SARS-CoV-2 Omicron variant: healthcare workers' perceptions and beliefs of vaccine effectiveness and advocacy: a national survey during the first week of the World Health Organization variant alert

Background: As COVID-19 Omicron variant spread in several countries, healthcare workers' (HCWs) perceptions of vaccine effectiveness, booster and worries warrant reassessment. Methods: Online questionnaire among HCWs in Saudi Arabia (KSA) was collected between Dec 1-6, 2021, aiming to assess their Omicron variant's perceptions, worries, and booster-vaccine advocacy. Results: Among the 1285 HCWs participants in the study, two-thirds were females, 41% were nurses,46.4% were physicians, and 50% worked in tertiary care hospitals. Vaccination was perceived to be the most effective way to prevent the spread of Omicron variant and future variants by 66.9%. The respondents perceived social distancing (78%), universal masking (77.8%), and avoiding unnecessary travel (71.4%), slightly superior to vaccination to prevent COVID-19 variants spread. Of the respondents, 99.5% received two doses of COVID-19 vaccine. Regarding the booster dose, 96% either received it or planned to receive it once they are eligible. 57.7% of the respondents agreed that Omicron could cause a new COVID-19 wave worldwide, 45.9% agreed it may cause another COVID-19 wave in Saudi Arabia and 46.1% indicated the possibility of another lockdown. Overall, the HCWs worry level of the Omicron variant correlated significantly and strongly with their perception of the effectiveness of vaccination and preventive measures. Male HCWs had a significant agreement with mandatory vaccination of all eligible adult populations while HCWs who are unwilling to receive the vaccine had a strong disagreement with mandatory vaccination. Conclusions: The current study was conducted in the first week of Omicron variant discovery in KSA and only two-thirds of HCWs felt that vaccination is the best option to prevent the variant spread, indicating the need to further motivation campaigns for vaccination and booster doses education among HCWs. HCWs had a strong belief in non-pharmacologic interventions that should be encouraged and augmented. It is important to further study and enhance coping strategies for HCWs as we move through the third year of the pandemic with more potential variants, to protect HCWs from fatigue and burnout.

A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis

Long diagnostic wait times hinder international efforts to address multi-drug resistance in M. tuberculosis. Pathogen whole genome sequencing, coupled with statistical and machine learning models, offers a promising solution. However, generalizability and clinical adoption have been limited in part by a lack of interpretability and verifiability, especially in deep learning methods. Here, we present a deep convolutional neural network (CNN) that predicts the antibiotic resistance phenotypes of M. tuberculosis isolates. The CNN performs with state-of-the-art levels of predictive accuracy. Evaluation of salient sequence features permits biologically meaningful interpretation and validation of the CNN’s predictions, with promising repercussions for functional variant discovery, clinical applicability, and translation to phenotype prediction in other organisms.

Genetic Variation and the Distribution of Variant Types in the Horse

Genetic variation is a key contributor to health and disease. Understanding the link between an individual’s genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.

Optimised multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer

Objective: Rapid, cost-effective identification of genetic variants in small candiate genomic regions remains a challenge, particularly for less well equipped or lower throughput laboratories. Application of Oxford Nanopore Technologies' MinION sequencer has the potential to fulfil this requirement. We have developed a multiplexing assay which pools PCR amplicons for MinION sequencing to enable sequencing of multiple templates from multiple individuals which could be applied to gene-targeted diagnostics. Methods: A combined strategy of barcoding and sample pooling was developed for simultaneous multiplex MinION sequencing of 100 PCR amplicons, spanning 30 loci in DNA isolated from 82 neurodevelopmental cases and family members. The target regions were chosen for further interegation because a potentially disease-causative variants had been identified in affected individuals by Illumina exome sequencing. The pooled MinION sequences were deconvoluted by aligning to custom references using the guppy aligner software. Results: Our multiplexing approach produced interpretable and expected sequence from 29 of the 30 targeted genetic loci. The sequence variant which was not correctly resolved in the MinION sequence was adjacent to a five nucleotide homopolymer. It is already known that homopolymers present a resolution problem with the MinION approach. Interstingly despite equimolar quantities of PCR amplicon pooled for sequencing, significant variation in the depth of coverage (139x - 21,499x; mean = 9,050, std err = 538.21) was observed. We observed independent relationships between depth of coverage and target length, and depth of coverage and GC content. These relationships demonstrate biases of the MinION sequencer for longer templates and those with lower GC content. Conclusion: We demonstrate an efficient approach for variant discovery or confirmation from short DNA templates using the MinION sequencing device. With less than 140x depth of coverage required for accurate genotyping, the methodology described here allows for rapid highly multiplexed targeted sequencing of large numbers of samples in a minimally equipped laboratory.

Integrating WES and RNA-Seq Data For Short Variant Discovery

The integration of omics has enormous potential that can be exploited for variant discovery. Several algorithms have been developed to detect somatic variants in an integrated fashion but, to our knowledge, there is still no strategy for germline variant calling. On this basis, we have developed a strategy to identify germline variants by integrating both WES and RNA-seq data. This integrated strategy identifies short variants (SNPs and indels) from raw sequence data, which are classified into six groups to improve variant interpretation: strong-evidence, DNA-only, RNA-only, allele-specific expression (ASE), RNA-editing and RNA-rescue variants. Four samples were analyzed and we show an increase in the number of identified variants without a great effect on performance compared to the exclusive use of WES data, allowing the validation of the variants identified by both types of data (strong-evidence variants), and the identification of RNA-editing and ASE. This integrated strategy provides a method to identify germline SNPs and indels from WES and RNA-seq data taking full advantage of both omics to broaden the range of identified variants and perform variant validation.

Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks.

Complex feline disease mapping using a dense genotyping array

The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.