Sample Size Calculations for Variant Surveillance in the Presence of Biological and Systematic Biases

As demonstrated during the SARS-CoV-2 pandemic, detecting and tracking the emergence and spread of pathogen variants is an important component of monitoring infectious disease outbreaks. Pathogen genome sequencing has emerged as the primary tool for variant characterization, so it is important to consider the number of sequences needed when designing surveillance programs or studies, both to ensure accurate conclusions and to optimize use of limited resources. However, current approaches to calculating sample size for variant monitoring often do not account for the biological and logistical processes that can bias which infections are detected and which samples are ultimately selected for sequencing. In this manuscript, we introduce a framework that models the full process from infection detection to variant characterization and demonstrate how to use this framework to calculate appropriate sample sizes for sequencing-based surveillance studies. We consider both cross-sectional and continuous sampling, and we have implemented our method in a publicly available tool that allows users to estimate necessary sample sizes given a specific aim (e.g., variant detection or measuring variant prevalence) and sampling method. Our framework is designed to be easy to use, while also flexible enough to be adapted to other pathogens and surveillance scenarios.

COVID-19: pathogen characteristics, natural and adaptive immune response mechanisms, genetic diversity and distribution

COVID-19 is a pandemic disease caused by a member of the Coronaviridae family, a beta-2 coronavirus named SARS-CoV-2. The COVID-19 pandemic lasting about 19 months has caused serious damage to the health of people on our planet – by the 13 of July 2021, more than 187.9 000 000 patients have been diagnosed and more than 4.0 mln patients died from infection (> 2.0 %). Scientists around the world are actively investigating the critically important molecular-genetic aspects of the biology of the pathogen (genome RNA structure, proteins properties) that are important for understanding the disease mechanisms, as well as the mechanisms of individual and collective immunological protection and vaccines development with non-specific prophylactics.

THE JOURNEY SO FAR AND THE ROADMAP AHEAD

Dear Reader, Current Covid times are introspection times, too. When the Human Genome Project was initiated in 1990, for determining the basic pairs that make up DNA and for identifying and mapping the entire genes of the human genome, the hue and cry made by the Indian NGOs kept India out of the project, at lease officially. Approximately, 20 research institutions globally, including some from China and Russia later, participated during the 13 years of the project, which concluded in 2003. The participating countries and institutions made major contributions and consequently became beneficiaries of great progress and major strides in genomic research. While China was already participating from 1990 and Russia joined in 2000, India realised the need and importance of moving into this field at the turn of the millennium. The 100K Pathogen Genome Project launched in 2012 in USA and the 100,000 Genomes Project, also of late 2012, by UK carried forward the genome project initiatives. The countries who took early initiatives were immensely benefited through major breakthroughs. For good (or bad?), China outpaced India in genomic research and was rewarded immensely through funding from major global investors. What about India? Better late than never. The DBT in India initiated the Genome India Project in January, 2020 with the aim of collecting a moderate 10,000 human genetic samples from across India to build a reference genome. Fortunately, the vociferous NGO lobbies have probably realised their folly in opposing the genome project participation by India in the 1990s and the Indian project of 2020 will hopefully progress.

A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini

Fusarium wilt of flax is an aggressive disease caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini. It is a challenging pathogen presenting a constant threat to flax production industry worldwide. Previously, we reported chromosome-level assemblies of 5 highly pathogenic F. oxysporum f. sp. lini strains. We sought to characterize the genomic architecture of the fungus and outline evolutionary mechanisms shaping the pathogen genome. Here, we reveal the complex multi-compartmentalized genome organization and uncover its diverse evolutionary dynamics, which boosts genetic diversity and facilitates host adaptation. In addition, our results suggest that host of functions implicated in the life cycle of mobile genetic elements are main contributors to dissimilarity between proteomes of different Fusaria. Finally, our experiments demonstrate that mobile genetics elements are expressed in planta upon infection, alluding to their role in pathogenicity. On the whole, these results pave the way for further in-depth studies of evolutionary forces shaping the host–pathogen interaction.

Case Report: Identification of SARS-CoV-2 in Cerebrospinal Fluid by Ultrahigh-Depth Sequencing in a Patient With Coronavirus Disease 2019 and Neurological Dysfunction

We reported that the complete genome sequence of SARS-Coronavirus-2 (SARS-CoV-2) was obtained from a cerebrospinal fluid (CSF) sample by ultrahigh-depth sequencing. Fourteen days after onset, seizures, maxillofacial convulsions, intractable hiccups and a significant increase in intracranial pressure developed in an adult coronavirus disease 2019 patient. The complete genome sequence of SARS-CoV-2 obtained from the cerebrospinal fluid indicates that SARS-CoV-2 can invade the central nervous system. In future, along with nervous system assessment, the pathogen genome detection and other indicators are needed for studying possible nervous system infection of SARS-CoV-2.

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22, which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVRA6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVRA1, AVRA7, AVRA10/AVRA22, and AVRA13, suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVRA1 and AVRA6 as well as allelic AVRA10 and AVRA22 is largely determined by the receptors’ C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVRA10 and five specific AVRA22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVRA effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.

Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus

ABSTRACT Acinetobacter baumannii and Stenotrophomonas maltophilia genomes were reconstructed from early-middle 20th-century human skeletal remains, maintained in natural history museums, using a metagenomic binning approach.

Genome-wide analyses reveal antibiotic resistance genes and mechanisms in pathogenic Pseudomonas bacteria

Background: The global emergence and re-emergence of antibiotic resistance among the Pseudomonas pathogens causes great problems to patients undergoing chemotherapy. However, there is limited comparative information on the antibiotic resistance genes (ARGs) and mechanisms across the Pseudomonas pathogenic groups. Methods: The complete genomes of five Pseudomonas pathogen groups, P. aeruginosa, P. fluorescens, P. putida, P. stutzeri and P. syringae, were analyzed for ARGs. Results: A significant number of ARGs were identified in the P. aeruginosa genome compared to the other Pseudomonas pathogens. The opportunistic pathogens P. stutzeri and P. putida were shown to be the closest to P. aeruginosa with an average nucleotide identity (%) of 80.30 and 79.52. The pathogen genome with the least hit was P. stutzeri. The four major antibiotic resistance mechanisms that include the efflux, inactivation, target alteration and efflux::target alteration were reported. Conclusion: The findings of this brief report could be useful in understanding the chemotherapeutics against antibiotic resistance strains of Pseudomonas pathogens