The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic

Lam, Anthony; Duchêne, Sebastián

doi:10.3390/v13010079

Cited by 3 publications

(2 citation statements)

References 32 publications

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“…The phylodynamic threshold has been rigorously explored in other pathogens, such as SARS-CoV-2 36 , but not explicitly in Y. pestis. The challenges in reconstructing intra-epidemic plague diversity have been noted previously.…”

Section: Resultsmentioning

confidence: 99%

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

et al. 2023

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Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.

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Section: Resultsmentioning

confidence: 99%

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

et al. 2023

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“…Although an epidemiological paradigm that combines molecular and native perspectives was provided, unevenly distributed and relatively inadequate genomic samples may bias the analytic results to some extent. In fact, sampling bias is inevitable in genomic surveillance and related research [93]. Therefore, in the process of deriving conclusions, we should try to combine the real-world pandemic situations and be cautious.…”

Section: Discussionmentioning

confidence: 99%

Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data

Zhu

Zeng²,

Saputro

et al. 2022

Virol J

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Background As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. Methods For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID’s EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. Results As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia’s daily infections during the period of March–May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. Conclusions SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential.

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Exploring the complexities of epigenetics in multiple sclerosis: A study involving meta-analysis of DNA methylation profiles, epigenetic drift, and rare epivariations

Baldrighi,

Cavagnola,

Sacco

et al. 2024

Multiple Sclerosis Journal - Experimental, Translational and Cl

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Background Multiple sclerosis (MS) is an autoimmune condition characterized by inflammatory and neurodegenerative traits. Recently, DNA methylation has emerged as a promising field of investigation for elucidating dynamics characterizing MS development and progression. Objectives This study aimed to comprehensively investigate the role of epigenetics in MS by analyzing the methylation profiles from blood and brain tissues from public datasets. Methods Employing a meta-analytical framework for differential methylation analyses, the study extended beyond conventional analyses to explore additional dimensions of epigenetic regulation, including epigenetic drift, age acceleration, and rare epivariations. Results Results of the differential methylation analysis were in line with previously reported findings. No significant differences were observed in age acceleration or global epigenetic drift between MS cases and controls. However, upon closer analysis at the gene level, distinctive patterns of epigenetic drift emerged, particularly within genes implicated in neural biological functions. Conclusions These findings underscore the role of epigenetic modifications in shaping MS pathology. Furthermore, the study unveiled the exclusive presence of rare epivariations within the MS cases, some of which involved genes previously linked to MS or other autoimmune diseases. This highlights the potential significance of rare genetic aberrations in driving MS susceptibility and progression.

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The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic

Cited by 3 publications

References 32 publications

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data

Exploring the complexities of epigenetics in multiple sclerosis: A study involving meta-analysis of DNA methylation profiles, epigenetic drift, and rare epivariations

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