Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BACKGROUND

We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases.

METHODS

We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.

RESULTS

No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5).

CONCLUSIONS

Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

Effects of the Coronavirus disease 2019 pandemic on routine pediatric immunization coverage rates at the main University Hospital in Saudi Arabia

OBJECTIVES

To investigate whether the coronavirus disease-2019 pandemic has had any effects on pediatric vaccination rates at the main university hospital in Saudi Arabia.

METHODS

A retrospective study conducted at King Saud University Medical City, Riyadh, Saudi Arabia using electronic health records. The vaccination statuses of all children who were scheduled for vaccinations at birth and at 2, 4, 6, 9, and 12 months during March, April and May between 2017 and 2020 were included in the study with total sample of 15,870 children, and comparisons between the cohorts were performed.

RESULTS

All vaccination visits during April and May 2020 were below the lower extremes except for the birth vaccinations. In March, April, and May 2020 there were respective drops in vaccination visits of 49.93%, 71.90% and 68.48% compared with the mean numbers of vaccination visits during the same months from 2017 to 2019. In comparisons of mean numbers of visits from March 2017 to May 2019 and March to May in 2020, the respective reductions in visits for birth and 2, 4, 6, 9 and 12-month vaccinations were 16.5%, 80.5%, 74.7%, 72.9%, 80.0% and 74.1%.

CONCLUSIONS

The huge impact of the coronavirus disease-2019 pandemic on childhood vaccinations will require urgent vaccination recovery plans with innovative approaches and future action plans to maintain vaccination coverage during any subsequent pandemics.

Pediatric residents' perceptions of the impact of the 24-hour on-call system on their well-being and education and patient safety. A national survey

Objectives:

To examine pediatric residents’ perceptions of the 24-hour in-hospital shift and its impact on their well-being and education and patient safety.

Methods:

A cross-sectional survey conducted with residents enrolled in pediatric residency programs across Saudi Arabia in February 2017 at the Saudi Commission For Health Specialties, Riyadh Saudi Arabia. We designed a self-administered questionnaire that was distributed using the Saudi Commission for Health Specialties E-mail groups. A 4-point Likert-type scale was used to rank the residents’ responses; and the relative importance index (RII) approach was used to analyze the relative contribution of each indicator to its main theme.

Results:

A total of 314 residents participated in the survey (response rate, 30%). Of these, 168 (53.6%) were females. When asked about their preferences regarding the 24-hour on-call system, 286 residents (91.1%) preferred not to continue with this system. Residents ranked several indicators that they perceived as a negative impact due to the 24-hour on-call system. The first ranked indicator was missing academic activities and elective rotations post-call (mean 3.10 [standard deviation 1.25], RII 90.94%), and the second was decreased performance and decision-making skills during night duty (mean 3.51 [standard deviation 1.0], RII 88.11%).

Conclusion:

We found that the 24-hour on-call system negatively impacts residents’ well-being and education and patient care. Pediatric residency training programs in Saudi Arabia should consider resident duty hour reform and evaluate new on-call models to improve resident well-being and training, as well as patient care.