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LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T6","span":{"begin":699,"end":708},"obj":"Disease"}],"attributes":[{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"}],"text":"Current report conducted careful examination of the sequences of 2019-nCoV, other CoV viruses and HIV-1 as well as GenBank database. Our results demonstrated no evidence that the sequences of these four inserts are HIV-1 specific or the 2019-nCoV viruses obtain these insertions from HIV-1. First, the results of blast search of these motifs against GenBank shows that the top 100 identical or highly homologous hits are all from host genes of mammalian, insects, bacterial and others. There are only a few hits on coronaviruses, but none of them are HIV-1 related. Blast against viral sequence database also showed these insertion sequences widely exist in all kinds of viruses from bacteriophage, influenza, to giant eukaryotic viruses (Table 1). More hits were found for coronaviruses and a few also hit on HIV-1 sequences than the search against the entire database (Table 1). However, while the 100% match between the insertion 1 and 2 sequences and the HIV sequences were found in 19 entries, the matches between the insertion 3 and 4 sequences and HIV-1 sequences were rather poor (from 42% to 88%). Moreover, the insertion 4 sequence ambiguously hit multiple different genes (gag, pol and env) in the HIV-1 genome, suggesting that similarities (as low as 42%) between them are too low to be reliable. Search these four insertion sequences against HIV-1 Sequence Database (https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html) yielded similar results. Sequences that completely match the insertion 3 and 4 sequences were not found in any HIV-1 sequences. This clearly shows that these insertioin sequences are widely present in living organisms including viruses, but not HIV-1 specific. All these regions in HIV-1 envelope glycoprotein are highly variable with many large insertions and deletions, indicating that they are not essential for biological functions of HIV-1 envelope glycoprotein. The detection of completely matched sequences of 1 and 2 insertions in only a few HIV-1 strains demonstrated that four insertions are very rare or not present among tens of thousands of natural HIV-1 sequences. This also explains why four insertion homolog sequences could only be independently found in different HIV-1 genomes [8]. Because of their poor identities to and rareness in the HIV-1 sequences, HIV-1 could not be the source for those insertion sequences in the 2019-nCoV genome.\nTable 1. Blast search results of four insertion sequences against sequence databases.\nDatabase Gene source Insertion 1 TNGTKR Insertion 2 HKNNKS Insertion 3 RSYLTPGDSSSG Insertion 4 QTNSPRRA\nWhole database CoV 2 (2) 0 3 (3) 2 (2)\nHIV-1 0 0 0 0\nProkaryotic 27 (27) 3 (3) 74 (0) 66 (1)\nEukaryotic 71 (71) 97 (97) 23 (0) 32 (1)\nOnly viral database CoV 3 (3) 3 (3) 5 (3) 3 (2)\nHIV-1 18 (18) 1 (1) 4 (0)* 6 (0)**\nOther Eukaryotic viruses 49 (2) 66 (8) 69 (0) 62 (0)\nProkaryotic viruses 29 (13) 30 (1) 21 (0) 28 (0)\nUnclassified virus 1 (1) 0 1 (0) 1 (0)\nTop 100 hits are analyzed and the numbers of 100% matches are shown in parentheses. * Similarity at 67%; ** Random hits in Gag, Pro and Env sequences with similarity between 42% and 88%."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T5","span":{"begin":1746,"end":1758},"obj":"Chemical"},{"id":"T6","span":{"begin":1903,"end":1915},"obj":"Chemical"},{"id":"T7","span":{"begin":3085,"end":3088},"obj":"Chemical"}],"attributes":[{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_50342"}],"text":"Current report conducted careful examination of the sequences of 2019-nCoV, other CoV viruses and HIV-1 as well as GenBank database. Our results demonstrated no evidence that the sequences of these four inserts are HIV-1 specific or the 2019-nCoV viruses obtain these insertions from HIV-1. First, the results of blast search of these motifs against GenBank shows that the top 100 identical or highly homologous hits are all from host genes of mammalian, insects, bacterial and others. There are only a few hits on coronaviruses, but none of them are HIV-1 related. Blast against viral sequence database also showed these insertion sequences widely exist in all kinds of viruses from bacteriophage, influenza, to giant eukaryotic viruses (Table 1). More hits were found for coronaviruses and a few also hit on HIV-1 sequences than the search against the entire database (Table 1). However, while the 100% match between the insertion 1 and 2 sequences and the HIV sequences were found in 19 entries, the matches between the insertion 3 and 4 sequences and HIV-1 sequences were rather poor (from 42% to 88%). Moreover, the insertion 4 sequence ambiguously hit multiple different genes (gag, pol and env) in the HIV-1 genome, suggesting that similarities (as low as 42%) between them are too low to be reliable. Search these four insertion sequences against HIV-1 Sequence Database (https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html) yielded similar results. Sequences that completely match the insertion 3 and 4 sequences were not found in any HIV-1 sequences. This clearly shows that these insertioin sequences are widely present in living organisms including viruses, but not HIV-1 specific. All these regions in HIV-1 envelope glycoprotein are highly variable with many large insertions and deletions, indicating that they are not essential for biological functions of HIV-1 envelope glycoprotein. The detection of completely matched sequences of 1 and 2 insertions in only a few HIV-1 strains demonstrated that four insertions are very rare or not present among tens of thousands of natural HIV-1 sequences. This also explains why four insertion homolog sequences could only be independently found in different HIV-1 genomes [8]. Because of their poor identities to and rareness in the HIV-1 sequences, HIV-1 could not be the source for those insertion sequences in the 2019-nCoV genome.\nTable 1. Blast search results of four insertion sequences against sequence databases.\nDatabase Gene source Insertion 1 TNGTKR Insertion 2 HKNNKS Insertion 3 RSYLTPGDSSSG Insertion 4 QTNSPRRA\nWhole database CoV 2 (2) 0 3 (3) 2 (2)\nHIV-1 0 0 0 0\nProkaryotic 27 (27) 3 (3) 74 (0) 66 (1)\nEukaryotic 71 (71) 97 (97) 23 (0) 32 (1)\nOnly viral database CoV 3 (3) 3 (3) 5 (3) 3 (2)\nHIV-1 18 (18) 1 (1) 4 (0)* 6 (0)**\nOther Eukaryotic viruses 49 (2) 66 (8) 69 (0) 62 (0)\nProkaryotic viruses 29 (13) 30 (1) 21 (0) 28 (0)\nUnclassified virus 1 (1) 0 1 (0) 1 (0)\nTop 100 hits are analyzed and the numbers of 100% matches are shown in parentheses. * Similarity at 67%; ** Random hits in Gag, Pro and Env sequences with similarity between 42% and 88%."}

LitCovid-sentences

LitCovid-PubTator