Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

Landscape of pharmacogenetic variants associated with non-insulin antidiabetic drugs in the Indian population

INTRODUCTION

Genetic variants contribute to differential responses to non-insulin antidiabetic drugs (NIADs), and consequently to variable plasma glucose control. Optimal control of plasma glucose is paramount to minimizing type 2 diabetes-related long-term complications. India's distinct genetic architecture and its exploding burden of type 2 diabetes warrants a population-specific survey of NIAD-associated pharmacogenetic (PGx) variants. The recent availability of large-scale whole genomes from the Indian population provides a unique opportunity to generate a population-specific map of NIAD-associated PGx variants.

RESEARCH DESIGN AND METHODS

We mined 1029 Indian whole genomes for PGx variants, drug-drug interaction (DDI) and drug-drug-gene interactions (DDGI) associated with 44 NIADs. Population-wise allele frequencies were estimated and compared using Fisher's exact test.

RESULTS

Overall, we found 76 known and 52 predicted deleterious common PGx variants associated with response to type 2 diabetes therapy among Indians. We report remarkable interethnic differences in the relative cumulative counts of decreased and increased response-associated alleles across NIAD classes. Indians and South Asians showed a significant excess of decreased metformin response-associated alleles compared with other global populations. Network analysis of shared PGx genes predicts high DDI risk during coadministration of NIADs with other metabolic disease drugs. We also predict an increased CYP2C19-mediated DDGI risk for CYP3A4/3A5-metabolized NIADs, saxagliptin, linagliptin and glyburide when coadministered with proton-pump inhibitors (PPIs).

CONCLUSIONS

Indians and South Asians have a distinct PGx profile for antidiabetes drugs, marked by an excess of poor treatment response-associated alleles for various NIAD classes. This suggests the possibility of a population-specific reduced drug response in atleast some NIADs. In addition, our findings provide an actionable resource for accelerating future diabetes PGx studies in Indians and South Asians and reconsidering NIAD dosing guidelines to ensure maximum efficacy and safety in the population.

Whole genome sequencing followed by functional analysis of genomic deletion encompassing ERCC8 and NDUFAF2 genes in a non-consanguineous Indian family reveals dysfunctional mitochondrial bioenergetics leading to infant mortality

Genomic investigations on an infant who presented with a putative mitochondrial disorder led to identification of compound heterozygous deletion with an overlapping region of ∼142 kb encompassing two nuclear encoded genes namely ERCC8 and NDUFAF2. Investigations on fetal-derived fibroblast culture demonstrated impaired bioenergetics and mitochondrial dysfunction, which explains the phenotype and observed infant mortality in the present study. The genetic findings from this study extended the utility of whole-genome sequencing as it led to development of a MLPA-based assay for carrier screening in the extended family and the prenatal testing aiding in the birth of two healthy children.

The genomic landscape of CYP2D6 variation in the Indian population

Aim: The CYP2D6 gene is highly polymorphic, causing large interindividual variability in the metabolism of several clinically important drugs. Materials & methods: The authors investigated the diversity and distribution of CYP2D6 alleles in Indians using whole genome sequences (N = 1518). Functional consequences were assessed using pathogenicity scores and molecular dynamics simulations. Results: The analysis revealed population-specific CYP2D6 alleles (*86, *7, *111, *112, *113, *99) and remarkable differences in variant and phenotype frequencies with global populations. The authors observed that one in three Indians could benefit from a dose alteration for psychiatric drugs with accurate CYP2D6 phenotyping. Molecular dynamics simulations revealed large conformational fluctuations, confirming the predicted reduced function of *86 and *113 alleles. Conclusion: The findings emphasize the utility of comprehensive CYP2D6 profiling for aiding precision public health.

Genetic landscape of human platelet antigen variants in the Indian population analysed from 1029 whole genomes

Genetic variants in human platelet antigens (HPAs) considered allo- or auto antigens are associated with various disorders, including neonatal alloimmune thrombocytopenia, platelet transfusion refractoriness and post-transfusion purpura. Although global differences in genotype frequencies were observed, the distributions of HPA variants in the Indian population are largely unknown. This study aims to explore the landscape of HPA variants in India to provide a basis for risk assessment and management of related complications. Population-specific frequencies of genetic variants associated with the 35 classes of HPAs (HPA-1 to HPA-35) were estimated by systematically analysing genomic variations of 1029 healthy Indian individuals as well as from global population genome datasets. Allele frequencies of the most clinically relevant HPA systems in the Indian population were found as follows, HPA-1a - 0.884, HPA-1b - 0.117, HPA-2a - 0.941, HPA-2b - 0.059, HPA-3a - 0.653, HPA-3b - 0.347, HPA-4a - 0.999, HPA-4b - 0.0010, HPA-5a - 0.923, HPA-5b - 0.077, HPA-6a - 0.998, HPA-6b - 0.002, HPA-15a - 0.582 and HPA-15b - 0.418. This study provides the first comprehensive analysis of HPA allele and genotype frequencies using large scale representative whole genome sequencing data of the Indian population.

Genetic landscape of human neutrophil antigen variants in India from population-scale genomes

Antibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia, transfusion-related acute lung injury, and other nonhemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. Ten genetic variants in four human genes encoding alleles of HNAs class I-V approved by the International Society of Blood Transfusion-Granulocyte Immunobiology Working Party were used in the analysis. Genetic variants from whole genome sequences of 1029 healthy Indian individuals corresponding to HNA alleles were analyzed. The frequencies of the variants were compared with global population datasets using an in-house computational pipeline. In HNA class I, allele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 encoding HNA-1a, HNA-1b, and HNA-1c were 0.07, 0.8, and 0.13, respectively. HNA class 3 alleles namely SLC44A2*01 (encoding HNA-3a) and SLC44A2*02 (encoding HNA-3b) were found at allele frequencies of 0.78 and 0.22, respectively. The frequencies of ITGAM*01 encoding HNA-4a and ITGAM*02 encoding HNA-4a were 0.95 and 0.05, respectively. Furthermore, allele frequencies of HNA class 5 alleles were 0.32 for ITGAL*01 (encoding HNA-5a) and 0.68 for ITGAL*02 (encoding HNA-5b). Interestingly, it was also found that rs2230433 variant deciding the HNA class 5 alleles, was highly prevalent (78.2%) in the Indian population compared with other global populations. This study presents the first comprehensive report of HNA allele and genotype frequencies in the Indian population using population genome datasets of 1029 individuals. Significant difference was observed in the prevalence of HNA5a and HNA5b in India in comparison to other global populations.

Whole-genome sequencing of 1029 Indian individuals reveals unique and rare structural variants

Structural variants contribute to genetic variability in human genomes and they can be presented in population-specific patterns. We aimed to understand the landscape of structural variants in the genomes of healthy Indian individuals and explore their potential implications in genetic disease conditions. For the identification of structural variants, a whole genome sequencing dataset of 1029 self-declared healthy Indian individuals from the IndiGen project was analysed. Further, these variants were evaluated for potential pathogenicity and their associations with genetic diseases. We also compared our identified variations with the existing global datasets. We generated a compendium of total 38,560 high-confident structural variants, comprising 28,393 deletions, 5030 duplications, 5038 insertions, and 99 inversions. Particularly, we identified around 55% of all these variants were found to be unique to the studied population. Further analysis revealed 134 deletions with predicted pathogenic/likely pathogenic effects and their affected genes were majorly enriched for neurological disease conditions, such as intellectual disability and neurodegenerative diseases. The IndiGenomes dataset helped us to understand the unique spectrum of structural variants in the Indian population. More than half of identified variants were not present in the publicly available global dataset on structural variants. Clinically important deletions identified in IndiGenomes might aid in improving the diagnosis of unsolved genetic diseases, particularly in neurological conditions. Along with basal allele frequency data and clinically important deletions, IndiGenomes data might serve as a baseline resource for future studies on genomic structural variant analysis in the Indian population.

1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants

BACKGROUND

The prevalence and genetic spectrum of cardiac channelopathies exhibit population-specific differences. We aimed to understand the spectrum of cardiac channelopathy-associated variations in India, which is characterised by a genetically diverse population and is largely understudied in the context of these disorders.

RESULTS

We utilised the IndiGenomes dataset comprising 1029 whole genomes from self-declared healthy individuals as a template to filter variants in 36 genes known to cause cardiac channelopathies. Our analysis revealed 186,782 variants, of which we filtered 470 variants that were identified as possibly pathogenic (440 nonsynonymous, 30 high-confidence predicted loss of function ). About 26% (124 out of 470) of these variants were unique to the Indian population as they were not reported in the global population datasets and published literature. Classification of 470 variants by ACMG/AMP guidelines unveiled 13 pathogenic/likely pathogenic (P/LP) variants mapping to 19 out of the 1029 individuals. Further query of 53 probands in an independent cohort of cardiac channelopathy, using exome sequencing, revealed the presence of 3 out of the 13 P/LP variants. The identification of p.G179Sfs*62, p.R823W and c.420 + 2 T > C variants in KCNQ1, KCNH2 and CASQ2 genes, respectively, validate the significance of the P/LP variants in the context of clinical applicability as well as for large-scale population analysis.

CONCLUSION

A compendium of ACMG/AMP classified cardiac channelopathy variants in 1029 self-declared healthy Indian population was created. A conservative genotypic prevalence was estimated to be 0.9-1.8% which poses a huge public health burden for a country with large population size like India. In the majority of cases, these disorders are manageable and the risk of sudden cardiac death can be alleviated by appropriate lifestyle modifications as well as treatment regimens/clinical interventions. Clinical utility of the obtained variants was demonstrated using a cardiac channelopathy patient cohort. Our study emphasises the need for large-scale population screening to identify at-risk individuals and take preventive measures. However, we suggest cautious clinical interpretation to be exercised by taking other cardiac channelopathy risk factors into account.

Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes

Background

Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient’s ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India.

Results

We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported.

Conclusion

With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00268-2.

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

Variants of concern responsible for SARS-CoV-2 vaccine breakthrough infections from India

Emerging reports of SARS‐CoV‐2 breakthrough infections entail methodical genomic surveillance for determining the efficacy of vaccines. This study elaborates genomic analysis of isolates from breakthrough infections following vaccination with AZD1222/Covishield and BBV152/Covaxin. Variants of concern B.1.617.2 and B.1.1.7 responsible for cases surge in April–May 2021 in Delhi, were the predominant lineages among breakthrough infections.

ESC: a comprehensive resource for SARS-CoV-2 immune escape variants

Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.

MitoLink: A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases: Observations from the GenomeAsia Pilot project

MitoLink is a generic, scalable and modular web-based workflow system developed to study genotype-phenotype correlations in human mitochondrial diseases. MitoLink integrates applications for assessment of genomic variation and currently houses genome-wide datasets from GenomeAsia Pilot project, gnomAD, ClinVar and DisGenNet. In this study, a reference list of nearly 3975 proteins (both nuclear and mitochondrial encoded) with mitochondrial function is reported. This protein set is mapped to disease associated variants in the GenomeAsia Pilot Project and DisGenNet and evaluated for pathogenicity as defined by ClinVar. Observations of shared genetic components in potential comorbidities are discussed from gene-disease network in Asian population, however, the platform is generic and can be applied to any population dataset. MitoLink is a unique customized workflow system that allows for systematic storage, extraction, analysis and visualization of genomic variation to understand genotype-phenotype correlations for mitochondrial diseases. Given the modularity of tool and data integration, MitoLink is a scalable system that can accommodate a diverse set of applications linked via standard data structure within the framework of Galaxy. MitoLink is built on FAIR principles and supports creation of reproducible workflows towards understanding genotype-phenotype correlations across several disease phenotypes globally.

An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

Sequencing of SARS-CoV-2 genomes is crucial for understanding the genetic epidemiology of the COVID-19 pandemic. It is also critical for understanding the evolution of the virus and also for the rapid development of diagnostic tools. The present protocol is a modification of the Illumina COVIDSeq test. We describe an amplicon-based next-generation sequencing approach with short turnaround time, adapted for bench-top sequencers like MiSeq, iSeq, and MiniSeq. For complete details on the use and execution of this protocol, please refer to Bhoyar et al. (2021).

Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes

Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.

Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes

COVID-19, the disease caused by the novel SARS-CoV-2 coronavirus, originated as an isolated outbreak in the Hubei province of China but soon created a global pandemic and is now a major threat to healthcare systems worldwide. Following the rapid human-to-human transmission of the infection, institutes around the world have made efforts to generate genome sequence data for the virus. With thousands of genome sequences for SARS-CoV-2 now available in the public domain, it is possible to analyze the sequences and gain a deeper understanding of the disease, its origin, and its epidemiology. Phylogenetic analysis is a potentially powerful tool for tracking the transmission pattern of the virus with a view to aiding identification of potential interventions. Toward this goal, we have created a comprehensive protocol for the analysis and phylogenetic clustering of SARS-CoV-2 genomes using Nextstrain, a powerful open-source tool for the real-time interactive visualization of genome sequencing data. Approaches to focus the phylogenetic clustering analysis on a particular region of interest are detailed in this protocol.

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.

IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes

With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.

Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays

An epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of the disease. Since the virus evolves by accumulating base substitutions, mutations in the viral genome could possibly affect the accuracy of RT-PCR-based detection assays. The recent availability of genomes of SARS-CoV-2 isolates motivated us to assess the presence and potential impact of variations in target sites of the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primer or probe sequences from literature and data available in the public domain. Our analysis revealed that a total of 5862 unique genetic variants mapped to at least one of the 132 primer or probe binding sites in the genome. A total of 29 unique variants were present in ≥ 1% of genomes from at least one of the continents (Asia, Africa, Australia, Europe, North America, and South America) that mapped to 36 unique primers or probes binding sites. Similarly, a total of 27 primer or probe binding sites had cumulative variants frequency of ≥ 1% in the global SARS-CoV-2 genomes. These included primers or probes sites which are used worldwide for molecular diagnosis as well as approved by national and international agencies. We also found 286 SARS-CoV-2 genomic regions with low variability at a continuous stretch of ≥ 20bps that could be potentially used for primer designing. This highlights the need for sequencing genomes of emerging pathogens to enable evidence-based policies for development and approval of diagnostics.

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

BACKGROUND

From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe.

METHODS

We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India.

RESULTS

We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade.

CONCLUSIONS

The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

MtBrowse: An integrative genomics browser for human mitochondrial DNA

The human mitochondrion is a unique semi-autonomous organelle with a genome of its own and also requires nuclear encoded components to carry out its functions. In addition to being the powerhouse of the cell, mitochondria plays a central role in several metabolic pathways. It is therefore challenging to delineate the cause-effect relationship in context of mitochondrial dysfunction. Several studies implicate mutations in mitochondrial DNA (mtDNA) in various complex diseases. The human mitochondrial DNA (mtDNA) encodes a set of 37 genes, 13 protein coding, 22 tRNAs and two ribosomal RNAs, which are essential structural and functional components of the electron transport chain. As mentioned above, variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. A large number of databases and prediction methods have been published to elucidate the role of human mitochondrial DNA in various disease phenotypes. However, there is no centralized resource to visualize this genotype-phenotype data. Towards this, we have developed MtBrowse: an integrative genomics browser for human mtDNA. As of now, MtBrowse has four categories - Gene, Disease, Reported variation and Variation prediction. These categories have 105 tracks and house data on mitochondrial reference genes, around 600 variants reported in literature with respect to various disease phenotypes and predictions for potential pathogenic variations in protein-coding genes. MtBrowse also hosts genomic variation data from over 5000 individuals on 22 disease phenotypes. MtBrowse may be accessed at http://ab-openlab.csir.res.in/cgi-bin/gb2/gbrowse.

Management practices associated with strongylid parasite prevalence on horse farms in rural counties of Kentucky

Anthelmintic resistance among cyathostomin parasites is a wide-spread problem. The parasite control guidelines written by the American Association of Equine Practitioners (AAEP) encourages the preservation of anthelmintic efficacy by reducing treatment frequency, using targeted deworming, and implementing environmental management practices. While there is knowledge regarding parasite management practices of affluent horse farms in the United States, surveys rarely explore the rural and underserved regions. The purpose of this study was to observe the management practices of horse farms in rural regions Kentucky, including working Amish farms, and determine factors associated with strongyle prevalence. A total of 160 horses among 38 owners from 28 different farms were enrolled in this study. A questionnaire survey regarding equine information, farm management, and deworming history was performed with each owner. Fecal samples were collected to determine fecal egg counts, perform coprocultures for subsequent strongyle larvae identification, and Strongylus vulgaris specific PCR. Serum samples were collected for the S. vulgaris antibody specific ELISA. The mean number of deworming treatments given in the last year was 2.1 with a 95% confidence interval of 1.9-2.3 with ivermectin being the most common active used. Statistical analysis showed horses treated within the last three months with a macrocylic lactone (ML) drug had significantly lower egg counts than horses treated with a ML 7-9 months ago (p = .0005). Despite the AAEP recommendations to reduce the overall number of treatments by using a surveillance-based approach and to no longer rotate treatments, only 17 horses reportedly had a fecal sample submitted for a fecal egg count and 65 horses were dewormed in a rotational manner. Horses whose owners utilized an informative deworming source (i.e., veterinarian, internet, magazine, local feed store) also had significantly lower counts (p = .0026). All coprocultures were negative for S. vulgaris while five horses were PCR positive. Interestingly, 95 horses tested ELISA positive for S. vulgaris. The strongyle egg counts of the working Amish horses were not significantly different from the other horses in this study and deworming practices including the use of efficacious drugs and low treatment frequencies were in accordance with the AAEP guidelines. This study was the first to summarize deworming management practices of rural regions in Kentucky, including a working Amish community. Overall, horse owners employed deworming practices recommended by the AAEP, however rotational deworming is still commonly implemented and fecal egg counts are rarely used.

Making robust assessments of specialist trainees' workplace performance

BACKGROUND

Workplace-based assessments should provide a reliable measure of trainee performance, but have met with mixed success. We proposed that using an entrustability scale, where supervisors scored trainees on the level of supervision required for the case would improve the utility of compulsory mini-clinical evaluation exercise (CEX) assessments in a large anaesthesia training program.

METHODS

We analysed mini-CEX scores from all Australian and New Zealand College of Anaesthetists trainees submitted to an online database over a 12-month period. Supervisors' scores were adjusted for the expected supervision requirement for the case for trainees at different stages of training. We used generalisability theory to determine score reliability.

RESULTS

7808 assessments were available for analysis. Supervision requirements decreased significantly (P < 0.05) with increased duration and level of training, supporting validity. We found moderate reliability (G > 0.7) with a feasible number of assessments. Adjusting scores against the expected supervision requirement considerably improved reliability, with G > 0.8 achieved with only nine assessments. Three per cent of trainees generated average mini-CEX scores below the expected standard.

CONCLUSIONS

Using an entrustment scoring system, where supervisors score trainees on the level of supervision required, mini-CEX scores demonstrated moderate reliability within a feasible number of assessments, and evidence of validity. When scores were adjusted against an expected standard, underperforming trainees could be identified, and reliability much improved. Taken together with other evidence on trainee ability, the mini-CEX is of sufficient reliability for inclusion in high stakes decisions on trainee progression towards independent specialist practice.

Reliability of the Direct Observation of Procedural Skills assessment tool for ultrasound-guided regional anaesthesia

Summary

The Direct Observation of Procedural Skills (DOPS) form is used as a workplace-based assessment tool in the current Australian and New Zealand College of Anaesthetists curriculum. The objective of this study was to evaluate the reliability of DOPS when used to score trainees performing ultrasound-guided regional anaesthesia. Reliability of an assessment tool is defined as the reproducibility of scores given by different assessors viewing the same trainee. Forty-nine anaesthetists were recruited to score two scripted videos of trainees performing a popliteal sciatic nerve block and an axillary brachial plexus block. Reliability, as measured by intraclass correlation coefficients, was −0.01 to 0.43 for the individual items in DOPS, and 0.15 for the ‘Overall Performance for this Procedure’ item. Assessors demonstrated consistency of scoring within DOPS, with significant correlation of sum of individual item scores with the ‘Overall Performance for this Procedure’ item (r=0.78 to 0.80, P <0.001), and with “yes” versus “no” responses to the ‘Was the procedure completed satisfactorily?’ item (W=24, P=0.0004, Video 1, and W=65, P=0.003, Video 2). While DOPS demonstrated a good degree of internal consistency in this setting, inter-rater reliability did not reach levels generally recommended for formative assessment tools. Feasibility of the form could be improved by removing the ‘Was the procedure completed satisfactorily?’ item without loss of information.

Can I leave the theatre? A key to more reliable workplace-based assessment

BACKGROUND

The value of workplace-based assessments such as the mini-clinical evaluation exercise (mini-CEX), and clinicians' confidence and engagement in the process, has been constrained by low reliability and limited capacity to identify underperforming trainees. We proposed that changing the way supervisors make judgements about trainees would improve score reliability and identification of underperformers. Anaesthetists regularly make decisions about the level of trainee independence with a case, based on how closely they need to supervise them. We therefore used this as the basis for a new scoring system.

METHODS

We analysed 338 mini-CEXs where supervisors scored trainees using the conventional system, and also scored trainee independence, based on the need for direct, or more distant, supervision. As supervisory requirements depend on case difficulty, we then compared the actual trainee independence score and the expected trainee independence score obtained externally.

RESULTS

Compared with the conventional scoring system used in previous studies, reliability was very substantially improved using a system based on a trainee's level of independence with a case. Reliability improved further when this score was corrected for case difficulty. Furthermore, the new scoring system overcame the previously identified problem of assessor leniency and identified a number of trainees performing below expectations.

CONCLUSIONS

Supervisors' judgements on trainee independence with a case, based on the need for direct or more distant supervision, can generate reliable scores of trainee ability without the need for an onerous number of assessments, identify trainees performing below expectations, and track trainee progress towards independent specialist practice.

Approaches to learning for the ANZCA Final Examination and validation of the revised Study Process Questionnaire in specialist medical training

When evaluating assessments, the impact on learning is often overlooked. Approaches to learning can be deep, surface and strategic. To provide insights into exam quality, we investigated the learning approaches taken by trainees preparing for the Australian and New Zealand College of Anaesthetists (ANZCA) Final Exam. The revised two-factor Study Process Questionnaire (R-SPQ-2F) was modified and validated for this context and was administered to ANZCA advanced trainees. Additional questions were asked about perceived value for anaesthetic practice, study time and approaches to learning for each exam component. Overall, 236 of 690 trainees responded (34%). Responses indicated both deep and surface approaches to learning with a clear preponderance of deep approaches. The anaesthetic viva was valued most highly and the multiple choice question component the least. Despite this, respondents spent the most time studying for the multiple choice questions. The traditionally low short answer questions pass rate could not be explained by limited study time, perceived lack of value or study approaches. Written responses suggested that preparation for multiple choice questions was characterised by a surface approach, with rote memorisation of past questions. Minimal reference was made to the ANZCA syllabus as a guide for learning. These findings indicate that, although trainees found the exam generally relevant to practice and adopted predominantly deep learning approaches, there was considerable variation between the four components. These results provide data with which to review the existing ANZCA Final Exam and comparative data for future studies of the revisions to the ANZCA curriculum and exam process.

Generalisability of Behavioural Skills in Simulated Anaesthetic Emergencies

A reliable assessment of clinical performance requires multiple cases, as performance varies between cases depending on previous experiences and knowledge of the case. However, behavioural attributes, including communication and teamwork, may be expected to be less dependent on specific case knowledge and thus be more stable across cases. This has implications for training and assessment design. In this study we measured the psychometric properties of assessment of behaviour in simulated anaesthetic emergencies.

Twenty anaesthesia trainees were rated in three simulated emergencies by four assessors. The psychometric properties of scores for behaviour were determined and were compared with scores for medical management and overall performance. We found that scores for behaviour were less dependent on the specific clinical context than the scores for overall performance and medical management, implying transferability of crisis management behaviours between cases.

Psychometric characteristics of simulation-based assessment in anaesthesia and accuracy of self-assessed scores

The purpose of this study was to define the psychometric properties of a simulation-based assessment of anaesthetists. Twenty-one anaesthetic trainees took part in three highly standardised simulations of anaesthetic emergencies. Scenarios were videotaped and rated independently by four judges. Trainees also assessed their own performance in the simulations. Results were analysed using generalisability theory to determine the influence of subject, case and judge on the variance in judges' scores and to determine the number of cases and judges required to produce a reliable result. Self-assessed scores were compared to the mean score of the judges. The results suggest that 12-15 cases are required to rank trainees reliably on their ability to manage simulated crises. Greater reliability is gained by increasing the number of cases than by increasing the number of judges. There was modest but significant correlation between self-assessed scores and external assessors' scores (rho = 0.321; p = 0.01). At the lower levels of performance, trainees consistently overrated their performance compared to those performing at higher levels (p = 0.0001).

Training the assessors for the General Medical Council's Performance Procedures

From July 1997, the General Medical Council (GMC) has had the power to investigate doctors whose performance is considered to be seriously deficient. Assessment procedures have been developed for all medical specialties to include peer review of performance in practice and tests of competence. Peer review is conducted by teams of at least two medical assessors and one lay assessor. A comprehensive training programme for assessors has been developed that simulates the context of a typical practice-based assessment and has been tailored for 12 medical specialties. The training includes the principles of assessment, familiarization with the assessment instruments and supervised practice in assessment methods used during the peer review visit. High fidelity is achieved through the use of actors who simulate third party interviewees and trained doctors who role play the assessee. A subgroup of assessors, selected to lead the assessment teams, undergo training in handling group dynamics, report writing and in defending the assessment report against legal challenge. Debriefing of assessors following real assessments has been strongly positive with regard to their preparedness and confidence in undertaking the assessment.

Sheffield Assessment Instrument for Letters (SAIL): performance assessment using outpatient letters

CONTEXT

Well-designed assessments of performance are urgently required for training doctors, and to provide indicators of the quality of practice.

OBJECTIVES

To design an assessment process that uses routine outpatient letters, and to evaluate its validity, feasibility, reliability (reproducibility and discrimination) and potential educational impact.

PARTICIPANTS

All 26 paediatric registrars in North Trent attending annual assessment panel in 1999 participated.

STUDY DESIGN

An assessment instrument (SAIL) was developed from a consensus framework for good practice in written communication. It comprises an 18-point checklist and a global rating scale. Three judges applied the instrument to 260 letters from the routine clinical practice of the 26 participants. Results We achieved consensus on good practice in written communication. This was in keeping with the published literature. All participants completed the assessment. Scoring took 3-6 min per judge per letter. The reliability coefficient in this test situation is 0.72. Modelling predicts that a coefficient of 0.8 (the threshold for high-stakes judgements about performance) can be achieved with more judges or letters. The assessment results are well suited to formative feedback.

CONCLUSIONS

SAIL uses letters as a face valid indicator of written communication performance. The instrument is feasible to use, and produces reliable results when applied to paediatric registrars to inform the annual Record of In-Training Assessment (RITA). Feedback from the assessment should help doctors to improve their written communication. Its use may extend to other specialities and settings including revalidation.

The General Medical Council's Performance Procedures: the development and implementation of tests of competence with examples from general practice

OBJECTIVE

This paper describes the development of the tests of competence used as part of the General Medical Council's assessment of potentially seriously deficient doctors. It is illustrated by reference to tests of knowledge and clinical and practical skills created for general practice. SUBJECTS AND TESTS: A notional sample of 30 volunteers in 'good standing' in the specialty (reference group), 27 practitioners referred to the procedures and four practitioners not referred but who were the focus of concern over their performance. Tests were constructed using available guidelines and a specially convened working group in the specialty.

METHODS

Standards were set using Angoff, modified contrasting group and global judgement methods, as appropriate.

RESULTS

Tests performed highly reliably, showed evidence of construct validity, intercorrelated at appropriate levels and, at the standards employed, demonstrated good separation of reference and referred groups. Likelihood ratios for above and below standard performance based on competence were large for each test. Seven of 27 doctors referred were shown not to be deficient in both phases of the performance assessment.

The assessment of poorly performing doctors: the development of the assessment programmes for the General Medical Council's Performance Procedures

BACKGROUND

Modernization of medical regulation has included the introduction of the Professional Performance Procedures by the UK General Medical Council in 1995. The Council now has the power to assess any registered practitioner whose performance may be seriously deficient, thus calling registration (licensure) into question. Problems arising from ill health or conduct are dealt with under separate programmes.

METHODS

This paper describes the development of the assessment programmes within the overall policy framework determined by the Council. Peer review of performance in the workplace (Phase 1) is followed by tests of competence (Phase 2) to reflect the relationship between clinical competence and performance. The theoretical and research basis for the approach are presented, and the relationship between the qualitative methods in Phase 1 and the quantitative methods in Phase 2 explored.

CONCLUSIONS

The approach is feasible, has been implemented and has stood legal challenge. The assessors judge and report all the evidence they collect and may not select from it. All their judgements are included and the voice of the lay assessor is preserved. Taken together, the output from both phases forms an important basis for remediation and training should it be required.

The General Medical Council's Performance Procedures: peer review of performance in the workplace

The General Medical Council procedures to assess the performance of doctors who may be seriously deficient include peer review of the doctor's practice at the workplace and tests of competence and skills. Peer reviews are conducted by three trained assessors, two from the same speciality as the doctor being assessed, with one lay assessor. The doctor completes a portfolio to describe his/her training, experience, the circumstances of practice and self rate his/her competence and familiarity in dealing with the common problems of his/her own discipline. The assessment includes a review of the doctor's medical records; discussion of cases selected from these records; observation of consultations for clinicians, or of relevant activities in non-clinicians; a tour of the doctor's workplace; interviews with at least 12 third parties (five nominated by the doctor); and structured interviews with the doctor. The content and structure of the peer review are designed to assess the doctor against the standards defined in Good Medical Practice, as applied to the doctor's speciality. The assessment methods are based on validated instruments and gather 700-1000 judgements on each doctor. Early experience of the peer review visits has confirmed their feasibility and effectiveness.