Modeling zoonotic and vector-borne viruses.

The 2013-2016 Ebola virus disease epidemic and the coronavirus disease 2019 pandemic galvanized tremendous growth in models for emerging zoonotic and vector-borne viruses. Therefore, we have reviewed the main goals and methods of models to guide scientists and decision-makers. The elements of models for emerging viruses vary across spectrums: from understanding the past to forecasting the future, using data across space and time, and using statistical versus mechanistic methods. Hybrid/ensemble models and artificial intelligence offer new opportunities for modeling. Despite this progress, challenges remain in translating models into actionable decisions, particularly in areas at highest risk for viral disease outbreaks. To address this issue, we must identify gaps in models for specific viruses, strengthen validation, and involve policymakers in model development.

Yellow fever in Ghana: Predicting emergence and ecology from historical outbreaks.

Understanding the epidemiology and ecology of yellow fever in endemic regions is critical for preventing future outbreaks. Ghana is a high-risk country for yellow fever. In this study we estimate the epidemiology, ecological cycles, and areas at risk for yellow fever in Ghana based on historical outbreaks. We identify 2371 cases and 887 deaths (case fatality rate 37.4%) from yellow fever reported in Ghana from 1910 to 2022. Since implementation of routine childhood vaccination in 1992, the estimated mean annual number of cases decreased by 81% and the geographic distribution of yellow fever cases also changed. While there have been multiple large historical outbreaks of yellow fever in Ghana from the urban cycle, recent outbreaks have originated among unvaccinated nomadic groups in rural areas with the sylvatic/savanna cycles. Using machine learning and an ecological niche modeling framework, we predict areas in Ghana that are similar to where prior yellow fever outbreaks have originated based on temperature, precipitation, landcover, elevation, and human population density. We find differences in predictions depending on the ecological cycles of outbreaks. Ultimately, these findings and methods could be used to inform further subnational risk assessments for yellow fever in Ghana and other high-risk countries.

Risk Factors for Hospitalization and Effect of Immunosuppression on Clinical Outcomes Among an Urban Cohort of Patients With Mpox.

Background: During the 2022 mpox outbreak most patients were managed as outpatients, but some required hospitalization. Uncontrolled human immunodeficiency virus (HIV) has been identified as a risk factor for severe mpox. Methods: Patients with mpox diagnosed or treated within the Johns Hopkins Health System between 1 June and 15 December 2022 were included. The primary outcome of interest was risk of hospitalization. Demographic features, comorbid conditions, treatment, and clinical outcomes were determined. Results: A total of 353 patients were tested or treated for mpox; 100 had mpox diagnosed or treated (median age, 35.3 years; 97.0% male; 57.0% black and 10.0% Hispanic; 46.0% people with HIV [PWH]). Seventeen patients (17.0%) required hospitalization, 10 of whom were PWH. Age >40 years, race, ethnicity, HIV status, insurance status, and body mass index >30 (calculated as weight in kilograms divided by height in meters squared) were not associated with hospitalization. Eight of 9 patients (88.9%) with immunosuppression were hospitalized. Immunosuppression was associated with hospitalization in univariate (odds ratio, 69.3 [95% confidence interval, 7.8-619.7]) and adjusted analysis (adjusted odds ratio, 94.8 [8.5-1060.1]). Two patients (11.8%) who were hospitalized required intensive care unit admission and died; both had uncontrolled HIV infection and CD4 T-cell counts <50/µL. Median cycle threshold values for the first positive mpox virus sample did not differ between those who were hospitalized and those who were not. Conclusions: Immunosuppression was a significant risk factor for hospitalization with mpox. PWH with CD4 T-cell counts <50/µL are at high risk of death due to mpox infection. Patients who are immunosuppressed should be considered for early and aggressive treatment of mpox, given the increased risk of hospitalization.

The Multiple Origins of Ebola Disease Outbreaks.

BACKGROUND: The origins of Ebola disease outbreaks remain enigmatic. Historically outbreaks have been attributed to spillover events from wildlife. However, recent data suggest that some outbreaks may originate from human-to-human transmission of prior outbreak strains instead of spillover. Clarifying the origins of Ebola disease outbreaks could improve detection and mitigation of future outbreaks. METHODS: We reviewed the origins of all Ebola disease outbreaks from 1976 to 2022 to analyze the earliest cases and characteristics of each outbreak. The epidemiology and phylogenetic relationships of outbreak strains were used to further identify the likely source of each outbreak. RESULTS: From 1976 to 2022 there were 35 Ebola disease outbreaks with 48 primary/index cases. While the majority of outbreaks were associated with wildlife spillover, resurgence of human-to-human transmission could account for roughly a quarter of outbreaks caused by Ebola virus. Larger outbreaks were more likely to lead to possible resurgence, and nosocomial transmission was associated with the majority of outbreaks. CONCLUSIONS: While spillover from wildlife has been a source for many Ebola disease outbreaks, multiple outbreaks may have originated from flare-ups of prior outbreak strains. Improving access to diagnostics as well as identifying groups at risk for resurgence of ebolaviruses will be crucial to preventing future outbreaks.

Passively scanned, single-fiber optical coherence tomography probes for gastrointestinal devices.

BACKGROUND/OBJECTIVES: Optical coherence tomography (OCT) uses low coherence interferometry to obtain depth-resolved tissue reflectivity profiles (M-mode) and transverse beam scanning to create images of two-dimensional tissue morphology (B-mode). Endoscopic OCT imaging probes typically employ proximal or distal mechanical beam scanning mechanisms that increase cost, complexity, and size. Here, we demonstrate in the gastrointestinal (GI) tracts of unsedated human patients, that a passive, single-fiber probe can be used to guide device placement, conduct device-tissue physical contact sensing, and obtain two-dimensional OCT images via M-to-B-mode conversion. MATERIALS AND METHODS: We designed and developed ultrasmall, manually scannable, side- and forward-viewing single fiber-optic probes that can capture M-mode OCT data. Side-viewing M-mode OCT probes were incorporated into brush biopsy devices designed to harvest the microbiome and forward-viewing M-mode OCT probes were integrated into devices that measure intestinal potential difference (IPD). The M-mode OCT probe-coupled devices were utilized in the GI tract in six unsedated patients in vivo. M-mode data were converted into B-mode images using an M-to-B-mode conversion algorithm. The effectiveness of physical contact sensing by the M-mode OCT probes was assessed by comparing the variances of the IPD values when the probe was in physical contact with the tissue versus when it was not. The capacity of forward- and side-viewing M-mode OCT probes to produce high-quality B-mode images was compared by computing the percentages of the M-to-B-mode images that showed close contact between the probe and the luminal surface. Passively scanned M-to-B-mode images were qualitatively compared to B-mode images obtained by mechanical scanning OCT tethered capsule endomicroscopy (TCE) imaging devices. RESULTS: The incorporation of M-mode OCT probes in these nonendoscopic GI devices safely and effectively enabled M-mode OCT imaging, facilitating real-time device placement guidance and contact sensing in vivo. Results showed that M-mode OCT contact sensing improved the variance of IPD measurements threefold and side-viewing probes increased M-to-B-mode image visibility by 10%. Images of the esophagus, stomach, and duodenum generated by the passively scanned probes and M-to-B-mode conversion were qualitatively superior to B-mode images obtained by mechanically scanning OCT TCE devices. CONCLUSION: These results show that passive, single optical fiber OCT probes can be effectively utilized for nonendoscopic device placement guidance, device contact sensing, and two-dimensional morphologic imaging in the human GI tract in vivo. Due to their small size, lower cost, and reduced complexity, these M-mode OCT probes may provide an easier avenue for the incorporation of OCT functionality into endoscopic/nonendoscopic devices.

COVID-19 data reporting systems in Africa reveal insights for future pandemics.

Globally, countries have used diverse methods to report data during the COVID-19 pandemic. Using international guidelines and principles of emergency management, we compare national data reporting systems in African countries in order to determine lessons for future pandemics. We analyse COVID-19 reporting practices across 54 African countries through 2020. Reporting systems were diverse and included summaries, press releases, situation reports and online dashboards. These systems were communicated via social media accounts and websites belonging to ministries of health and public health. Data variables from the reports included event detection (cases/deaths/recoveries), risk assessment (demographics/co-morbidities) and response (total tests/hospitalisations). Of countries with reporting systems, 36/53 (67.9%) had recurrent situation reports and/or online dashboards which provided more extensive data. All of these systems reported cases, deaths and recoveries. However, few systems contained risk assessment and response data, with only 5/36 (13.9%) reporting patient co-morbidities and 9/36 (25%) including total hospitalisations. Further evaluation of reporting practices in Cameroon, Egypt, Kenya, Senegal and South Africa as examples from different sub-regions revealed differences in reporting healthcare capacity and preparedness data. Improving the standardisation and accessibility of national data reporting systems could augment research and decision-making, as well as increase public awareness and transparency for national governments.

Clinical presentation, complications, and outcomes of hospitalized COVID-19 patients in an academic center with a centralized palliative care consult service.

BACKGROUND AND AIMS: Palliative care is a critical component of the response of a healthcare system to a pandemic. We present risk factors associated with mortality and highlight an operational palliative care consult service in facilitating early identification of risk factors to guide goal-concordant care and rational utilization of finite healthcare resources during a pandemic. METHODS: In this case series of 100 consecutive patients hospitalized with COVID-19, we analyzed clinical data, treatment including palliative care, and outcomes in patients with SARS-CoV-2 infection admitted to three hospitals in Seattle, Washington. We compared data between patients who were discharged and non-survivors. RESULTS: Age (OR 4.67 [1.43, 15.32] ages 65-79; OR 3.96 [1.05, 14.89] ages 80-97), dementia (OR 5.62 [1.60, 19.74]), and transfer from a congregate living facility (OR 5.40 [2.07, 14.07]), as well hypoxemia and tachypnea (OR 7.00 [2.91, 22.41]; OR 2.78 [1.11, 6.97]) were associated with mortality. Forty-one (41%) patients required intensive care and 22 (22%) invasive mechanical ventilation. Forty-six (46%) patients were seen by the palliative care service, resulting in a change of resuscitation status in 54% of admitted patients. Fifty-eight (58%) patients recovered and were discharged, 34 (34%) died, and eight (8%) remained hospitalized, of which seven ultimately survived and one died. CONCLUSIONS: Older age, dementia, and congregate living were associated with mortality. Early discussions of goals of care facilitated by an operational palliative care consult service can effectively guide goal-concordant care in patients at high risk for mortality during a pandemic. Development of a functional palliative care consult service is an important component of pandemic planning.

Zoonoses and global epidemics.

PURPOSE OF REVIEW: The purpose of the review is to summarize recent advances in understanding the origins, drivers and clinical context of zoonotic disease epidemics and pandemics. In addition, we aimed to highlight the role of clinicians in identifying sentinel cases of zoonotic disease outbreaks. RECENT FINDINGS: The majority of emerging infectious disease events over recent decades, including the COVID-19 pandemic, have been caused by zoonotic viruses and bacteria. In particular, coronaviruses, haemorrhagic fever viruses, arboviruses and influenza A viruses have caused significant epidemics globally. There have been recent advances in understanding the origins and drivers of zoonotic epidemics, yet there are gaps in diagnostic capacity and clinical training about zoonoses. SUMMARY: Identifying the origins of zoonotic pathogens, understanding factors influencing disease transmission and improving the diagnostic capacity of clinicians will be crucial to early detection and prevention of further epidemics of zoonoses.

Regional vulnerability for COVID-19 in Cameroon.

INTRODUCTION: few studies have assessed risk for coronavirus disease 2019 (COVID-19) within African countries. Here we examine differences in vulnerability to COVID-19 among the ten administrative regions and two major cities of Cameroon based on epidemiological risk factors and access to healthcare resources. METHODS: regional epidemiological and healthcare access vulnerability indices were created and compared with cumulative COVID-19 cases, case fatality rates, co-morbidities, and healthcare resources in Cameroon. RESULTS: based on epidemiological risk factors, populations in the East Region, Douala (in the Littoral Region), West Region, and Yaoundé (in the Center Region) are at highest risk for COVID-19. Meanwhile, the North, Far North, East, and Adamawa Regions had the most healthcare access vulnerability. COVID-19 cases per population were highest in the Center, Littoral, and East Regions. Case fatality rates were greatest in the North Region. Potential co-morbidities with greater prevalence among COVID-19 patients included male sex, hypertension, and diabetes. CONCLUSION: epidemiological risk factors for COVID-19 and access to healthcare varies between the regions of Cameroon. These discrepancies are potentially reflected in regional differences of COVID-19 cases and case fatality rates. In particular, the East Region has high epidemiological risk factors and low healthcare accessibility compared to other regions. Understanding the relationships between epidemiological risk factors, access to healthcare resources, and COVID-19 cases in Cameroon could aid decision-making among national policymakers and inform further research.

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer.

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis. The infection was not cleared after the first treatment with convalescent plasma, suggesting a limited effect on SARS-CoV-2 in the upper respiratory tract of this individual. Several weeks after a second convalescent plasma transfusion, SARS-CoV-2 RNA was no longer detected. We observed marked within-host genomic evolution of SARS-CoV-2 with continuous turnover of dominant viral variants. However, replication kinetics in Vero E6 cells and primary human alveolar epithelial tissues were not affected. Our data indicate that certain immunocompromised individuals may shed infectious virus longer than previously recognized. Detection of subgenomic RNA is recommended in persistently SARS-CoV-2-positive individuals as a proxy for shedding of infectious virus.

Effectiveness of N95 Respirator Decontamination and Reuse against SARS-CoV-2 Virus.

The coronavirus pandemic has created worldwide shortages of N95 respirators. We analyzed 4 decontamination methods for effectiveness in deactivating severe acute respiratory syndrome coronavirus 2 virus and effect on respirator function. Our results indicate that N95 respirators can be decontaminated and reused, but the integrity of respirator fit and seal must be maintained.

Regional vulnerability for COVID-19 in Cameroon

Introduction: few studies have assessed risk for coronavirus disease 2019 (COVID-19) within African countries. Here we examine differences in vulnerability to COVID-19 among the ten administrative Regions and two major cities of Cameroon based on epidemiological risk factors and access to healthcare resources. Methods: regional epidemiological and healthcare access vulnerability indices were created and compared with cumulative COVID-19 cases, case fatality rates, co-morbidities, and healthcare resources in Cameroon. Results: based on epidemiological risk factors, populations in the East Region, Douala (in the Littoral Region), West Region, and Yaoundé (in the Center Region) are at highest risk for COVID-19. Meanwhile, the North, Far North, East, and Adamawa Regions had the most healthcare access vulnerability. COVID-19 cases per population were highest in the Center, Littoral, and East Regions. Case fatality rates were greatest in the North Region. Potential co-morbidities with greater prevalence among COVID-19 patients included male sex, hypertension, and diabetes. Conclusion: epidemiological risk factors for COVID-19 and access to healthcare varies between the Regions of Cameroon. These discrepancies are potentially reflected in regional differences of COVID-19 cases and case fatality rates. In particular, the East Region has high epidemiological risk factors and low healthcare accessibility compared to other Regions. Understanding the relationships between epidemiological risk factors, access to healthcare resources, and COVID-19 cases in Cameroon could aid decision-making among national policymakers and inform further research

Nosocomial Transmission of Emerging Viruses via Aerosol-Generating Medical Procedures.

Recent nosocomial transmission events of emerging and re-emerging viruses, including Ebola virus, Middle East respiratory syndrome coronavirus, Nipah virus, and Crimean-Congo hemorrhagic fever orthonairovirus, have highlighted the risk of nosocomial transmission of emerging viruses in health-care settings. In particular, concerns and precautions have increased regarding the use of aerosol-generating medical procedures when treating patients with such viral infections. In spite of increasing associations between aerosol-generating medical procedures and the nosocomial transmission of viruses, we still have a poor understanding of the risks of specific procedures and viruses. In order to identify which aerosol-generating medical procedures and emerging viruses pose a high risk to health-care workers, we explore the mechanisms of aerosol-generating medical procedures, as well as the transmission pathways and characteristics of highly pathogenic viruses associated with nosocomial transmission. We then propose how research, both in clinical and experimental settings, could advance current infection control guidelines.

Neisseria gonorrhoeae as a Rare Cause of Preseptal Cellulitis.

Neisseria gonorrhoeae is a rare cause of preseptal cellulitis, but infections can be severe. Rapid diagnosis is critical and can be expedited by nucleic acid amplification tests. Contact isolation precautions are encouraged for hospitalized patients with gonococcal preseptal cellulitis and a prolonged course of antibiotics is recommended.

Translating Predictions of Zoonotic Viruses for Policymakers.

Recent outbreaks of Ebola virus disease and Zika virus disease highlight the need for disseminating accurate predictions of emerging zoonotic viruses to national governments for disease surveillance and response. Although there are published maps for many emerging zoonotic viruses, it is unknown if there is agreement among different models or if they are concordant with national expert opinion. Therefore, we reviewed existing predictions for five high priority emerging zoonotic viruses with national experts in Cameroon to investigate these issues and determine how to make predictions more useful for national policymakers. Predictive maps relied primarily on environmental parameters and species distribution models. Rift Valley fever virus and Crimean-Congo hemorrhagic fever virus predictions differed from national expert opinion, potentially because of local livestock movements. Our findings reveal that involving national experts could elicit additional data to improve predictions of emerging pathogens as well as help repackage predictions for policymakers.