Reduced Pathogenicity and Transmission Potential of Omicron BA.1 and BA.2 Sublineages Compared with the Early Severe Acute Respiratory Syndrome Coronavirus 2 D614G Variant in Syrian Hamsters.

BACKGROUND: The epidemiological advantage of Omicron variant is evidenced by its rapid spread and the ability to outcompete prior variants. Among Omicron sublineages, early outbreaks were dominated by BA.1, while BA.2 has gained dominance since February 2022. The relative pathogenicity and transmissibility of BA.1 and BA.2 have not been fully defined. METHODS: We compared viral loads and clinical signs in Syrian hamsters after infection with BA.1, BA.2, or D614G variant. A competitive transmission model and next-generation sequencing were used to compare the relative transmission potential of BA.1 and BA.2. RESULTS: BA.1 and BA.2 caused no apparent clinical signs, while D614G caused more than 10% weight loss. Higher viral loads were detected in nasal wash samples and nasal turbinate and lung tissues from BA.1-inoculated hamsters compared with BA.2-inoculated hamsters. No aerosol transmission was observed for BA.1 or BA.2 under the experimental condition in which D614G transmitted efficiently. BA.1 and BA.2 were able to transmit among hamsters via direct contact; however, BA.1 transmitted more efficiently than BA.2 under the competitive transmission model. No recombination was detected from direct contacts exposed simultaneously to BA.1 and BA.2. CONCLUSIONS: Omicron BA.1 and BA.2 demonstrated attenuated pathogenicity and reduced transmission potential in hamsters compared with early SARS-CoV-2 strains.

Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022.

We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021-February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5' end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed.

Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021.

We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler in a quarantine hotel in Hong Kong, China. The Omicron variant was also detected in a fully vaccinated traveler staying in a room across the corridor from the index patient, suggesting transmission despite strict quarantine precautions.

Monitoring International Travelers Arriving in Hong Kong for Genomic Surveillance of SARS-CoV-2.

We sequenced ≈50% of coronavirus disease cases imported to Hong Kong during March-July 2021 and identified 70 cases caused by Delta variants of severe acute respiratory syndrome coronavirus 2. The genomic diversity detected in Hong Kong was similar to global diversity, suggesting travel hubs can play a substantial role in surveillance.

Development and Implementation of a Multicomponent Protocol to Promote Sleep and Reduce Delirium in a Medical Intensive Care Unit.

BACKGROUND: Evidence suggests that poor sleep increases risk of delirium. Because delirium is associated with poor outcomes, institutions have developed protocols to improve sleep in critically ill patients. OBJECTIVE: To assess the impact of implementing a multicomponent sleep protocol. METHODS: In this prospective, preimplementation and postimplementation evaluation, adult patients admitted to the medical intensive care unit (ICU) over 42 days were included. Outcomes evaluated included median delirium-free days, median Richards-Campbell Sleep Questionnaire (RCSQ) score, median optimal sleep nights, duration of mechanical ventilation (MV), ICU and hospital length of stay (LOS), and in-hospital mortality. RESULTS: The preimplementation group included 78 patients and postimplementation group, 84 patients. There was no difference in median delirium-free days (1 day [interquartile range, IQR, = 0-2.5] vs 1 day [IQR = 0-2]; P = 0.48), median RCSQ score (59.4 [IQR = 43.2-71.6] vs 61.2 [IQR = 49.9-75.5]; P = 0.20), median optimal sleep nights (1 night [IQR = 0-2] vs 1 night [IQR = 0-2]; P = 0.95), and in-hospital mortality (16.7% vs 17.9%, P = 1.00). Duration of MV (8 days [IQR = 4-10] vs 4 days [IQR = 2-7]; P = 0.03) and hospital LOS (13 days [IQR = 7-22.3] vs 8 days [IQR = 6-17]; P = 0.05) were shorter in the postimplementation group, but both were similar between groups after adjusting for age and severity of illness. CONCLUSIONS AND RELEVANCE: This report demonstrates that implementation of a multicomponent sleep protocol in everyday ICU care is feasible, but limitations exist when evaluating impact on measurable outcomes. Additional evaluations are needed to identify the most meaningful interventions and best practices for quantifying impact on patient outcomes.

SARS-CoV-2 Superspread in Fitness Center, Hong Kong, China, March 2021.

To investigate a superspreading event at a fitness center in Hong Kong, China, we used genomic sequencing to analyze 102 reverse transcription PCR-confirmed cases of severe acute respiratory syndrome coronavirus 2 infection. Our finding highlights the risk for virus transmission in confined spaces with poor ventilation and limited public health interventions.

Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong.

We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.

Intermediate Care Units: A Survey of Organization Practices Across the United States.

PURPOSE: Intermediate care units (IMCUs) represent an alternative care setting with nurse staffing levels between those of the general ward and the intensive care unit (ICU). Despite rising prevalence, little is known about IMCU practices across US hospitals. The purpose of this study is to characterize utilization patterns and assess for variation. MATERIALS AND METHODS: A 14-item survey was distributed to a random nationwide sample of pulmonary and critical care physicians between January and April 2017. RESULTS: A total of 51 physicians from 24 different states completed the survey. Each response represented a unique institution, the majority of which were public (59%), academic (73%), and contained at least 1 IMCU (65%). Of the IMCUs surveyed, 58% operated as 1 mixed unit that admitted medical, cardiac, and surgical patients as opposed to having separate subspecialty units. Ninety-one percent of units admitted step-down patients from the ICU, but 39% of units accepted a mix of step-up patients, step-down patients, postoperative patients, and patients from the emergency department. Intensivists managed care in 21% of units whereas 36% had no intensivist involvement. CONCLUSION: Organization practices vary considerably between IMCUs across institutions. The impact of different organization practices on patient outcomes should be assessed.

Motor neuron disease, TDP-43 pathology, and memory deficits in mice expressing ALS-FTD-linked UBQLN2 mutations.

Missense mutations in ubiquilin 2 (UBQLN2) cause ALS with frontotemporal dementia (ALS-FTD). Animal models of ALS are useful for understanding the mechanisms of pathogenesis and for preclinical investigations. However, previous rodent models carrying UBQLN2 mutations failed to manifest any sign of motor neuron disease. Here, we show that lines of mice expressing either the ALS-FTD-linked P497S or P506T UBQLN2 mutations have cognitive deficits, shortened lifespans, and develop motor neuron disease, mimicking the human disease. Neuropathologic analysis of the mice with end-stage disease revealed the accumulation of ubiquitinated inclusions in the brain and spinal cord, astrocytosis, a reduction in the number of hippocampal neurons, and reduced staining of TAR-DNA binding protein 43 in the nucleus, with concomitant formation of ubiquitin+ inclusions in the cytoplasm of spinal motor neurons. Moreover, both lines displayed denervation muscle atrophy and age-dependent loss of motor neurons that correlated with a reduction in the number of large-caliber axons. By contrast, two mouse lines expressing WT UBQLN2 were mostly devoid of clinical and pathological signs of disease. These UBQLN2 mouse models provide valuable tools for identifying the mechanisms underlying ALS-FTD pathogenesis and for investigating therapeutic strategies to halt disease.

ALS-linked mutations in ubiquilin-2 or hnRNPA1 reduce interaction between ubiquilin-2 and hnRNPA1.

Amyotrophic lateral sclerosis (ALS)-linked mutations in UBQLN2 and some members of the heterogeneous nuclear ribonucleoproteins (hnRNPs) family cause ALS. Most mutations in UBQLN2 are missense mutations that occur in and around a PXX repeat motif located in the central domain of the encoded protein. However, neither the function of the PXX motif nor the mechanism by which mutations in UBQLN2 cause ALS is known. We screened a yeast two-hybrid library using the central domain of ubiquilin-2 hoping to identify proteins whose binding is affected by the UBQLN2 mutations. Three such interactors were identified-hnRNPA1, hnRNPA3 and hnRNPU-all members of the hnRNP family. The interacting region in each of these proteins was their glycine-rich domain, the domain most frequently mutated in hnRNP-related proteins that cause ALS. We focused on hnRNPA1, because a mutation in the protein causes ALS. We confirmed the interaction between wild-type (WT) ubiquilin-2 and hnRNPA1 proteins in vitro and in cells. In contrast, all five ALS mutations in ubiquilin-2 that we examined had reduced binding with WT hnRNPA1. In addition, hnRNPA1 carrying the D262V missense mutation that causes ALS failed to bind WT ubiquilin-2. Overexpression of ubiquilin-2 containing the ALS mutations increased cell death and, for several of the mutants, this correlated with increased translocation of hnRNPA1 to the cytoplasm. Knockdown of ubiquilin-2 led to increased turnover of hnRNPA1, indicating ubiquilin-2 functions to stabilize hnRNPA1. The discovery that ubiquilin-2 interacts with hnRNP proteins and that mutation in either protein disrupts interaction suggests a connection between proteostasis and RNA metabolism.

Utilization of rapid response resources and outcomes in a comprehensive cancer center*.

OBJECTIVE: To compare the differences in characteristics and outcomes of cancer center patients with other subspecialty medical patients reviewed by rapid response teams. DESIGN: A retrospective cohort study of hospitalized general medicine patients, subspecialty medicine patients, and oncology patients requiring rapid response team activation over a 2-year period from September 2009 to August 2011. PATIENTS: Five hundred fifty-seven subspecialty medical patients required rapid response team intervention. SETTING: A single academic medical center in the southeastern United States (800+ bed) with a dedicated 50-bed inpatient comprehensive cancer care center. INTERVENTIONS: Data abstraction from computerized medical records and a hospital quality improvement rapid response database. MEASUREMENTS AND MAIN RESULTS: Of the 557 patients, 135 were cancer center patients. Cancer center patients had a significantly higher Charlson Comorbidity Score (4.4 vs 2.9, < 0.001). Cancer center patients had a significantly longer hospitalization period prior to rapid response team activation (11.4 vs 6.1 d, p < 0.001). There was no significant difference between proportions of patients requiring ICU transfer between the two groups (odds ratio, 1.2; 95% CI, 0.8-1.8). Cancer center patients had a significantly higher in-hospital mortality compared with the other subspecialty medical patients (33% vs 18%; odds ratio, 2.2; 95% CI, 1.50-3.5). If the rapid response team event required an ICU transfer, this finding was more pronounced (56% vs 23%; odds ratio, 4.0; 95% CI, 2.0-7.8). The utilization of rapid response team resources during the 2-year period studied was also much higher for the oncology patients with 37.34 activations per 1,000 patient discharges compared with 20.86 per 1,000 patient discharges for the general medical patients. CONCLUSIONS: Oncology patients requiring rapid response team activation have a significantly higher in-hospital mortality rate, particularly if the rapid response team requires ICU transfer. Oncology patients also utilize rapid response team resources at a much higher rate.

Lung transplant outcomes in cystic fibrosis patients with pre-operative Mycobacterium abscessus respiratory infections.

BACKGROUND: Mycobacterium abscessus in cystic fibrosis (CF) patients is considered a contraindication to lung transplantation. We examine the post-transplant outcomes of CF patients with M. abscessus pre-transplant. METHODS: CF patients transplanted at the University of North Carolina from 1992 to 2012 were retrospectively examined. Patients with at least one respiratory sample positive for M. abscessus prior to transplantation were included. Data collected included age, FEV1, body mass index (BMI), systemic steroid use, diabetes mellitus, ventilatory assistance, co-existent CF pathogens, imaging, post-transplant complications, and survival. RESULTS (N = 13): At transplant, mean age was 24.6 yr, mean BMI was 18.1 kg/m(2), six had 3+ positive smears for M. abscessus, and three were ventilator dependent. All met American Thoracic Society microbiological criteria for disease pre-transplant. Three patients developed M. abscessus-related complications, with clearance of the organism following treatment. Survival post-transplant shows 77% alive at one yr, 64% at three yr, and 50% at five yr; none died of M. abscessus. The survival data showed no statistically significant difference (p = 0.8) compared with a contemporaneously transplanted population of CF patients without M. abscessus (n = 154). CONCLUSION: Lung transplantation, with favorable survival, is possible in CF patients with M. abscessus. Even if M. abscessus recurs, local control and clearance is possible.

The impact of glaucoma referral refinement criteria on referral to, and first-visit discharge rates from, the hospital eye service: the Health Innovation & Education Cluster (HIEC) Glaucoma Pathways project.

PURPOSE: To assess the impact of referral refinement criteria on the number of patients referred to, and first-visit discharges from, the Hospital Eye Service (HES) in relation to the National Institute for Health & Clinical Excellence (NICE) Glaucoma Guidelines, Joint College Group Guidance (JCG) and the NICE commissioning guidance. METHODS: All low-risk (one risk factor: suspicious optic disc, abnormal visual field (VF), raised intra-ocular pressure (IOP) (22-28 mmHg) or IOP asymmetry (>5 mmHg) and high-risk (more than one risk factor, shallow anterior chamber or IOP >28 mmHg) referrals to the HES from 2006 to 2011 were analysed. Low-risk referrals were seen by Optometrists with a specialist interest in glaucoma and high-risk referrals were referred directly to the HES. RESULTS: Two thousand nine hundred and twelve patient records were analysed. The highest Consultant first-visit discharge rates were for referrals based on IOP alone (45% for IOP 22-28 mmHg) and IOP asymmetry (53%), VF defect alone (46%) and for abnormal IOP and VF (54%). The lowest first-visit discharge rates were for referrals for suspicious optic disc (19%) and IOP >28 mmHg (22%). 73% of patients aged 65-80 and 60% of patients aged >80 who were referred by the OSI due to an IOP between 22-28 mmHg would have satisfied the JCG criteria for non-referral. For patients referred with an IOP >28 mmHg and an otherwise normal examination, adherence to the NICE commissioning guidance would have resulted in 6% fewer referrals. In 2010 this scheme reduced the number of patients attending the HES by 15%, which resulted in a saving of £16 258 (13%). CONCLUSION: The results support that referrals for a raised IOP alone or in combination with an abnormal VF be classified as low-risk and undergo referral refinement. Adherence to the JCG and the NICE commissioning guidance as onward referral criteria for specialist optometrists in this referral refinement scheme would result in fewer referrals.

Respiratory diseases: meeting the challenges of screening, prevention, and treatment.

Respiratory conditions, both acute and chronic, continue to have a significant impact on worldwide health because of their high prevalence, the high disease burden they place on individual health, and their enormous cost to the health care system. There are also unmeasured indirect economic costs due to loss of productivity. Despite advances in our understanding of the complex pathophysiology of respiratory diseases, as well as the availability of relatively straightforward primary prevention measures, the prevalence of chronic respiratory diseases continues to rise. In addition, periodic outbreaks of acute infectious respiratory conditions result in significant cost and even mortality, and the incidence of these conditions fluctuates widely from year to year. Although we have seen recent developments in medical therapies for respiratory diseases, and there are established and well-publicized disease management guidelines, morbidity and mortality remain high. One intervention that has lagged behind has been smoking prevention and cessation, which is the mainstay of prevention for chronic obstructive pulmonary disease and lung cancer. The persistence of these conditions underscores vulnerabilities within our national and regional health care systems. Several of the articles in this issue of the NCMJ describe innovative programs to address these challenges.

In-Hospital Code Status Updates: Trends Over Time and the Impact of COVID-19.

OBJECTIVE: The primary objective was to evaluate if the percentage of patients with missing or inaccurate code status documentation at a Trauma Level 1 hospital could be reduced through daily updates. The secondary objective was to examine if patient preferences for DNR changed during the COVID-19 pandemic. METHODS: This retrospective study, spanning March 2019 to December 2022, compared the code status in ICU and ED patients drawn from two data sets. The first was based on historical electronic medical records (EHR), and the second involved daily updates of code status following patient admission. RESULTS: Implementing daily updates upon admission was more effective in ICUs than in the ED in reducing missing code status documentation. Around 20% of patients without a specific code status chose DNR under the new system. During COVID-19, a decrease in ICU patients choosing DNR and an increase in full code (FC) choices were observed. CONCLUSION: This study highlights the importance of regular updates and discussions regarding code status to enhance patient care and resource allocation in ICU and ED settings. The COVID-19 pandemic's influence on shifting patient preferences towards full code status underscores the need for adaptable documentation practices. Emphasizing patient education about DNR implications and benefits is key to supporting informed decisions that reflect individual health contexts and values. This approach will help balance the considerations for DNR and full code choices, especially during health care crises.

Development of multiplex RT-ddPCR assays for detection of SARS-CoV-2 and other common respiratory virus infections.

BACKGROUND: Measures for mitigation of Coronavirus Disease 2019 (COVID-19) were set to reduce the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 and other respiratory viruses share similar transmission routes and some common clinical manifestations. Co-circulation of SARS-CoV-2 and other common respiratory viruses is imminent. Therefore, development of multiplex assays for detecting these respiratory viruses is essential for being prepared for future outbreaks of respiratory viruses. METHODS: A panel of three reverse transcription droplet digital PCR (RT-ddPCR) assays were developed to detect 15 different human respiratory viruses. Evaluations of its performance were demonstrated. A total of 100 local and 98 imported COVID-19 cases in Hong Kong were screened for co-infection with other common respiratory viruses. RESULTS: All detected viral targets showed distinct signal clusters using the multiplex RT-ddPCR assays. These assays have a broad range of linearity and good intra-/inter-assay reproducibility for each target. The lower limits of quantification for all targets were ≤46 copies per reaction. Six imported cases of COVID-19 were found to be co-infected with other respiratory viruses, whereas no local case of co-infection was observed. CONCLUSIONS: The multiplex RT-ddPCR assays were demonstrated to be useful for screening of respiratory virus co-infections. The strict preventive measures applied in Hong Kong may be effective in limiting the circulation of other human respiratory viruses. The multiplex assays developed in this study can achieve a robust detection method for clinical and research purposes.

Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.

Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.

Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong.

Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.

TOXOPLASMA GONDII PREVALENCE, PARTIAL GENOTYPES, AND SPATIAL VARIATION IN NORTH AMERICAN RIVER OTTERS (LONTRA CANADENSIS) IN THE UPPER PENINSULA OF MICHIGAN, USA.

Toxoplasma gondii is a ubiquitous parasitic protozoan that poses a health threat to wildlife and human health worldwide. Oocysts shed into the environment in felid host feces may persist for several years. Runoff from rainfall and snowmelt may carry the oocysts into waterways. Semiaquatic mammals such as the Northern American river otter (Lontra canadensis) are particularly at risk of exposure, as they may encounter infective stages in both terrestrial and aquatic environments. Despite this risk, only a small number of studies have examined the prevalence of T. gondii in US river otter populations. Tongue tissue was sampled from 124 otters from the Upper Peninsula of Michigan submitted by trappers to the Michigan Department of Natural Resources in the 2018-19 harvest season. Following DNA extraction, a portion of the B1 T. gondii gene was amplified with PCR. A subset of positive samples was genotyped for comparison with known T. gondii sequences. Of the 124 tongue samples, 35 (28%) were positive for T. gondii. Prevalence did not differ significantly between sexes or age classes across the entire study area. Most (53.8%) of the genotyped samples were type 4 (type 12), a genotype commonly found in North American wildlife. Genotypes 127 and 197 were also found. Three clusters of T. gondii prevalence were identified through SaTScan analysis, although they were not significant. When modeling prevalence of T. gondii with covariates at individual otter locations, the top three models included the presence of Sarcocystis, area of exotic plants, area of agriculture, and sex of the otter. Our results suggest that T. gondii is widespread in otter populations in the Upper Peninsula of Michigan.

Within-host diversity of SARS-CoV-2 lineages and effect of vaccination.

Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.