HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.

Access to accurate viral genomes is important to downstream data analysis. Third-generation sequencing (TGS) has recently become a popular platform for virus sequencing because of its long read length. However, its per-base error rate, which is higher than next-generation sequencing, can lead to genomes with errors. Polishing tools are thus needed to correct errors either before or after sequence assembly. Despite promising results of available polishing tools, there is still room to improve the error correction performance to perform more accurate genome assembly. The errors, particularly those in coding regions, can hamper analysis such as linage identification and variant monitoring. In this work, we developed a novel pipeline, HMMPolish, for correcting (polishing) errors in protein-coding regions of known RNA viruses. This tool can be applied to either raw TGS reads or the assembled sequences of the target virus. By utilizing profile Hidden Markov Models of protein families/domains in known viruses, HMMPolish can correct errors that are ignored by available polishers. We extensively validated HMMPolish on 34 datasets that covered four clinically important viruses, including HIV-1, influenza-A, norovirus, and severe acute respiratory syndrome coronavirus 2. These datasets contain reads with different properties, such as sequencing depth and platforms (PacBio or Nanopore). The benchmark results against popular/representative polishers show that HMMPolish competes favorably on error correction in coding regions of known RNA viruses.

Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Subvariant BA.2 in a Single-Source Community Outbreak.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single-source BA.2 outbreak in a housing estate. METHODS: We analyzed the epidemiological information on a community outbreak of BA.2 (STY outbreak). We performed whole viral genome sequencing using the Oxford Nanopore MinION device. We calculated the doubling time of the outbreak within a housing estate. RESULTS: The STY outbreak involved a total of 768 individuals as of 5 February 2022, including 432 residents, visitors, or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate had a short doubling time of 1.28 days (95% confidence interval: .560-1.935). The outbreak was promptly controlled with the lockdown of 3 buildings within the housing estate. Whole-genome sequencing was performed for 133 patients in the STY outbreak, including 106 residents of the KC Estate. All 133 sequences from the STY outbreak belonged to the BA.2 sublineage, and phylogenetic analysis showed that these sequences cluster together. All individuals in the STY cluster had the unique mutation C12525T. CONCLUSIONS: Our study highlights the exceptionally high transmissibility of the Omicron variant BA.2 sublineage in Hong Kong, where stringent measures are implemented as part of the elimination strategy. Continual genomic surveillance is crucial in monitoring the emergence of epidemiologically important Omicron sublineages.

Probable Animal-to-Human Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant AY.127 Causing a Pet Shop-Related Coronavirus Disease 2019 (COVID-19) Outbreak in Hong Kong.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect human and other mammals, including hamsters. Syrian (Mesocricetus auratus) and dwarf (Phodopus sp.) hamsters are susceptible to SARS-CoV-2 infection in the laboratory setting. However, pet shop-related Coronavirus Disease 2019 (COVID-19) outbreaks have not been reported. METHODS: We conducted an investigation of a pet shop-related COVID-19 outbreak due to Delta variant AY.127 involving at least 3 patients in Hong Kong. We tested samples collected from the patients, environment, and hamsters linked to this outbreak and performed whole genome sequencing analysis of the reverse transcription polymerase chain reaction (RT-PCR)-positive samples. RESULTS: The patients included a pet shop keeper (Patient 1), a female customer of the pet shop (Patient 2), and the husband of Patient 2 (Patient 3). Investigation showed that 17.2% (5/29) and 25.5% (13/51) environmental specimens collected from the pet shop and its related warehouse, respectively, tested positive for SARS-CoV-2 RNA by RT-PCR. Among euthanized hamsters randomly collected from the storehouse, 3% (3/100) tested positive for SARS-CoV-2 RNA by RT-PCR and seropositive for anti-SARS-CoV-2 antibody by enzyme immunoassay. Whole genome analysis showed that although all genomes from the outbreak belonged to the Delta variant AY.127, there were at least 3 nucleotide differences among the genomes from different patients and the hamster cages. Genomic analysis suggests that multiple strains have emerged within the hamster population, and these different strains have likely transmitted to human either via direct contact or via the environment. CONCLUSIONS: Our study demonstrated probable hamster-to-human transmission of SARS-CoV-2. As pet trading is common around the world, this can represent a route of international spread of this pandemic virus.

Rationale and guidance for strengthening infection prevention and control measures and antimicrobial stewardship programs in Bangladesh: a study protocol.

BACKGROUND: Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are major global health challenges. Drug-resistant infectious diseases continue to rise in developing countries, driven by shortfalls in infection control measures, antibiotic misuse, and scarcity of reliable diagnostics. These escalating global challenges have highlighted the importance of strengthening fundamental infection prevention and control (IPC) measures and implementing effective antimicrobial stewardship programs (ASP). This study aims to present a framework for enhancing IPC measures and ASP efforts to reduce the HAI and AMR burden in Bangladesh. METHODS: This implementation approach will employ a mixed-methods strategy, combining both quantitative and qualitative data from 12 tertiary hospitals in Bangladesh. A baseline assessment will be conducted using the Infection Prevention and Control Assessment Framework (IPCAF) developed by the WHO. We will record IPC practices through direct observations of hand hygiene, personal protective equipment (PPE) utilization, and hospital ward IPC infrastructure. Additionally, data on healthcare providers' knowledge, attitudes, and practices regarding IPC and antibiotic prescribing will be collected using both structured questionnaires and qualitative interviews. We will also assist the hospital leadership with establishing and/or strengthening IPC and ASP committees. Based on baseline assessments of each healthcare facility, tailored interventions and quality improvement projects will be designed and implemented. An end-line assessment will also be conducted after 12 months of intervention using the same assessment tools. The findings will be compared with the baseline to determine changes in IPC and antibiotic stewardship practices. DISCUSSION: Comprehensive assessments of healthcare facilities in low-resource settings are crucial for strengthening IPC measures and ASP activities,. This approach to assessing existing IPC and ASP activities will provide policy-relevant data for addressing current shortfalls. Moreover, this framework proposes identifying institutionally-tailored solutions, which will ensure that response activities are appropriately contextualized, aligned with stakeholder priorities, and offer sustainable solutions. CONCLUSION: Findings from this study can guide the design and implementation of feasible and sustainable interventions in resource-constrained healthcare settings to address gaps in existing IPC and ASP activities. Therefore, this protocol will be applicable across a broad range of settings to improve IPC and ASP and reduce the burden of hospital-acquired infections and AMR.

Multi-scale pixel-based image fusion using multivariate empirical mode decomposition.

A novel scheme to perform the fusion of multiple images using the multivariate empirical mode decomposition (MEMD) algorithm is proposed. Standard multi-scale fusion techniques make a priori assumptions regarding input data, whereas standard univariate empirical mode decomposition (EMD)-based fusion techniques suffer from inherent mode mixing and mode misalignment issues, characterized respectively by either a single intrinsic mode function (IMF) containing multiple scales or the same indexed IMFs corresponding to multiple input images carrying different frequency information. We show that MEMD overcomes these problems by being fully data adaptive and by aligning common frequency scales from multiple channels, thus enabling their comparison at a pixel level and subsequent fusion at multiple data scales. We then demonstrate the potential of the proposed scheme on a large dataset of real-world multi-exposure and multi-focus images and compare the results against those obtained from standard fusion algorithms, including the principal component analysis (PCA), discrete wavelet transform (DWT) and non-subsampled contourlet transform (NCT). A variety of image fusion quality measures are employed for the objective evaluation of the proposed method. We also report the results of a hypothesis testing approach on our large image dataset to identify statistically-significant performance differences.

Antibiotic use in tertiary care hospitals in Bangladesh: Revealing the extent through a point prevalence survey.

BACKGROUND: Prevalent use of antibiotics in hospitals results in antimicrobial resistance (AMR), rising mortality, and substantial financial burden. This study assessed the current pattern of antibiotic use among inpatients in tertiary hospitals in Bangladesh. METHODS: Between August and November 2022, we conducted a point prevalence survey in 4 tertiary hospitals in Dhaka, Bangladesh. The World Health Organization-directed point prevalence survey methodology and tools were followed for the data collection. Descriptive and multivariate statistics were performed using Stata version 15. RESULTS: Of 1,063 hospitalized patients, antibiotics were prescribed to 73.5% (781/1063, 95% confidence interval: 70.8-76.1) of patients. A total of 1,164 antibiotics were prescribed, and 49.1% of patients consumed multiple antibiotics. Only 31.4% of patients were prescribed antibiotics based on microbiology results. The reasons for antibiotic prescribing were mentioned only in 19.3% of patients. Infants (adjusted odds ratio: 8.52, P-value: <.001) and neonates (adjusted odds ratio: 4.32, P-value: <.001) were more likely to consume antibiotics compared to adults. Cephalosporins accounted for the majority (54.0%) of antibiotics used in hospitals. None of the hospitals had any antibiotic use guidelines. CONCLUSIONS: Consumption of Watch group antibiotics empirically among all age groups demonstrates irrational antibiotic usage in Bangladeshi hospitals. Implementation of a tailored stewardship program, antibiotic use guidelines, and prescriber-patient awareness could improve the rational use of antibiotics.

Tailoring NiCoCu layered double hydroxide with Ag-citrate/polyaniline/functionalized SWCNTs nanocomposites for supercapacitor applications.

Supercapacitors have substantially altered the landscape of sophisticated energy storage devices with their exceptional power density along with prolonged cyclic stability. On the contrary, their energy density remains low, requiring research to compete with conventional battery storage devices. This study addresses the disparities between energy and power densities in energy storage technologies by exploring the integration of layered double hydroxides (LDH) and highly conductive materials to develop an innovative energy storage system. Four electrodes were fabricated via a hydrothermal process using NiCoCu LDH, Ag-citrate, PANI, and f-SWCNTs. The optimal electrode demonstrated exceptional electrochemical properties; at 0.5 A g-1, it possessed specific capacitances of 807 F g-1, twice as high as those of the pure sample. The constructed asymmetric supercapacitor device attained energy densities of 62.15 W h kg-1 and 22.44 W h kg-1, corresponding to power densities of 1275 W kg-1 and 11 900 W kg-1, respectively. Furthermore, it maintained 100% cyclic stability and a coulombic efficiency of 95% for 4000 charge-discharge cycles. The concept of a supercapacitor of the hybrid grade was reinforced by power law investigations, which unveiled b-values in the interval of 0.5 to 1. This research emphasizes the considerable potential of supercapacitor-grade NiCoCu LDH/Ag-citrate-PANI-f-SWCNTs nanocomposites for superior rate performance, robust cycle stability, and enhanced energy storage capacity.

Enhancing supercapacitor performance of Ni-Co-Mn metal-organic frameworks by compositing it with polyaniline and reduced graphene oxide.

Metal-organic frameworks (MOFs) are one of the most sought-after materials in the domain of supercapacitors and can be tailored to accommodate diverse compositions, making them amenable to facile functionalization. However, their intrinsic specific capacitance as well as energy density is minimal, which hinders their usage for advanced energy storage applications. Therefore, herein, we have prepared six electrodes, i.e., Ni-Co-Mn MOFs, polyaniline (PANI), and reduced graphene oxide (rGO) along with their novel nanocomposites, i.e., C1, C2, and C3, comprising MOFs : PANI : rGO in a mass ratio of 100 : 1 : 0.5, 100 : 1 : 1, and 100 : 1 : 10, respectively. The polyaniline conducting polymer and rGO enabled efficient electron transport, enhanced charge storage processes, substantial surface area facilitating higher loading of active materials, promoting electrochemical reactions, and ultimately enhanced nanocomposite system performance. As a result, scanning electron microscopy (SEM) and X-ray diffraction (XRD) techniques confirmed the successful synthesis and revealed distinct morphological features of the materials. Following electrochemical testing, it was observed that composition C2 exhibited the highest performance, demonstrating a groundbreaking specific capacitance of 1007 F g-1 at 1 A g-1. The device showed a good energy density of 25.11 W h kg-1 and a power density of 860 W kg-1. Remarkably, the device demonstrated a capacity retention of 115% after 1500 cycles, which is a clear indication of the wettability factor, according to the literature. The power law indicated b-values in a range of 0.58-0.64, verifying the hybrid-type behavior of supercapacitors.

Molecular interactions of 4-acetoxy-plakinamine B with peripheral anionic and other catalytic subsites of the aromatic gorge of acetylcholinesterase: computational and structural insights.

CONTEXT: A steroidal alkaloid, 4-acetoxy-plakinamine B (4APB), is a recently discovered marine natural product with inhibitory effect against acetylcholinesterase (AChE), but its mechanism of interaction with the enzyme remains to be elucidated. OBJECTIVE: The main objective was to study molecular binding mode of the compound, its interactions with catalytic subsites and molecular mechanism behind its significant inhibitory effect. MATERIALS AND METHODS: All possible interactions of ligands in the binding sites were analyzed using FRED 2.1 and the OMEGA pre-generated multi-conformer library. RESULTS: Dipole-dipole interactions were observed between the secondary amino group of 4APB and Ser200 at a distance of 3.91 Å and also with Gly117 and Gly118. A further dipole-dipole interaction was between Arg289 and the heterocyclic nitrogen. Hydrogen bonding interactions were observed between Tyr130 and secondary amino and C-4 acetyl groups as well as between heterocyclic nitrogen and Phe288 at a distance of 3.04 Å. Hydrophobic interactions were evident between rings C/D of 4APB and with Phe288, Phe330 and Phe331. The computational studies revealed 4APB's critical molecular interaction with amino acids of peripheral active (PAS) and anionic (AS) subsites. DISCUSSION: Our data provided molecular evidence for the mixed competitive inhibitory effect of 4APB. For lead optimization, structural insights revealed the N-methyl group of 4APB could be replaced by NH2 moiety to generate a more favorable hydrogen bonding with Glu199. A polar group insertion such as NH2 or OH at certain sites of the 4APB skeleton is also recommended. CONCLUSION: These computational insights explained the mixed-competitive enzyme kinetic behavior of 4APB. This study outlines a strategy for designing novel derivatives of 4APB with potentially better AChE inhibitory activities through interaction at the PAS and AS sites.

Uptake of Influenza Vaccine and Factors Associated with Influenza Vaccination among Healthcare Workers in Tertiary Care Hospitals in Bangladesh: A Multicenter Cross-Sectional Study.

Influenza, highly contagious in hospital settings, imposes a substantial disease burden globally, and influenza vaccination is critical for healthcare workers (HCWs) to prevent this illness. This study assessed influenza vaccine uptake, including its associated factors among HCWs of tertiary care hospitals in Bangladesh. Between September and December 2020, this multicenter study included 2046 HCWs from 11 hospitals. Face-to-face interviews were conducted using a semi-structured questionnaire to collect data from physicians, nurses, and cleaning and administrative staff for the survey. Only 13.8% (283/2046) of HCWs received the influenza vaccine, of which the majority (76.7%, 217/283) received it for free from the hospital. Nurses had the highest (20.0%, 187/934) influenza vaccine coverage, followed by physicians at 13.5% (71/526), whereas cleaning staff had the lowest at 6.0% (19/318). Among unvaccinated HCWs, the desire to get vaccinated was high (86.2%), with half of the respondents even being willing to pay for it. The HCWs who were aware of the influenza vaccine were over five times more likely to get the vaccine (OR 5.63; 95% CI: 1.04, 1.88) compared to those who were not. HCWs in Bangladesh were vaccinated against influenza at a very low rate. Free and mandatory influenza vaccination programs should be initiated to optimize vaccine coverage among HCWs.

Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance.

BACKGROUND: Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CLpro) inhibitors which have been approved for the treatment of COVID-19 in 2021 and 2022, respectively. Previous studies have identified 3CLpro mutations that are associated with reduced susceptibility to these antivirals. The aim of the current study was to estimate the global prevalence of 3CLpro inhibitor-resistant SARS-CoV-2 strains. METHODS: We compiled a list of 3CLpro mutations which have been associated with nirmatrelvir or ensitrelvir resistance based on either viral replication or 3CLpro activity assays, and determined their prevalence among 13.4 million sequences deposited in GISAID as of December 14, 2022, about 1 year after the approval of nirmatrelvir-ritonavir. We analyzed the prevalence for different time periods, SARS-CoV-2 lineages and geographical locations. FINDINGS: Overall, 0.5% (67,095/13,446,588) of the sequences contained at least one mutation that was shown to affect the inhibitory activity of nirmatrelvir or ensitrelvir on viral replication or 3CLpro activity. We did not observe any increasing trend of resistance after the widespread clinical use of nirmatrelvir-ritonavir. G15S (2070 per million) and T21I (1386 per million) were the most prevalent mutations, and these mutations were dominant in some SARS-CoV-2 lineages. E166V and S144E, previously shown to affect the inhibitory activity of nirmatrelvir on viral replication or protease activity by > 100-folds, were found in <1 per million sequences. INTERPRETATION: Our data suggest that 3CLpro inhibitor resistance is currently rare. However, continuous global genotypic and phenotypic surveillance would be crucial in the early detection of resistant mutants. FUNDING: Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, the Emergency Key Program of Guangzhou Laboratory (See acknowledgements for full list).

Case of steroid refractory dengue myositis responsive to intravenous immunoglobulins.

Dengue is an arbovirus infection that usually presents with the symptoms of high-grade fever, myalgia and rash. Dengue is spread by the Aedes aegypti mosquito and frequent outbreaks are being reported in regions like Pakistan, India and Sri Lanka. Although muscle ache is quite common with dengue fever, overt myositis is of very rare occurrence. Here, we report a case of a young girl who presented to us with serologically confirmed dengue infection, and having bilateral upper and lower limb weakness. Her raised creatine kinase, along with her electromyography pattern was suggestive of myositis. Her condition was steroid-resistant and responded only to intravenous immunoglobulin. She was discharged in a stable condition.

The Effects of Social Distance and Asymmetric Reward and Punishment on Individual Cooperative Behavior in Dilemma Situations.

The behavior decisions in social dilemmas are highlighted in sociological, economic, and social psychological studies. Across two studies, the iterated prisoner's dilemma is used as a basic paradigm to explore the effects of social distance and asymmetric reward and punishment on an individual's cooperative behavior. Experiment 1 (N = 80) used a 2 (social distance: intimacy vs. strangeness) × 2 (symmetry of rewards: symmetric rewards vs. asymmetric rewards) within-subject design and demonstrated that when there were only two options, namely, cooperation and defection, cooperative behavior was influenced by social distance and symmetry of rewards, respectively, and the interaction was not significant. Experiment 2 (N = 80) used a 2 (social distance: intimacy vs. strangeness) × 2 (symmetry of punishment: symmetric punishment vs. asymmetric punishment) within-subject design and showed that the cooperative behavior of participants decreased when the punishment option was added, and the two levels of symmetry and asymmetry were set. Specifically, compared with the symmetric punishment group, the asymmetric punishment group was more likely to choose a defection strategy and less likely to use a punishment strategy. Moreover, there was a marginal interaction effect between social distance and symmetry of punishment, and symmetry of punishment was a significant mediator in the relationship between social distance and individual cooperation. Specifically, asymmetric punishment reduced only the cooperation rate (CR) between participants and their friends. In conclusion, in dilemma situations, asymmetric reward did not influence individual cooperative behavior at different social distances, while asymmetric punishment did, because the sense of loss was more likely to awaken an individual's social comparison motives.

A highly stable electrode with low electrode-skin impedance for wearable brain-computer interface.

To date, brain-computer interfaces (BCIs) have proved to play a key role in many medical applications, for example, the rehabilitation of stroke patients. For post-stroke rehabilitation, the BCIs require the EEG electrodes to precisely translate the brain signals of patients into intended movements of the paralyzed limb for months. However, the gold standard silver/silver-chloride electrodes cannot satisfy the requirements for long-term stability and preparation-free recording capability in wearable EEG devices, thus limiting the versatility of EEG in wearable BCI applications over time outside the rehabilitation center. Here, we design a long-term stable and low electrode-skin interfacial impedance conductive polymer-hydrogel EEG electrode that maintains a lower impedance value than gel-based electrodes for 29 days. With this technology, EEG-based long-term and wearable BCIs could be realized in the near future. To demonstrate this, our designed electrode is applied for a wireless single-channel EEG device that detects changes in alpha rhythms in eye-open/eye-close conditions. In addition, we validate that the designed electrodes could capture oscillatory rhythms in motor imagery protocols as well as low-frequency time-locked event-related potentials from healthy subjects, with similar or better performance than gel-based electrodes. Finally, we demonstrate the use of the designed electrode in online BCI-based functional electrical stimulation, which could be used for post-stroke rehabilitation.

Hepatitis B Vaccination Coverage among Bangladeshi Healthcare Workers: Findings from Tertiary Care Hospitals.

Healthcare workers (HCWs) are at a four-fold higher risk of being infected with the hepatitis B virus in hospital settings. This study investigated the hepatitis B vaccination coverage among Bangladeshi HCWs in selected tertiary care hospitals. Between September 2020 to January 2021, a multicenter cross-sectional study was conducted in 11 hospitals across Bangladesh. Participants included physicians, nurses, cleaners, and administrative staff. A semi-structured questionnaire was used to collect data through face-to-face interviews. Descriptive and multivariate statistics were used to analyze the data. The overall hepatitis B vaccination coverage was 66.6% (1363/2046) among HCWs, with cleaning staff having the lowest at 38.8%. Among the unvaccinated, 89.2% of HCWs desired to receive the free vaccine in the near future. In the last year, over one-fourth of staff (27.9%) had at least one history of needlestick injury. Only 9.8% HCWs were found to have attended training on hepatitis B virus prevention and management in the previous two years. Multivariate analysis revealed that physicians (AOR: 7.13, 95% CI: 4.94-10.30) and nurses (AOR: 6.00, 95% CI: 4.09-8.81) were more likely to be vaccinated against hepatitis B than cleaners and administrative staff. Low uptake of hepatitis B vaccination among HCWs suggests policies that require vaccination are needed to achieve optimum vaccine coverage.

Hospitalization and Mortality by Vaccination Status among COVID-19 Patients Aged ≥ 25 Years in Bangladesh: Results from a Multicenter Cross-Sectional Study.

The COVID-19 pandemic has inflicted a massive disease burden globally, involving 623 million confirmed cases with 6.55 million deaths, and in Bangladesh, over 2.02 million clinically confirmed cases of COVID-19, with 29,371 deaths, have been reported. Evidence showed that vaccines significantly reduced infection, severity, and mortality across a wide age range of populations. This study investigated the hospitalization and mortality by vaccination status among COVID-19 patients in Bangladesh and identified the vaccine's effectiveness against severe outcomes in real-world settings. Between August and December 2021, we conducted this cross-sectional survey among 783 RT-PCR-confirmed COVID-19 hospitalized patients admitted to three dedicated COVID-19 hospitals in Bangladesh. The study used a semi-structured questionnaire to collect information. We reviewed the patient's records and gathered COVID-19 immunization status from the study participants or their caregivers. Patients with incomplete or partial data from the record were excluded from enrollment. Logistic regression analyses were performed to determine the association between key variables with a patient's vaccination status and mortality. The study revealed that overall hospitalization, severity, and morality were significantly high among unvaccinated study participants. Only one-fourth (25%) of hospitalized patients were found COVID-19 vaccinated. Morality among unvaccinated COVID-19 study participants was significantly higher (AOR: 7.17) than the vaccinated (11.17% vs. 1.53%). Severity was found to be seven times higher among unvaccinated patients. Vaccination coverage was higher in urban areas (29.8%) compared to rural parts (20.8%), and vaccine uptake was lower among female study participants (22.7%) than male (27.6%). The study highlighted the importance of COVID-19 vaccines in reducing mortality, hospitalization, and other severe consequences. We found a gap in vaccination coverage between urban and rural settings. The findings would encourage the entire population toward immunization and aid the policymakers in the ground reality so that more initiatives are taken to improve vaccination coverage among the pocket population.

Infection prevention and control in tertiary care hospitals of Bangladesh: results from WHO infection prevention and control assessment framework (IPCAF).

INTRODUCTION: Infection prevention and control (IPC) in healthcare settings is imperative for the safety of patients as well as healthcare providers. To measure current IPC activities, resources, and gaps at the facility level, WHO has developed the Infection Prevention and Control Assessment Framework (IPCAF). This study aimed to assess the existing IPC level of selected tertiary care hospitals in Bangladesh during the COVID-19 pandemic using IPCAF to explore their strengths and deficits. METHODS: Between September and December 2020, we assessed 11 tertiary-care hospitals across Bangladesh. We collected the information from IPC focal person and/or hospital administrator from each hospital using the IPCAF assessment tool.. The score was calculated based on eight core components and was used to categorize the hospitals into four distinct IPC levels- Inadequate, Basic, Intermediate, and Advanced. Key performance metrics were summarized within and between hospitals. RESULTS: The overall median IPCAF score was 355.0 (IQR: 252.5-397.5) out of 800. The majority (73%) of hospitals scored as 'Basic' IPC level, while only 18% of hospitals were categorized as 'Intermediate'. Most hospitals had IPC guidelines as well as environments, materials and equipments. Although 64% of hospitals had IPC orientation and training program for new employees, only 30% of hospitals had regular IPC training program for the staff. None of the hospitals had an IPC surveillance system with standard surveillance case definitions to track HAIs. Around 90% of hospitals did not have an active IPC monitoring and audit system. Half of the hospitals had inadequate staffing considering the workload. Bed occupancy of one patient per bed in all units was found in 55% of hospitals. About 73% of hospitals had functional hand hygiene stations, but sufficient toilets were available in only 37% of hospitals. CONCLUSION: The majority of sampled tertiary care hospitals demonstrate inadequate IPC level to ensure the safety of healthcare workers, patients, and visitors. Quality improvement programs and feedback mechanisms should be implemented to strengthen all IPC core components, particularly IPC surveillance, monitoring, education, and training, to improve healthcare safety and resilience.

Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong.

Monitoring population protective immunity against SARS-CoV-2 variants is critical for risk assessment. We hypothesize that Hong Kong's explosive Omicron BA.2 outbreak in early 2022 could be explained by low herd immunity. Our seroprevalence study using sera collected from January to December 2021 shows a very low prevalence of neutralizing antibodies (NAb) against ancestral virus among older adults. The age group-specific prevalence of NAb generally correlates with the vaccination uptake rate, but older adults have a much lower NAb seropositive rate than vaccination uptake rate. For all age groups, the seroprevalence of NAb against Omicron variant is much lower than that against the ancestral virus. Our study suggests that this BA.2 outbreak and the exceptionally high case-fatality rate in the ≥80 year-old age group (9.2%) could be attributed to the lack of protective immunity in the population, especially among the vulnerable older adults, and that ongoing sero-surveillance is essential.