Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study

BACKGROUND

Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.

AIM

To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study.

METHODS

For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis.

FINDINGS

The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT.

CONCLUSION

Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.

Analysis of protein profile of tomato root infected with Fusarium oxysporum f. sp lycopersici

Fusarium wilt caused by Fusarium oxysporum f. sp lycopersici (Fol) is one of the main diseases affecting tomatoes. The BHRS 2,3 genotype of tomato is, however, resistant to this disease. A proteomic approach was used to understand the defense mechanisms of this genotype using the tomato root, the first tissue that interacts with the fungus, as a target. Protein was extracted and separated by two-dimensional electrophoresis followed by staining with Coomassie brilliant blue. The proteins were identified by MALDI-TOF/TOF mass spectrometry. A total of 22 proteins were identified, 21 of which showed differential expression with 12 proteins being upregulated and nine being downregulated. Plants responded to the pathogen with increased expression of pathogenesis-related proteins. We noted the induction of proteins involved in hypersensitivity reaction and other defense mechanisms. The expression of proteins of primary metabolism related to energy production, however, decreased, as did the expression of two proteins related to defense against abiotic stress. These results demonstrate the presence of important mechanisms for defense against Fol in the tomato genotype BHRS 2,3.

CYP2E1 RsaI and 96-bp insertion genetic polymorphisms associated with risk for colorectal cancer

We investigated a possible association between alcoholism, cigarette smoking, obesity and CYP2E1 RsaI and 96-bp insertion genetic polymorphisms with risk for colorectal cancer (CRC). Patients with CRC (70 women and 61 men) were matched for gender and age to 206 healthy controls. The mean age of the two groups was 62 years. Meat intake, cigarette smoking and alcohol drinking were assessed using a specific frequency questionnaire. The body mass index was also calculated. DNA was extracted from peripheral blood; RsaI polymorphism genotypes were evaluated by PCR-RFLP and 96-bp insertion genetic polymorphisms were evaluated by specific primers. The distributions of CYP2E1 RsaI c1/c1, c1/c2 and c2/c2 genotypes were 90.2, 9.2 and 0.6%, respectively, in controls and 83.9, 13.7 and 2.4% in CRC cases. Allele c2 was associated with increased risk for CRC [odds ratio (OR) = 1.88, 95% confidence interval (95%CI) = 1.02-3.45]. The CYP2E1 RsaI c2/c2 genotype was associated with an increased risk for rectal cancer (OR = 3.23, 95%CI = 1.26-9.03). The 96-bp insertion was slightly more frequent in the CRC group (9.3 vs 11.4%, P = 0.19), especially in females (6.4 vs 11.5%, P = 0.34). Smoking, alcohol drinking or high intake of red meat and CYP2E1 polymorphisms were not associated with increased risk for CRC. The 96-bp insertion was marginally more frequent (P = 0.07) in undernourished CRC subjects. We concluded that the risk for CRC is higher among individuals with allele c2. The CYP2E1 RsaI c2/c2 genotype was associated with an increased risk for rectal cancer.

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops

Completed genome sequences provide templates for the design of genome analysis tools in orphan species lacking sequence information. To demonstrate this principle, we designed 384 PCR primer pairs to conserved exonic regions flanking introns, using Sorghum/Pennisetum expressed sequence tag alignments to the Oryza genome. Conserved-intron scanning primers (CISPs) amplified single-copy loci at 37% to 80% success rates in taxa that sample much of the approximately 50-million years of Poaceae divergence. While the conserved nature of exons fostered cross-taxon amplification, the lesser evolutionary constraints on introns enhanced single-nucleotide polymorphism detection. For example, in eight rice (Oryza sativa) genotypes, polymorphism averaged 12.1 per kb in introns but only 3.6 per kb in exons. Curiously, among 124 CISPs evaluated across Oryza, Sorghum, Pennisetum, Cynodon, Eragrostis, Zea, Triticum, and Hordeum, 23 (18.5%) seemed to be subject to rigid intron size constraints that were independent of per-nucleotide DNA sequence variation. Furthermore, we identified 487 conserved-noncoding sequence motifs in 129 CISP loci. A large CISP set (6,062 primer pairs, amplifying introns from 1,676 genes) designed using an automated pipeline showed generally higher abundance in recombinogenic than in nonrecombinogenic regions of the rice genome, thus providing relatively even distribution along genetic maps. CISPs are an effective means to explore poorly characterized genomes for both DNA polymorphism and noncoding sequence conservation on a genome-wide or candidate gene basis, and also provide anchor points for comparative genomics across a diverse range of species.