VGsim: scalable viral genealogy simulator for global pandemic
Shchur V., Spirin V., Pokrovskiy V., Burovski E., De Maio N., Corbett-Detig R.
As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from all continents. More than one million viral sequences are publicly available as of April 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification and investigating the spread of new variants conferring transmissibility and immunity evasion advantages to the virus. To validate new methods and to verify results resulting from these vast datasets, one needs an efficient simulator able to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses this problem. The simulation process is split into two phases. During the forward run the algorithm generates a chain of events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape. The code is freely available at https://github.com/Genomics-HSE/VGsim.
Research target: Mathematics Biology Computer Science Medical and Health Sciences
Priority areas: IT and mathematics
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The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed ...
Added: July 17, 2020
, , et al., SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia / . 2022.
Added: January 13, 2022
, , et al., The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia / Cold Spring Harbor Laboratory. Series 005140 "Medrxiv". 2021.
Background Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries. Aim Here, we aim to study the emergence and spread of the Delta lineage in Russia. Methods We use a phylogeographic approach to infer imports of Delta ...
Added: December 6, 2021
, , et al., PeerJ 2020 Vol. 8 Article e9994
Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions ...
Added: September 17, 2020
Endocytosis and Transcytosis of SARS-CoV-2 Across the Intestinal Epithelium and Other Tissue Barriers
, , , Frontiers in Immunology 2021 Vol. 12 Article 636966
Since 2003, the world has been confronted with three new betacoronaviruses that cause human respiratory infections: SARS-CoV, which causes severe acute respiratory syndrome (SARS), MERS-CoV, which causes Middle East respiratory syndrome (MERS), and SARS-CoV-2, which causes Coronavirus Disease 2019 (COVID-19). The mechanisms of coronavirus transmission and dissemination in the human body determine the diagnostic and ...
Added: September 7, 2021
, , et al., Virus Evolution 2022 Vol. 8 No. 1 Article veac017
Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to the emergence of multiple sublineages, most of which are well-mixed between countries. By contrast, here we show that nearly the entire Delta epidemic in Russia has probably descended from a single import event, or ...
Added: June 4, 2022
, , et al., Биотехнология 2020 Т. 36 № 5 С. 6-12
Real-time RT-PCR currently remains a gold standard for early COVID-19 diagnostics. However Loop-mediated isothermal amplification (LAMP) method outperform real-time RT-PCR in simplicity because it doesn't require expensive lab equipment and trained personnel, and in speed. LAMP-based diagnostic kits for COVID-19 testing are already exist, but LAMP-based tests have not been widely accepted yet. The method has great potential for ...
Added: October 14, 2020
Ингибитор деметилаз семейства KDM5 — KDOAM-25 — снижает проникновение псевдотипированных вирусных частиц SARS-CoV-2 в клетки
, , et al., Клеточные технологии в биологии и медицине 2023 № 1 С. 40-46
We studied the effect of KDM5 family demethylase inhibitors (JIB-04, PBIT, and KDOAM-25) on the penetration of SARS-CoV-2 pseudotyped viruses into differentiated Caco-2 cells and HEK293T cells with ACE2 hyperexpression. The above drugs were not cytotoxic. Only KDOAM-25 significantly reduced viral entry into cells. At the same time, the level of ACE2 mRNA expression in Caco-2 significantly increased, while TMPRSS2 expression ...
Added: November 2, 2022
Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2
, , et al., Plos One 2020 Vol. 15 No. 7 P. e0235987
Development of novel approaches for regulating the expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) is becoming increasingly important within the context of the ongoing COVID-19 pandemic since these enzymes play a crucial role in cell infection. In this work we searched for putative ACE2 and TMPRSS2 expression regulation networks mediated ...
Added: July 29, 2020
, , et al., Вестник Российского государственного медицинского университета 2020 № 2 С. 17-20
Coronavirus SARS-CoV-2, the cause of the COVID-19 pandemic, enters the cell by binding the cell surface proteins: angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). The expression of these proteins varies significantly in individual organs and tissues of the human body. One of the proteins’ expression regulation mechanisms is based on the activity ...
Added: May 6, 2020
М. : МАКС Пресс, 2013
В 2013 году Московский университет проводит очередной, крупнейший в Евразии Международный молодежный научный форум, центральным мероприятием которого является юбилейная, XX молодежная научная конференция студентов, аспирантов и молодых ученых. Сопредседателями организационного комитета Форума являются ректор Московского университета, вице-президент РАН, академик РАН В.А.Садовничий и Министр образования и науки Российской Федерации Д.В. Ливанов. Проведению Форума традиционно оказывают поддержку Исполком ...
Added: April 16, 2015
, Ижевск : Ижевский институт компьютерных исследований, 2018
Предлагаемая книга является полноцветным изданием и относится к вычислительной нейродинамике. В ней изложены базовые понятия электрофизиологии нейронов и основы математического моделирования нейронной активности методами нелинейной динамики. Все главы этой книги представляют собой законченные разделы, в которых материал излагается доступным языком, с постепенным усложнением. Широкое использование геометрической и иллюстративной интерпретации основных математических понятий теории динамических систем делает книгу доступной широкому кругу читателей. ...
Added: February 25, 2019
, , et al., Journal of Computational Biology 2013 Vol. 20 No. 4 P. 359-371
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in ...
Added: March 21, 2014
Пятая Международная конференция «Системный анализ и информационные технологии» САИТ-2013 (19–25 сентября 2013 г., г.Красноярск, Россия): Труды конференции. В 2-х т.
Красноярск : ИВМ СО РАН, 2013
Труды Пятой Международной конференции «Системный анализ и информационные технологии» САИТ-2013 (19–25 сентября 2013 г., г.Красноярск, Россия): ...
Added: November 18, 2013
Selected works from the BIOMAT Consortium Lectures, Moscow 2017 This book brings together carefully selected, peer-reviewed works on mathematical biology presented at the BIOMAT International Symposium on Mathematical and Computational Biology, which was held at the Institute of Numerical Mathematics, Russian Academy of Sciences, in October 2017, in Moscow. Topics covered include, but are not limited ...
Added: November 19, 2018
, , et al., Nature Communications 2021 Vol. 12 P. 1-13
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from at least 67 ...
Added: January 28, 2021
, , et al., Journal of Computational Biology 2013 Vol. 20 No. 10 P. 714-737
Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, ...
Added: March 21, 2014
, , Математическая биология и биоинформатика 2015 Т. 10 № 1 С. 54-59
пространственная структура РНК, мультиплет, стем, псевдоузел, линк, граф ...
Added: March 30, 2015
Сборник трудов 43-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2019"
Added: January 15, 2020
Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure
, , , Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2018.
Estimation of the relationship between DNA sequences is one of the most important problems in genomics. Understanding these relationships is central to de- mographic inference, correction of population structure in GWAS, identifying signals of selection etc. The data structure containing the full information about sample genealogy is called the ancestral recombination graph (ARG). However, ARG ...
Added: February 7, 2019
, , Cross - Cultural Research 2007 Vol. 41 P. 307-335
This article hypothesizes that in societies where spouses are considered to have relatively equal status, they are more likely to be intimate with one another than in societies where there is spousal status inequality. The authors ask: What are the core attributes of intimacy between husband and wife cross-culturally? And what sociocultural norms and practices are ...
Added: March 8, 2013
Прогнозирование развития эпидемии COVID-19 в странах европейского союза с использованием энтропийно-рандомизированного подхода
, , , Информатика и автоматизация (Труды СПИИРАН) 2021 Т. 20 № 5 С. 1010-1033
© St. Petersburg Federal Research Center of the Russian Academy of Sciences.The paper is devoted to the forecasting of the COVID-19 epidemic by the novel method of randomized machine learning. This method is based on the idea of estimation of probability distributions of model parameters and noises on real data. Entropy-optimal distributions correspond to the ...
Added: October 28, 2022
, , , Математическая биология и биоинформатика 2012 Т. 7 № 2 С. 567-571
Предложена классификация элементов вторичной структуры РНК, которая является обобщением классификации петель, предложенной Мэтьюзом и Тернером. Эта классификация позволяет единообразно описывать структуры как содержащие, так и не содержащие псевдоузлы. ...
Added: January 30, 2013
, , et al., Topology of cognitive maps / Cornell University. Series Computer Science "arxiv.org". 2022.
In present paper we test different approaches to reconstructing the topology of the physical space from neural activity data in A1 fields of mice brains, in particular, having a Cognitome-focused approach in mind. Animals were placed in different new environments and discovered them while their physical and neural activity was recorded. We discuss possible approaches ...
Added: November 17, 2022