Rapid, high-throughput, cost-effective whole-genome sequencing of SARS-CoV-2 using a condensed library preparation of the Illumina DNA Prep kit.

The ongoing COVID-19 pandemic necessitates cost-effective, high-throughput, and timely whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses for outbreak investigations, identifying variants of concern (VoC), characterizing vaccine breakthrough infections, and public health surveillance. In addition, the enormous demand for WGS on supply chains and the resulting shortages of laboratory supplies necessitated the use of low-reagent and low-consumable methods. Here, we report an optimized library preparation method (the BCCDC cutdown method) that can be used in a high-throughput scenario, where one technologist can perform 576 library preparations (6 plates of 96 samples) over the course of one 8-hour shift. The same protocol can also be used in a rapid turnaround time scenario, from primary samples (up to 96 samples) to loading on a sequencer in an 8-hour shift. This new method uses Freed et al.'s 1,200 bp primer sets (Biol Methods Protoc 5:bpaa014, 2020, https://doi.org/10.1093/biomethods/bpaa014) and a modified and condensed Illumina DNA Prep workflow (Illumina, CA, USA). Compared to the original protocol, the application of this new method using hundreds of clinical specimens demonstrated equivalent results to the full-length DNA Prep workflow at 45% of the cost, 15% of consumables required (such as pipet tips), 25% of manual hands-on time, and 15% of on-instrument time if performing on a liquid handler, with no compromise in sequence quality. Results demonstrate that this new method is a rapid, simple, cost-effective, and high-quality SARS-CoV-2 WGS protocol. IMPORTANCE: Sequencing has played an invaluable role in the response to the COVID-19 pandemic. Ongoing work in this area, however, demands optimization of laboratory workflow to increase sequencing capacity, improve turnaround time, and reduce cost without compromising sequence quality. This report describes an optimized DNA library preparation method for improved whole-genome sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen. The workflow advantages summarized here include significant time, cost, and consumable savings, which suggest that this new method is an efficient, scalable, and pragmatic alternative for SARS-CoV-2 whole-genome sequencing.

Naturally acquired antibody against Haemophilus influenzae type a in pediatric saliva.

We developed a salivary assay for the detection of naturally acquired IgA antibody against Haemophilus influenzae type a (Hia) capsular polysaccharide in healthy Indigenous children from Northwestern Ontario, Canada. Hia-specific IgA antibody was detected in the saliva of 93% of Indigenous children aged 2-7 years.

Influenza Vaccine Effectiveness by A(H3N2) Phylogenetic Subcluster and Prior Vaccination History: 2016-2017 and 2017-2018 Epidemics in Canada.

BACKGROUND: The influenza A(H3N2) vaccine was updated from clade 3C.3a in 2015-2016 to 3C.2a for 2016-2017 and 2017-2018. Circulating 3C.2a viruses showed considerable hemagglutinin glycoprotein diversification and the egg-adapted vaccine also bore mutations. METHODS: Vaccine effectiveness (VE) in 2016-2017 and 2017-2018 was assessed by test-negative design, explored by A(H3N2) phylogenetic subcluster and prior season's vaccination history. RESULTS: In 2016-2017, A(H3N2) VE was 36% (95% confidence interval [CI], 18%-50%), comparable with (43%; 95% CI, 24%-58%) or without (33%; 95% CI, -21% to 62%) prior season's vaccination. In 2017-2018, VE was 14% (95% CI, -8% to 31%), lower with (9%; 95% CI, -18% to 30%) versus without (45%; 95% CI, -7% to 71%) prior season's vaccination. In 2016-2017, VE against predominant clade 3C.2a1 viruses was 33% (95% CI, 11%-50%): 18% (95% CI, -40% to 52%) for 3C.2a1a defined by a pivotal T135K loss of glycosylation; 60% (95% CI, 19%-81%) for 3C.2a1b (without T135K); and 31% (95% CI, 2%-51%) for other 3C.2a1 variants (with/without T135K). VE against 3C.2a2 viruses was 45% (95% CI, 2%-70%) in 2016-2017 but 15% (95% CI, -7% to 33%) in 2017-2018 when 3C.2a2 predominated. VE against 3C.2a1b in 2017-2018 was 37% (95% CI, -57% to 75%), lower at 12% (95% CI, -129% to 67%) for a new 3C.2a1b subcluster (n = 28) also bearing T135K. CONCLUSIONS: Exploring VE by phylogenetic subcluster and prior vaccination history reveals informative heterogeneity. Pivotal mutations affecting glycosylation sites, and repeat vaccination using unchanged antigen, may reduce VE.

Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens.

Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.

Epidemiology of Burkholderia Infections in People with Cystic Fibrosis in Canada between 2000 and 2017.

Rationale: Infections by Burkholderia species bacteria in cystic fibrosis (CF) may be transmissible, necessitating infection control measures, and remain a serious cause of morbidity and mortality. The last major study of Burkholderia epidemiology in Canada included cases up until July 2000 and was marked by the dominance of a limited number of epidemic clones of Burkholderia cenocepacia.Objectives: Describe the nationwide epidemiology of Burkholderia species infections in people with cystic fibrosis in Canada over the 17-year period since 2000.Methods: Isolates were collected from across Canada between August 2000 and July 2017 and identified to the species and, for isolates between 2015 and 2017, strain level.Results: We analyzed 1,362 Burkholderia isolates from at least 396 people with CF. Forty-nine percent (n = 666) of all isolates and 47% (n = 179) of new incident infections were identified as B. multivorans. The incidence of Burkholderia infection in the Canadian CF population did not change between 2000 and 2017 at 6 cases per 1,000 annually. Multilocus sequence typing analysis suggested minimal sharing of clones in Canada.Conclusions: The epidemiology of Burkholderia in CF in Canada has shifted from limited numbers of epidemic strains of B. cenocepacia to largely nonclonal isolates of B. multivorans, B. cenocepacia, and other species. Despite widespread infection control, however, Burkholderia species bacteria continue to be acquired by people with CF at an unchanged rate, posing a continued hazard.

Influenza Classification Suite: An automated Galaxy workflow for rapid influenza sequence analysis.

Influenza viruses continually evolve to evade population immunity, and the different lineages are assigned into clades based on shared mutations. We have developed a publicly available computational workflow, the Influenza Classification Suite, for rapid clade mapping of sequenced influenza viruses. This suite provides a user-friendly workflow implemented in Galaxy to automate clade calling and antigenic site extraction. Workflow input includes clade definition and amino acid index array files, which can be customized to identify any clades of interest. The Influenza Classification Suite provides rapid, high-resolution understanding of circulating influenza strain evolution to inform influenza vaccine effectiveness and the need for potential vaccine reformulation.

Vaccine Effectiveness Against Lineage-matched and -mismatched Influenza B Viruses Across 8 Seasons in Canada, 2010-2011 to 2017-2018.

Vaccine effectiveness (VE) against influenza B was derived separately for Victoria and Yamagata lineages across 8 seasons (2010-2011 to 2017-2018) in Canada when trivalent influenza vaccine was predominantly used. VE was ≥50% regardless of lineage match to circulating viruses, except when the vaccine strain was unchanged from the prior season.

Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018.

Using a test-negative design, we assessed interim vaccine effectiveness (VE) for the 2017/18 epidemic of co-circulating influenza A(H3N2) and B(Yamagata) viruses. Adjusted VE for influenza A(H3N2), driven by a predominant subgroup of clade 3C.2a viruses with T131K + R142K + R261Q substitutions, was low at 17% (95% confidence interval (CI): -14 to 40). Adjusted VE for influenza B was higher at 55% (95% CI: 38 to 68) despite prominent use of trivalent vaccine containing lineage-mismatched influenza B(Victoria) antigen, suggesting cross-lineage protection.

Anterior cervical interbody constructs: effect of a repetitive compressive force on the endplate.

Graft subsidence following anterior cervical reconstruction can result in the loss of sagittal balance and recurring foraminal stenosis. This study examined the implant-endplate interface using a cyclic fatigue loading protocol in an attempt to model the subsidence seen in vivo. The superior endplate from 30 cervical vertebrae (C3 to T1) were harvested and biomechanically tested in axial compression with one of three implants: Fibular allograft; titanium mesh cage packed with cancellous chips; and trabecular metal. Each construct was cyclically loaded from 50 to 250 N for 10,000 cycles. Nondestructive cyclic loading of the cervical endplate-implant construct resulted in a stiffer construct independent of the type of the interbody implant tested. The trabecular metal construct demonstrated significantly more axial stability and significantly less subsidence in comparison to the titanium mesh construct. Although the allograft construct resulted in more subsidence than the trabecular metal construct, the difference was not significant and no difference was found when comparing axial stability. For all constructs, the majority of the subsidence during the cyclic testing occurred during the first 500 cycles and was followed by a more gradual settling in the remaining 9,500 cycles.

Electromagnetic effects on forearm disuse osteopenia: a randomized, double-blind, sham-controlled study.

A randomized, double-blind, sham-controlled, feasibility and dosing study was undertaken to determine if a common pulsing electromagnetic field (PEMF) treatment could moderate the substantial osteopenia that occurs after forearm disuse. Ninety-nine subjects were randomized into four groups after a distal radius fracture, or carpal surgery requiring immobilization in a cast. Active or identical sham PEMF transducers were worn on the distal forearm for 1, 2, or 4 h/day for 8 weeks starting after cast removal ("baseline") when bone density continues to decline. Bone mineral density (BMD) and bone geometry were measured in the distal forearm by dual energy X-ray absorptiometry (DXA) and peripheral quantitative computed tomography (pQCT) at entry ("baseline") and 8, 16, and 24 weeks later. Significant average BMD losses after baseline were observed in the affected forearm at all time points (5-7% distally and 3-4% for the radius/ulna shaft). However, after adjusting for age, gender, and baseline BMD there was no evidence of a positive effect of active versus sham PEMF treatment on bone loss by DXA or pQCT for subjects completing all visits (n = 82, ∼20 per group) and for an intent-to-treat analysis (n = 99). Regardless of PEMF exposure, serum bone-specific alkaline phosphatase (BSAP) was normal at baseline and 8 weeks, while serum c-terminal collagen teleopeptide (CTX-1) was markedly elevated at baseline and less so at 8 weeks. Although there was substantial variability in disuse osteopenia, these results suggested that the particular PEMF waveform and durations applied did not affect the continuing substantial disuse bone loss in these subjects.

Distal radius strength: a comparison of DXA-derived vs pQCT-measured parameters in adolescent females.

Although quantitative computed tomography (QCT) is considered the gold standard for in vivo densitometry, dual-energy X-ray absorptiometry (DXA) scans assess larger bone regions and are more appropriate for pediatric longitudinal studies. Unfortunately, DXA does not yield specific bone architectural output. To address this issue in healthy, postmenarcheal girls, Sievänen's distal radius formulae [1996] were applied to derive indices of bone geometry, volumetric bone mineral density (vBMD), and strength from DXA data; results were compared to peripheral quantitative computed tomography (pQCT) output. Contemporaneous scans were performed on the left, distal radii of 35 gymnasts, ex-gymnasts, and nongymnasts (aged 13.3-20.4 yr, mean 16.6 yr). For 4% and 33% regions, pQCT measured cross-sectional areas (CSAs) and vBMD; comparable DXA indices were generated at ultradistal and 1/3 regions. Index of structural strength in axial compression was calculated from 4% pQCT and DXA output for comparison; 33% pQCT strength-strain index was compared to 1/3 DXA section modulus. Sievänen DXA indices were significantly, positively correlated with pQCT output (R=+0.61 to +0.98; p<0.0001). At the distal radius, in healthy postmenarcheal girls, Sievänen's method yielded potentially useful DXA indices of diaphyseal cortical CSA and bone strength at both the diaphysis (section modulus) and the metaphysis (index of structural strength in axial compression).