The 2022<i>Nucleic Acids Research</i>database issue and the online molecular biology database collection

Rigden, Daniel J.; Fernández, Xosé M.

doi:10.1093/nar/gkab1195

Cited by 48 publications

(22 citation statements)

References 110 publications

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“…Our observations of biallelic variant positions are consistent with those from other studies describing subconsensus SNPs or iSNVs [30][31][32][33][34][35][36][37][38]. To determine how often biallelic variations were included in SARS-CoV-2 sequences submitted to international repositories, we randomly selected and analyzed 110 additional COVID-19 infections (Supplemental Table 4) reported from 18 different laboratories or consortia with raw sequence data available in the sequence read archive (SRA) [39]; the same ³80% coverage, ³100X read-depth inclusion threshold was applied. Results summarized in Supplemental Fig.…”

Section: Consensus Sequences and Sars-cov-2 Strain Polymorphismsupporting

confidence: 81%

COVID-19 Infection and Transmission Includes Complex Sequence Diversity

Chan

Jones

Linger

et al. 2022

Preprint

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SARS-CoV-2 whole genome sequencing has played an important role in documenting the emergence of polymorphisms in the viral genome and its continuing evolution during the COVID-19 pandemic. Here we present data from over 360 patients to characterize the complex sequence diversity of individual infections identified during multiple variant surges (e.g., Alpha and Delta; requiring ≥ 80% genome coverage and ≥100X read depth). Across our survey, we observed significantly increasing SARS-CoV-2 sequence diversity during the pandemic and frequent occurrence of multiple biallelic sequence polymorphisms in all infections. This sequence polymorphism shows that SARS-CoV-2 infections are heterogeneous mixtures. Convention for reporting microbial pathogens guides investigators to report a majority consensus sequence. In our study, we found that this approach would under-report at least 79% of the observed sequence variation. As we find that this sequence heterogeneity is efficiently transmitted from donors to recipients, our findings illustrate that infection complexity must be monitored and reported more completely to understand SARS-CoV-2 infection and transmission dynamics involving both immunocompetent and immunocompromised patients. Many of the nucleotide changes that would not be reported in a majority consensus sequence have now been observed as lineage defining SNPs in Omicron BA.1 and/or BA.2 variants. This suggests that minority alleles in earlier SARS-CoV-2 infections may play an important role in the continuing evolution of new variants of concern.AUTHOR SUMMARYEvolution of the virus causing COVID-19 (SARS-CoV-2) has been associated with significant transmission surges. With evolution of SARS-CoV-2, evidence has accumulated regarding increased transmissibility of lineages, varying severity of illness, evasion of vaccines and diagnostic tests. Continuous tracking of SARS-CoV-2 lineage evolution distills very large and complex viral sequence data sets down to consensus sequences that report the majority nucleotide at each of over 29,000 positions in the SARS-CoV-2 genome. We observe that this eliminates considerable sequence variation and leads to a significant underestimation of SARS-CoV-2 infection diversity and transmission complexity. Additionally, concentration on the majority consensus sequence diverts attention from genetic variation that may contribute significantly to the continuing evolution of the COVID-19 pandemic.

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Section: Consensus Sequences and Sars-cov-2 Strain Polymorphismsupporting

confidence: 81%

COVID-19 Infection and Transmission Includes Complex Sequence Diversity

Chan

Jones

Linger

et al. 2022

Preprint

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“…Hence, caution must be exercised when using gene expression as a proxy for protein expression. Background on various experimental techniques, an overview of how PPI databases are built, and a recent list of PPI databases can be found here [3] , [32] . Some examples of PPI databases are shown in Table 2 .…”

Section: Data Availability and Qualitymentioning

confidence: 99%

“…The emergence and growth of network medicine in the last decade has been facilitated by the growth of publicly-accessible molecular datasets [1] . Various kinds of interactions such as protein-protein interactions (PPIs), transcription factor-gene regulatory interactions, perturbation effects of drugs and small molecules on gene expression, etc., have been systematically documented [2] , [3] , [4] . These interactions can be represented as networks or graphs, which are composed of a set of nodes, also called vertices, representing the discrete interacting entities (whose nature depends on the type of data under study), and a set of links, also called edges, representing physical or functional interactions between nodes.…”

Section: Introductionmentioning

confidence: 99%

Construction and contextualization approaches for protein-protein interaction networks

Badkas

Landtsheer²,

Sauter³

2022

Computational and Structural Biotechnology Journal

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“…Due to their significance, each year, since 1999, the Nucleic Acids Research journal reviews new biological databases, eliminates discontinued URLs, and updates an existing compilation of them. This resource can be freely consulted at https://www.oxfordjournals.org/nar/database/c/, rendering a current total of 1637 databases for the early 2021 issue [9] and 1645 for the following one [10],…”

Section: Relevance Of Databases and Scientific Repositories: The Spec...mentioning

confidence: 99%

“…A clear example of this was illustrated by the emergence of biological databases, such as LitCovid, which reached more than 85,000 publications on the subject by December the 31 st , 2020 [14]. In the latest Nucleic Acids Research review issue [10], seven new databases inspired by the COVID-19 pandemic were added:…”

Section: The Role Of Covid-19 In the Increase Of Published Materialsmentioning

confidence: 99%

COVID-19 Times: Impact on Information Generation and Data Sharing

Rodríguez-Flores¹,

Gómez-Manzo²,

Marcial-Quino³

et al. 2022

AIT

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At the beginning of 2020, human activities were interrupted by a new virus, identified as SARS-CoV-2, which causes COVID-19 disease. The scientific area was no exception: for a certain period, researchers around the world were forced to leave their laboratories and work remotely. There was a global necessity for finding alternatives focused on generating knowledge and publishing data, so repositories of scientific information, such as databases, represented strong support. In the specific case of life sciences, different strategies allowed rapid compilation of data and its sharing worldwide. Therefore, in this work, the impact of the SARS-CoV-2 pandemic on the amount of peer-reviewed and published papers during COVID-19 times was analyzed along with the role of databases. Our results pointed out that an increase in the number of papers belonging to different knowledge fields took place, with the medical field being the most significant. On the other hand, the complete genome of the new virus was sequenced, and repositories were created with sufficient data for monitoring, preventing, and controlling its dissemination. This was the case for the generation of vaccines in addition to potential candidates for drugs against COVID-19. However, although in 2021, vaccines allowed us to gradually return to our activities, databases and the generation of other repositories remain a key point for facing new strains and adapting to a new reality. Finally, this paper discusses joint efforts to tackle the obstacles of the pandemic, not only from a medical but also from the point of view regarding the fight against misinformation.

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The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Cited by 48 publications

References 110 publications

COVID-19 Infection and Transmission Includes Complex Sequence Diversity

COVID-19 Infection and Transmission Includes Complex Sequence Diversity

Construction and contextualization approaches for protein-protein interaction networks

COVID-19 Times: Impact on Information Generation and Data Sharing

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