (e.g. contacts of index cases or contacts of contacts of index cases), or the setting where contacts are traced (e.g. the household or the workplace). We performed a systematic review of the evidence regarding the comparative effectiveness of contact tracing interventions. 78 studies were included in the review, 12 observational (ten ecological studies, one retrospective cohort study and one pre-post study with two patient cohorts) and 66 mathematical modelling studies. Based on the results from six of the 12 observational studies, contact tracing can be effective at controlling COVID-19. Two high quality ecological studies showed the incremental effectiveness of adding digital contact tracing to manual contact tracing. One ecological study of intermediate quality showed that increases in contact tracing were associated with a drop in COVID-19 mortality, and a pre-post study of acceptable quality showed that prompt contact tracing of contacts of COVID-19 case clusters / symptomatic individuals led to a reduction in the reproduction number R. Within the seven observational studies exploring the effectiveness of contact tracing in the context of the implementation of other non-pharmaceutical interventions, contact tracing was found to have an effect on COVID-19 epidemic control in two studies and not in the remaining five studies. However, a limitation in many of these studies is the lack of description of the extent of implementation of contact tracing interventions. Based on the results from the mathematical modelling studies, we identified the following highly effective policies: (1) manual contact tracing with high tracing coverage and either medium-term immunity, highly efficacious isolation/quarantine and/ or physical distancing (2) hybrid manual and digital contact tracing with high app adoption with highly effective isolation/ quarantine and social distancing, (3) secondary contact tracing, (4) eliminating contact tracing delays, (5) bidirectional contact tracing, (6) contact tracing with high coverage in reopening educational institutions. We also highlighted the role of social distancing to enhance the effectiveness of some of these interventions in the context of 2020 lockdown reopening. While limited, the evidence from observational studies shows a role for manual and digital contact tracing in controlling the COVID-19 epidemic. More empirical studies accounting for the extent of contact tracing implementation are required.

Assessment of 2021/22 influenza epidemic scenarios in Italy during SARS-CoV-2 outbreak.

Global mitigation strategies to tackle the threat posed by SARS-CoV-2 have produced a significant decrease of the severity of 2020/21 seasonal influenza, which might result in a reduced population natural immunity for the upcoming 2021/22 influenza season. To predict the spread of influenza virus in Italy and the impact of prevention and control measures, we present an age-structured Susceptible-Exposed-Infectious-Removed (SEIR) model including the role of social mixing patterns and the impact of age-stratified vaccination strategies and Non-Pharmaceutical Interventions (NPIs) such as school closures, partial lockdown, as well as the adoption of personal protective equipment and the practice of hand hygiene. We find that vaccination campaigns with standard coverage would produce a remarkable mitigation of the spread of the disease in moderate influenza seasons, making the adoption of NPIs unnecessary. However, in case of severe seasonal epidemics, a standard vaccination coverage would not be sufficiently effective in fighting the epidemic, thus implying that a combination with the adoption of NPIs is necessary to contain the disease. Alternatively, our results show that the enhancement of the vaccination coverage would reduce the need to adopt NPIs, thus limiting the economic and social impacts that NPIs might produce. Our results highlight the need to respond to the influenza epidemic by strengthening the vaccination coverage.

Stemming the Shadow Pandemic: Integrating Sociolegal Services in Contact Tracing and Beyond.

The COVID-19 pandemic has shed light on the challenges of complying with public health guidance to isolate or quarantine without access to adequate income, housing, food, and other resources. When people cannot safely isolate or quarantine during an outbreak of infectious disease, a critical public health strategy fails. This article proposes integrating sociolegal needs screening and services into contact tracing as a way to mitigate public health harms and pandemic-related health inequities.

A Novel Social Distancing Approach for Limiting the Number of Vehicles in Smart Buildings Using LiFi Hybrid-Network.

The coronavirus (COVID-19) has arisen as one of the most severe problems due to its ongoing mutations as well as the absence of a suitable cure for this virus. The virus primarily spreads and replicates itself throughout huge groups of individuals through daily touch, which regretfully can happen in several unanticipated way. As a result, the sole viable attempts to constrain the spread of this new virus are to preserve social distance, perform contact tracing, utilize suitable safety gear, and enforce quarantine measures. In order to control the virus's proliferation, scientists and officials are considering using several social distancing models to detect possible diseased individuals as well as extremely risky areas to sustain separation and lockdown procedures. However, models and systems in the existing studies heavily depend on the human factor only and reveal serious privacy vulnerabilities. In addition, no social distancing model/technique was found for monitoring, tracking, and scheduling vehicles for smart buildings as a social distancing approach so far. In this study, a new system design that performs real-time monitoring, tracking, and scheduling of vehicles for smart buildings is proposed for the first time named the social distancing approach for limiting the number of vehicles (SDA-LNV). The proposed model employs LiFi technology as a wireless transmission medium for the first time in the social distance (SD) approach. The proposed work is considered as Vehicle-to-infrastructure (V2I) communication. It might aid authorities in counting the volume of likely affected people. In addition, the proposed system design is expected to help reduce the infection rate inside buildings in areas where traditional social distancing techniques are not used or applicable.