Implementation of Health Policies in the COVID-19 Pandemic Phases of Myanmar and How the Population Approach Influenced Their Success Rate

The impact of the COVID-19 pandemic is continuing in developing countries, and post-pandemic individuals are still suffering mentally and physically. Many researchers have tried to find the causes and risks that can impact the spread of disease. Among the causes and risks identified, socioeconomic factors and health policies played an important role in determining the transmission of the disease. However, the significance of these factors for the spread of infection is different depending on the country. In this editorial, we discuss the implementation of health policies in Myanmar and their effect on infection transmission.

Health surveillance for SARS-CoV-2: infection spread and vaccination coverage in the schools of Modena province, Italy

Introduction

In Italy, over 4.8 million individuals aged 0-19 years have been infected with SARS-CoV-2. This study aims to evaluate the spread of SARS-CoV-2 within schools in Modena province and the influence of anti-SARS-CoV-2 vaccination coverage.

Methods

We performed a survey in the period 1 September-15 December 2021, involving student population aged 0-19 years and related teachers screened for SARS-CoV-2 infection using nasopharyngeal swab after the detection of an index case within their class. During the study period, vaccination against SARS-CoV-2 was actively offered to all subjects aged ≥12 years.

Results

A total of 13,934 subjects were tested, 12,534 students and 1,400 teachers (594 classes). We identified a total of 594 and 779 index and secondary cases, respectively. We found that 9.8% of students and 10.6% of teachers were positive for SARS-CoV-2. Overall at the test time, 32.5% were vaccinated with at least one dose of anti-SARS-CoV-2 vaccine. Among secondary cases, 7.8% were vaccinated compared to 34.9% among negative tested subjects. A higher secondary attack rate was for non-vaccinated subjects rather than vaccinated ones (8.1% vs. 1.4%). Higher secondary attack rates were reported for subjects attending infant and primary school (5.9 and 9.6%, respectively). Lower secondary attack rates were for those who attended middle school (4.9%) and especially high school (1.7%).

Conclusion

Our results highlight the differential spread of the infection within various educational settings and that the vaccination, available in the study period for the population aged ≥12, have mitigated SARS-CoV-2 spread in high and middle schools.

Immunosuppression and Opportunistic Infections: A Rare Case Report of Nocardia Osteomyelitis of the Pelvis

Patients with a long-standing history of immunosuppression are at significantly increased risk of opportunistic infections. One such group of organisms that may cause these types of infections includes the Nocardia genus, a gram-positive, filamentous rod that demonstrates a branching pattern, is urease-producing and has acid-fast properties. The disease profile of Nocardia varies with manifestations ranging from cutaneous infection to severe pulmonary or central nervous system (CNS) infections, and rarely, osteomyelitis. In this case report, we present an 87-year-old female with persistent left gluteal and lumbar pain, generalized body aches, chills, and fevers diagnosed with Nocardia asiatica osteomyelitis of the pelvis, likely secondary to dissemination from pulmonary cavitary disease in an immunosuppressed host with chronic neutropenia. On magnetic resonance imaging (MRI), the patient was found to have heterogeneous enhancement, central necrosis, and loss of cortical margins of the left iliac wing, alongside a rim-enhancing soft tissue mass from the left iliac bone into the left gluteal soft tissues and left paraspinal musculature representing an abscess. She was promptly treated with surgical irrigation and drainage with surgical wound cultures growing Nocardia asiatica. She received treatment with trimethoprim-sulfamethoxazole antibiotics with symptom improvement and is following up with an infectious disease physician outpatient. Management of osteomyelitis, like in this case, involves long-term antibiotics with the potential need for surgical intervention. There are few reported cases of extrapulmonary Nocardia infections, particularly osteomyelitis, demonstrating the importance of their inclusion in the literature to better serve patients to allow for timely intervention for rare and life-threatening conditions. In immunocompromised hosts, the differential diagnosis should include opportunistic infections and less common pathogens, especially in those with atypical presentations, including gluteal and leg pain.

Protecting Older Adult Residents in Care Facilities Against Influenza and COVID-19 Using the Influenza Communication, Advice and Reporting (FluCARE) App: Prospective Cohort Mixed Methods Study

BACKGROUND

Early detection and response to influenza and COVID-19 outbreaks in aged care facilities (ACFs) are critical to minimizing health impacts. The Sydney Local Health District (SLHD) Public Health Unit (PHU) has developed and implemented a novel web-based app with integrated functions for online line listings, detection algorithms, and automatic notifications to responders, to assist ACFs in outbreak response. The goal of the Influenza Outbreak Communication, Advice and Reporting (FluCARE) app is to reduce time delays to notifications, which we hope will reduce the spread, duration, and health impacts of an influenza or COVID-19 outbreak, as well as ease workload burdens on ACF staff.

OBJECTIVE

The specific aims of the study were to (1) evaluate the acceptability and user satisfaction of the implementation and use of FluCARE in helping ACFs recognize, notify, and manage influenza and COVID-19 outbreaks in their facility; (2) identify the safety of FluCARE and any potential adverse outcomes of using the app; and (3) identify any perceived barriers or facilitators to the implementation and use of FluCARE from the ACF user perspective.

METHODS

The FluCARE app was piloted from September 2019 to December 2020 in the SLHD. Associated implementation included promotion and engagement, user training, and operational policies. Participating ACF staff were invited to complete a posttraining survey. Staff were also invited to complete a postpilot evaluation survey that included the user Mobile Application Rating Scale (uMARS) measuring app acceptance, utility, and barriers and facilitators to use. An issues log was also prospectively maintained to assess safety. Survey data were analyzed descriptively or via content analysis where appropriate.

RESULTS

Surveys were completed by 31 consenting users from 27 ACFs. FluCARE was rated 3.91 of 5 overall on the uMARS. Of the 31 users, 25 (80%) would definitely use FluCARE for future outbreaks, and all users agreed that the app was useful for identifying influenza and COVID-19 outbreaks at their facilities. There were no reported critical issues with incorrect or missed outbreak detection. User training, particularly online training modules, and technical support were identified as key facilitators to FluCARE use.

CONCLUSIONS

FluCARE is an acceptable, useful, and safe app to assist ACF staff with early detection and response to influenza and COVID-19 outbreaks. This study supports feasibility for ongoing implementation and efficacy evaluation, followed by scale-up into other health districts in New South Wales.

Identifying Hot Spots of Tuberculosis in Nigeria Using an Early Warning Outbreak Recognition System: Retrospective Analysis of Implications for Active Case Finding Interventions

BACKGROUND

Undiagnosed tuberculosis (TB) cases are the major challenge to TB control in Nigeria. An early warning outbreak recognition system (EWORS) is a system that is primarily used to detect infectious disease outbreaks; this system can be used as a case-based geospatial tool for the real-time identification of hot spot areas with clusters of TB patients. TB screening targeted at such hot spots should yield more TB cases than screening targeted at non-hot spots.

OBJECTIVE

We aimed to demonstrate the effectiveness of an EWORS for TB hot spot mapping as a tool for detecting areas with increased TB case yields in high TB-burden states of Nigeria.

METHODS

KNCV Tuberculosis Foundation Nigeria deployed an EWORS to 14 high-burden states in Nigeria. The system used an advanced surveillance mechanism to identify TB patients' residences in clusters, enabling it to predict areas with elevated disease spread (ie, hot spots) at the ward level. TB screening outreach using the World Health Organization 4-symptom screening method was conducted in 121 hot spot wards and 213 non-hot spot wards selected from the same communities. Presumptive cases identified were evaluated for TB using the GeneXpert instrument or chest X-ray. Confirmed TB cases from both areas were linked to treatment. Data from the hot spot and non-hot spot wards were analyzed retrospectively for this study.

RESULTS

During the 16-month intervention, a total of 1,962,042 persons (n=734,384, 37.4% male, n=1,227,658, 62.6% female) and 2,025,286 persons (n=701,103, 34.6% male, n=1,324,183, 65.4% female) participated in the community TB screening outreaches in the hot spot and non-hot spot areas, respectively. Presumptive cases among all patients screened were 268,264 (N=3,987,328, 6.7%) and confirmed TB cases were 22,618 (N=222,270, 10.1%). The number needed to screen to diagnose a TB case in the hot spot and non-hot spot areas was 146 and 193 per 10,000 people, respectively.

CONCLUSIONS

Active TB case finding in EWORS-mapped hot spot areas yielded higher TB cases than the non-hot spot areas in the 14 high-burden states of Nigeria. With the application of EWORS, the precision of diagnosing TB among presumptive cases increased from 0.077 to 0.103, and the number of presumptive cases needed to diagnose a TB case decreased from 14.047 to 10.255 per 10,000 people.

Disinfection of Virtual Reality Devices in Health Care Settings: In Vitro Assessment and Survey Study

BACKGROUND

Virtual reality (VR) devices are increasingly used in health care settings. The use among patients has the potential to unintentionally transmit pathogens between patients and hospital staff. No standard operating procedure for disinfection exists to ensure safe use between patients.

OBJECTIVE

This study aims to determine the efficacy of disinfectants on VR devices in order to ensure safe use in health care settings.

METHODS

Three types of bacteria were inoculated onto porous and nonporous surfaces of 2 VR devices: the Meta Oculus Quest and Meta Oculus Quest 2. Disinfection was performed using either isopropyl alcohol or alcohol-free quaternary ammonium wipes. A quantitative culture was used to assess the adequacy of disinfection. A survey was separately sent out to VR device technicians at other pediatric health care institutes to compare the methods of disinfection and how they were established.

RESULTS

Both products achieved adequate disinfection of the treated surfaces; however, a greater log-kill was achieved on nonporous surfaces than on the porous surfaces. Alcohol performed better than quaternary ammonium on porous surfaces. The survey respondents reported a wide variability in disinfection processes with only 1 person reporting an established standard operating procedure.

CONCLUSIONS

Disinfection can be achieved through the use of either isopropyl alcohol or quaternary ammonium products. Porous surfaces showed lesser log-kill rates than the nonporous surfaces, indicating that the use of an added barrier may be of benefit and should be a point of future research. Given the variability in the disinfection process across health care systems, a standard operating procedure is proposed.

Evaluating Epidemiological Risk by Using Open Contact Tracing Data: Correlational Study

Background

During the 2020s, there has been extensive debate about the possibility of using contact tracing (CT) to contain the SARS-CoV-2 pandemic, and concerns have been raised about data security and privacy. Little has been said about the effectiveness of CT. In this paper, we present a real data analysis of a CT experiment that was conducted in Italy for 8 months and involved more than 100,000 CT app users.

Objective

We aimed to discuss the technical and health aspects of using a centralized approach. We also aimed to show the correlation between the acquired contact data and the number of SARS-CoV-2–positive cases. Finally, we aimed to analyze CT data to define population behaviors and show the potential applications of real CT data.

Methods

We collected, analyzed, and evaluated CT data on the duration, persistence, and frequency of contacts over several months of observation. A statistical test was conducted to determine whether there was a correlation between indices of behavior that were calculated from the data and the number of new SARS-CoV-2 infections in the population (new SARS-CoV-2–positive cases).

Results

We found evidence of a correlation between a weighted measure of contacts and the number of new SARS-CoV-2–positive cases (Pearson coefficient=0.86), thereby paving the road to better and more accurate data analyses and spread predictions.

Conclusions

Our data have been used to determine the most relevant epidemiological parameters and can be used to develop an agent-based system for simulating the effects of restrictions and vaccinations. Further, we demonstrated our system's ability to identify the physical locations where the probability of infection is the highest. All the data we collected are available to the scientific community for further analysis.

Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.

Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to almost every country on the globe, and each country is reporting the symptomatic presentation of their patients to give better insight into the various clinical presentations of SARS-CoV-2. However, the epidemiological literature from Pakistan is scanty.

Methods

We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. Patients' demographics, symptoms, travel and contact history, and outcomes were recorded. All statistical analysis was performed using the Statistical Package for the Social Sciences (SPSS) version 22 (IBM SPSS Statistics for Windows, IBM Corp, Armonk, NY).

Results

Most of the patients were male (64.6%), the majority (43.3%) belonging to the 21- to 40-year age group. Most of the patients (65.5%) were residents of Gulshan Iqbal. A total of 15.8% of the patients were admitted to the hospital, and 3.9% of patients expired. The three most common presenting symptoms were fever (74.8%), cough (60.4%), and flu (35.5%). The majority of patients (89.3%) gave a history of contact with SARS-CoV-2 patients.

Conclusion

The number of SARS-CoV-2 cases is rapidly increasing in Karachi, Pakistan. There is a need to educate the population about the most common sign and symptoms of the virus so that individuals can identify these symptoms and get themselves tested. The concerned authorities should devise an adequate and effective plan to flatten the infectivity curve.

Infectio: a Generic Framework for Computational Simulation of Virus Transmission between Cells

Infectio presents a generalized platform to analyze virus infection spread between cells. It allows the simulation of plaque phenotypes from image-based assays. Viral plaques are the result of virus spreading from primary infected cells to neighboring cells. This is a complex process and involves neighborhood effects at cell-cell contact sites or fluid dynamics in the extracellular medium. Infectio differentiates between two major modes of virus transmission between cells, allowing in silico testing of hypotheses about spreading mechanisms of any virus which can be grown in cell cultures, based on experimentally measured parameters, such as infection intensity or cell killing. The results of these tests can be compared with experimental data and allow interpretations with regard to biophysical mechanisms. Infectio also facilitates characterizations of the mode of action of therapeutic agents, such as oncolytic viruses or other infectious or cytotoxic agents.

Viruses spread between cells, tissues, and organisms by cell-free and cell-cell mechanisms, depending on the cell type, the nature of the virus, or the phase of the infection cycle. The mode of viral transmission has a large impact on disease development, the outcome of antiviral therapies or the efficacy of gene therapy protocols. The transmission mode of viruses can be addressed in tissue culture systems using live-cell imaging. Yet even in relatively simple cell cultures, the mechanisms of viral transmission are difficult to distinguish. Here we present a cross-platform software framework called “Infectio,” which is capable of simulating transmission phenotypes in tissue culture of virtually any virus. Infectio can estimate interdependent biological parameters, for example for vaccinia virus infection, and differentiate between cell-cell and cell-free virus spreading. Infectio assists in elucidating virus transmission mechanisms, a feature useful for designing strategies of perturbing or enhancing viral transmission. The complexity of the Infectio software is low compared to that of other software commonly used to quantitate features of cell biological images, which yields stable and relatively error-free output from Infectio. The software is open source (GPLv3 license), and operates on the major platforms (Windows, Mac, and Linux). The complete source code can be downloaded from http://infectio.github.io/index.html.

IMPORTANCE Infectio presents a generalized platform to analyze virus infection spread between cells. It allows the simulation of plaque phenotypes from image-based assays. Viral plaques are the result of virus spreading from primary infected cells to neighboring cells. This is a complex process and involves neighborhood effects at cell-cell contact sites or fluid dynamics in the extracellular medium. Infectio differentiates between two major modes of virus transmission between cells, allowing in silico testing of hypotheses about spreading mechanisms of any virus which can be grown in cell cultures, based on experimentally measured parameters, such as infection intensity or cell killing. The results of these tests can be compared with experimental data and allow interpretations with regard to biophysical mechanisms. Infectio also facilitates characterizations of the mode of action of therapeutic agents, such as oncolytic viruses or other infectious or cytotoxic agents.

Visualizing infection spread: dual-color fluorescent reporting of virus-host interactions

Although the molecular mechanisms by which host cells defend themselves against viral infection have been studied in great depth, and countermeasures viruses employ to suppress such defensive responses have been widely documented, relatively little attention has been devoted toward elucidating how such interactions between virus and host are resolved over multiple rounds of infection. Here, we describe the design, synthesis, and validation of a dual-color fluorescent reporter system to study how viral infections spread through a host cell monolayer and how the cellular innate immune system mounts an antiviral response. We employed recombinant, red fluorescent protein expressing mutants of a prototypical RNA virus, vesicular stomatitis virus to enable identification and tracking of infected cells. Further, we generated stable reporter cells that use green fluorescent protein to report on the expression of IFIT2, an interferon stimulated gene involved in the interference of viral protein translation, and a marker of antiviral defense activation. The presence of the fluorescent protein reporters had minimal effects on the normal behavior of the cells or viruses. Moreover, expression of the virus and cell reporters correlated with the kinetics of viral replication and activation of an anti-viral response, respectively. This two-color system enabled us to track and quantify in live cells how viral replication and activation of host defensive responses play out over multiple rounds of infection. Initial study of propagating infections demonstrated that antiviral activation over multiple rounds was critical for slowing and ultimately halting the spread of infection.