Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks

Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.

Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study

IntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of rapid (<48h) and 4 weeks of longer-turnaround (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected [≥]48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.

Defining the need for faculty development in assessment.

BACKGROUND: High-quality workplace-based assessments are essential for competency-based surgical education. We explored education leaders' perceptions regarding faculty competence in assessment. METHODS: Surgical education leaders were surveyed regarding which areas faculty needed improvement, and knowledge of assessment tools. Respondents were queried on specific skills regarding (a)importance in resident/medical student education (b)competence of faculty in assessment and feedback. RESULTS: Surveys (n = 636) were emailed, 103 responded most faculty needed improvement in: verbal (86%) and written (83%) feedback, assessing operative skill (49%) and preparation for procedures (50%). Cholecystectomy, trauma laparotomy, inguinal herniorrhaphy were "very-extremely important" in resident education (99%), but 21-24% thought faculty "moderately to not-at-all" competent in assessment. This gap was larger for non-technical skills. Regarding assessment tools, 56% used OSATS, 49% Zwisch; most were unfamiliar with all non-technical tools. SUMMARY: These data demonstrate a significant perceived gap in competence of faculty in assessment and feedback, and unfamiliarity with assessment tools. This can inform faculty development to support competency-based surgical education.

SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. MethodsWe collected viral sequences and clinical data of patients admitted with SARS-CoV-2 and hospital-onset COVID-19 infections (HOCIs), sampled 16/11/2020 - 10/01/2021, from eight hospitals participating in the COG-UK-HOCI study. Associations between the variant and the outcomes of all-cause mortality and intensive therapy unit (ITU) admission were evaluated using mixed effects Cox models adjusted by age, sex, comorbidities, care home residence, pregnancy and ethnicity. ResultsSequences were obtained from 2341 inpatients (HOCI cases = 786) and analysis of clinical outcomes was carried out in 2147 inpatients with all data available. The hazard ratio (HR) for mortality of B.1.1.7 compared to other lineages was 1.01 (95% CI 0.79-1.28, P=0.94) and for ITU admission was 1.01 (95% CI 0.75-1.37, P=0.96). Analysis of sex-specific effects of B.1.1.7 identified increased risk of mortality (HR 1.30, 95% CI 0.95-1.78) and ITU admission (HR 1.82, 95% CI 1.15-2.90) in females infected with the variant but not males (mortality HR 0.82, 95% CI 0.61-1.10; ITU HR 0.74, 95% CI 0.52-1.04). ConclusionsIn common with smaller studies of patients hospitalised with SARS-CoV-2 we did not find an overall increase in mortality or ITU admission associated with B.1.1.7 compared to other lineages. However, women with B.1.1.7 may be at an increased risk of admission to intensive care and at modestly increased risk of mortality.

Molnupiravir (EIDD-2801) inhibits SARS-CoV2 replication in Syrian hamsters model

Favipiravir and Molnupiravir, orally available antivirals, have been reported to exert antiviral activity against SARS-CoV2. In recent days preliminary efficacy data have been reported in COVID-19 patients. We here studied the combined antiviral effect of the drugs in the SARS-CoV2 hamster infection model. We first demonstrate that Molnupiravir can reduce infectious virus titers in lungs of infected animals in a dose-dependent manner by up to 3.5 log10 which is associated with a marked improvement of virus-induced lung pathology. When animals are treated with a combination of suboptimal doses of Molnupiravir and Favipiravir (that each alone result in respectively a 1.3 log10 and 1.1 log10 reduction of infectious virus titers in the lungs), a marked combined potency is observed. Infectious virus titers in the lungs of animals treated with the combo are on average reduced by 4.5 log10 and infectious virus are no longer detected in the lungs of 60% of treated infected animals. Both drugs result in an increased mutation frequency of the remaining viral RNA recovered from the lungs. In the combo-treated hamsters an increased frequency of C-to-T and G-to-A mutations in the viral RNA is observed as compared to the single treatment groups which may explain the pronounced antiviral potency of the combination. Our findings may lay the basis for the design of clinical studies to test the efficacy of the combination of Molnupiravir and Favipiravir in the treatment of COVID-19.

Remdesivir induced viral RNA and subgenomic RNA suppression, and evolution of viral variants in SARS-CoV-2 infected patients.

While changes in SARS-CoV-2 viral load over time have been documented, detailed information on the impact of remdesivir and how it might alter intra-host viral evolution is limited. Sequential viral loads and deep sequencing of SARS-CoV-2 recovered from the upper respiratory tract of hospitalised children revealed that remdesivir treatment suppressed viral RNA levels in one patient but not in a second infected with an identical strain. Evidence of drug resistance to explain this difference was not found. Reduced levels of subgenomic (sg) RNA during treatment of the second patient, suggest an additional effect of remdesivir on viral replication that is independent of viral RNA levels. Haplotype reconstruction uncovered persistent SARS-CoV-2 variant genotypes in four patients. We conclude that these are likely to have arisen from within-host evolution, and not co-transmission, although superinfection cannot be excluded in one case. Sample-to-sample heterogeneity in the abundances of variant genotypes is best explained by the presence of discrete viral populations in the lung with incomplete population sampling in diagnostic swabs. Such compartmentalisation is well described in serious lung infections caused by influenza and Mycobacterium tuberculosis and has been associated with poor drug penetration, suboptimal treatment and drug resistance. Our data provide evidence that remdesivir is able to suppress SARS-CoV-2 replication in vivo but that its efficacy may be compromised by factors reducing penetration into the lung. Based on data from influenza and Mycobacterium tuberculosis lung infections we conclude that early use of remdesivir combined with other agents should now be evaluated. Summary SentenceDeep sequencing of longitudinal samples from SARS-CoV-2 infected paediatric patients identifies evidence of remdesivir-associated inhibition of viral replication in vivo and uncovers evidence of within host evolution of distinct viral genotypes.

SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.

Genetic and Environmental Factors Contributing to Visceral Adiposity in Asian Populations

Obesity-associated metabolic illnesses are increasing at an alarming rate in Asian countries. A common feature observed in the Asian population is a higher incidence of abdominal obesity—the “skinny-fat” Asian syndrome. In this review, we critically evaluate the relative roles of genetics and environmental factors on fat distribution in Asian populations. While there is an upward trend in obesity among most Asian countries, it appears particularly conspicuous in Malaysia. We propose a novel theory, the Malaysian gene-environment multiplier hypothesis, which explains how ancestral variations in feast-and-famine cycles contribute to inherited genetic predispositions that, when acted on by modern-day stressors—most notably, urbanization, westernization, lifestyle changes, dietary transitions, cultural pressures, and stress—contribute to increased visceral adiposity in Asian populations. At present, the major determinants contributing to visceral adiposity in Asians are far from conclusive, but we seek to highlight critical areas for further research.

Genetic and Environmental Factors Contributing to Visceral Adiposity in Asian Populations

Obesity-associated metabolic illnesses are increasing at an alarming rate in Asian countries. A common feature observed in the Asian population is a higher incidence of abdominal obesity—the “skinny-fat” Asian syndrome. In this review, we critically evaluate the relative roles of genetics and environmental factors on fat distribution in Asian populations. While there is an upward trend in obesity among most Asian countries, it appears particularly conspicuous in Malaysia. We propose a novel theory, the Malaysian gene-environment multiplier hypothesis, which explains how ancestral variations in feast-and-famine cycles contribute to inherited genetic predispositions that, when acted on by modern-day stressors—most notably, urbanization, westernization, lifestyle changes, dietary transitions, cultural pressures, and stress—contribute to increased visceral adiposity in Asian populations. At present, the major determinants contributing to visceral adiposity in Asians are far from conclusive, but we seek to highlight critical areas for further research.

"Taking Training to the Next Level": The American College of Surgeons Committee on Residency Training Survey.

OBJECTIVE: The American College of Surgeons (ACS) appointed a committee of leaders from the ACS, Association of Program Directors in Surgery, Accreditation Council for Graduate Medical Education, and American Board of Surgery to define key challenges facing surgery resident training programs and to explore solutions. The committee wanted to solicit the perspectives of surgery resident program directors (PDs) given their pivotal role in residency training. DESIGN: Two surveys were developed, pilot tested, and administered to PDs following Institutional Review Board approval. PDs from 247 Accreditation Council for Graduate Medical Education-accredited general surgery programs were randomized to receive 1 of the 2 surveys. Bias analyses were conducted, and adjusted Pearson χ2 tests were used to test for differences in response patterns by program type and size. SETTING: All accredited general surgery programs in the United States were included in the sampling frame of the survey; 10 programs with initial or withdrawn accreditation were excluded from the sampling frame. PARTICIPANTS: A total of 135 PDs responded, resulting in a 54.7% response rate (Survey A: n = 67 and Survey B: n = 68). The respondent sample was determined to be representative of program type and size. RESULTS: Nearly 52% of PD responses were from university-based programs, and 41% had over 6 residents per graduating cohort. More than 61% of PDs reported that, compared to 10 years ago, both entering and graduating residents are less prepared in technical skills. PDs expressed significant concerns regarding the effect of duty-hour restrictions on the overall preparation of graduating residents (61%) and quality of patient care (57%). The current 5-year training structure was viewed as needing a significant or extensive increase in opportunities for resident autonomy (63%), and the greatest barriers to resident autonomy were viewed to be patient preferences not to be cared for by residents (68%), liability concerns (68%), and Centers for Medicare and Medicaid Services regulations (65%). Although 64% of PDs believe that moderate or significant changes are needed in the current structure of residency training, 35% believe that no changes in the structure are needed. When asked for their 1 best recommendation regarding the structure of surgical residency, only 22% of PDs selected retaining the current 5-year structure. The greatest percentage of PDs (28%) selected the "4 + 2" model as their 1 best recommendation for the structure to be used. In the area of faculty development, 56% of PDs supported a significant or extensive increase in Train the Teacher programs, and 41% supported a significant or extensive increase in faculty certification in education. CONCLUSIONS: Information regarding the valuable perspectives of PDs gathered through these surveys should help in implementing important changes in residency training and faculty development. These efforts will need to be pursued collaboratively with involvement of key stakeholders, including the organizations represented on this ACS committee.

Flavour preferences in youth versus adults: a review.

OBJECTIVE: To understand the available evidence of how children and adults differ in their preferences for flavours that may be used in tobacco products. DATA SOURCES: A total of 474 articles published between 1931 and August 2015 were retrieved through searches conducted in PubMed, EMBASE, Web of Science and PsycINFO. STUDY SELECTION AND EXTRACTION: A 2-phase relevancy review process resulted in the identification of 59 articles and information was extracted by 2 independent reviewers. DATA SYNTHESIS: Findings were grouped by taste and smell preferences, which are important components of overall flavour. For taste, evidence is summarised in the following categories: sweet, salty, sour, bitter, umami and fat; within each of them, findings are organised by age categories. For smell, evidence is summarised as follows: fruit/herbal/spices, tobacco and coffee and other odours. Major findings from this search indicated that sweet preference in children and adolescents was higher than in adults. Examples of preferred food-related tastes and odours for young people included cherry, candy, strawberry, orange, apple and cinnamon. Currently, all these are used to flavour cigars, cartridges for electronic cigarettes, hookah (waterpipe) and smokeless tobacco products. CONCLUSIONS: Infants and children exhibited elevated sweet and salty preference relative to adults. Age-related changes in bitter, sour, umami and fat taste were not clear and more research would be useful. 'Sweet' food odours were highly preferred by children. Tobacco products in flavours preferred by young people may impact tobacco use and initiation, while flavours preferred by adults may impact product switching or dual use.