DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.

In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations. Moreover, tree topology and the incorporation of population parameters (phylodynamics) can be useful in reconstructing the evolutionary dynamics of an epidemic across space and time among individuals. We now demonstrate the utility of phylodynamic trees for transmission modeling and forecasting, developing a phylogeny-based deep learning system, referred to as DeepDynaForecast. Our approach leverages a primal-dual graph learning structure with shortcut multi-layer aggregation, which is suited for the early identification and prediction of transmission dynamics in emerging high-risk groups. We demonstrate the accuracy of DeepDynaForecast using simulated outbreak data and the utility of the learned model using empirical, large-scale data from the human immunodeficiency virus epidemic in Florida between 2012 and 2020. Our framework is available as open-source software (MIT license) at github.com/lab-smile/DeepDynaForcast.

Neurovascular Complications of Iatrogenic Fusarium solani Meningitis.

A multinational outbreak of nosocomial fusarium meningitis occurred among immunocompetent patients who had undergone surgery with epidural anesthesia in Mexico. The pathogen involved had a high predilection for the brain stem and vertebrobasilar arterial system and was associated with high mortality from vessel injury. Effective treatment options remain limited; in vitro susceptibility testing of the organism suggested that it is resistant to all currently approved antifungal medications in the United States. To highlight the severe complications associated with fusarium infection acquired in this manner, we report data, clinical courses, and outcomes from 13 patients in the outbreak who presented with symptoms after a median delay of 39 days.

From "Immunity Debt" to "Immunity Theft"-How COVID-19 Might Be Tied to Recent Respiratory Disease Surges.

This Medical News story discusses the relationship between the COVID-19 pandemic and recent increases in other respiratory diseases.

The episodic resurgence of highly pathogenic avian influenza H5 virus.

Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, increasingly causing mass mortality in wild birds and poultry and incidental infections in mammals1-3. However, the ecological and virological properties that underscore future mitigation strategies still remain unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the origins of resurgent HPAI H5 and reveal significant shifts in virus ecology and evolution. Outbreak data show key resurgent events in 2016-2017 and 2020-2021, contributing to the emergence and panzootic spread of H5N1 in 2021-2022. Genomic analysis reveals that the 2016-2017 epizootics originated in Asia, where HPAI H5 reservoirs are endemic. In 2020-2021, 2.3.4.4b H5N8 viruses emerged in African poultry, featuring mutations altering HA structure and receptor binding. In 2021-2022, a new H5N1 virus evolved through reassortment in wild birds in Europe, undergoing further reassortment with low-pathogenic avian influenza in wild and domestic birds during global dissemination. These results highlight a shift in the HPAI H5 epicentre beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential. As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic-bird-wild-bird interface. Elimination strategies in domestic birds therefore remain a high priority to limit future epizootics.

Study of efficacy and antibody duration to fourth-dose booster of Ad5-nCoV or inactivated SARS-CoV-2 vaccine in Chinese adults: a prospective cohort study.

Introduction: China experienced a record surge of coronavirus disease 2019 cases in December 2022, during the pandemic. Methods: We conducted a randomized, parallel-controlled prospective cohort study to evaluate efficacy and antibody duration after a fourth-dose booster with Ad5-nCoV or inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine. Results: A total of 191 participants aged ≥18 years who had completed a three-dose regimen of the inactivated SARS-CoV-2 vaccine 6 months earlier were recruited to receive the intramuscular Ad5-nCoV booster or the inactivated SARS-CoV-2 vaccine. The Ad5-nCoV group had significantly higher antibody levels compared with the inactivated vaccine group at 6 months after the fourth vaccination dose. After the pandemic, the breakthrough infection rate for the Ad5-nCoV and the inactivated vaccine groups was 77.89% and 78.13%, respectively. Survival curve analysis (p = 0.872) and multivariable logistic regression analysis (p = 0.956) showed no statistically significant differences in breakthrough infection between the two groups. Discussion: Compared with a homologous fourth dose, a heterologous fourth dose of Ad5-nCoV elicited a higher immunogenic response in healthy adults who had been immunized with three doses of inactivated vaccine. Nevertheless, the efficacy of the two vaccine types was equivalent after the pandemic.

Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda.

IMPORTANCE: Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013-2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.

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.

Covid-19 Surveillance Testing and Resident Outcomes in Nursing Homes.

BACKGROUND: Despite widespread adoption of surveillance testing for coronavirus disease 2019 (Covid-19) among staff members in skilled nursing facilities, evidence is limited regarding its relationship with outcomes among facility residents. METHODS: Using data obtained from 2020 to 2022, we performed a retrospective cohort study of testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among staff members in 13,424 skilled nursing facilities during three pandemic periods: before vaccine approval, before the B.1.1.529 (omicron) variant wave, and during the omicron wave. We assessed staff testing volumes during weeks without Covid-19 cases relative to other skilled nursing facilities in the same county, along with Covid-19 cases and deaths among residents during potential outbreaks (defined as the occurrence of a case after 2 weeks with no cases). We reported adjusted differences in outcomes between high-testing facilities (90th percentile of test volume) and low-testing facilities (10th percentile). The two primary outcomes were the weekly cumulative number of Covid-19 cases and related deaths among residents during potential outbreaks. RESULTS: During the overall study period, 519.7 cases of Covid-19 per 100 potential outbreaks were reported among residents of high-testing facilities as compared with 591.2 cases among residents of low-testing facilities (adjusted difference, -71.5; 95% confidence interval [CI], -91.3 to -51.6). During the same period, 42.7 deaths per 100 potential outbreaks occurred in high-testing facilities as compared with 49.8 deaths in low-testing facilities (adjusted difference, -7.1; 95% CI, -11.0 to -3.2). Before vaccine availability, high- and low-testing facilities had 759.9 cases and 1060.2 cases, respectively, per 100 potential outbreaks (adjusted difference, -300.3; 95% CI, -377.1 to -223.5), along with 125.2 and 166.8 deaths (adjusted difference, -41.6; 95% CI, -57.8 to -25.5). Before the omicron wave, the numbers of cases and deaths were similar in high- and low-testing facilities; during the omicron wave, high-testing facilities had fewer cases among residents, but deaths were similar in the two groups. CONCLUSIONS: Greater surveillance testing of staff members at skilled nursing facilities was associated with clinically meaningful reductions in Covid-19 cases and deaths among residents, particularly before vaccine availability.

Otolaryngologic manifestations of Mpox: the Atlanta outbreak.

BACKGROUND: In 2022, Mpox (MPX) has become clinically relevant as otolaryngologists are evaluating this exotic disease process due to its many otolaryngologic manifestations. AIMS/OBJECTIVE: To characterize our cohort of otolaryngology-relevant MPX confirmed cases. MATERIALS AND METHODS: A descriptive case series was performed via retrospective review. Adult patients who underwent inpatient or emergency department otolaryngology consultation at an Emory University-affiliated tertiary care level hospital for MPX were included. RESULTS: Seven patients (age 18-58 years; median 32 years) were identified. All patients were male. Six patients (86%) were black and six patients (86%) were HIV positive with varied immunocompetence. Otolaryngology was consulted for lymphadenopathy (n = 2), pharyngeal involvement (n = 1), and airway evaluation (n = 4). All 6 patients with active MPX developed the classic rash, which developed after oropharyngeal symptoms in 3 patients. Three patients had laryngeal involvement. CONCLUSION: MPX manifests with symptoms requiring otolaryngology expertise, especially when the airway is involved. Infectious disease consultation is key. Mpox can be identified with a specific constellation of demographic identifiers and physical exam findings, which is key to determining appropriate treatment and protection for the consulting otolaryngologist. SIGNIFICANCE: This is the first otolaryngologic study of Mpox and first description of Mpox laryngeal involvement.