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Persistent minimal sequences of SARS-CoV-2.

ABSTRACT: MOTIVATION:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis, and therapeutics are of great importance. RESULTS:Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. Additionally, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. AVAILABILITY AND IMPLEMENTATION:https://github.com/cobilab/eagle. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Pratas D

PROVIDER: S-EPMC7559010 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Persistent minimal sequences of SARS-CoV-2.

Pratas Diogo D Silva Jorge M JM

Bioinformatics (Oxford, England) 20210101 21

<h4>Motivation</h4>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis and therapeutics are of great importance.<h4>Results</h4>Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four ...[more]

PMID: 32730589

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Project description:Environmental contamination caused by COVID-19 patients could be a medium of transmission. Previous reports of SARS-CoV-2 in environmental surfaces were about short-term contamination. This study investigated SARS-CoV-2 RNA existence in room-temperature and low-temperature environments long after exposure (>28 days). A department store, where a COVID-19 outbreak was occurred in January 2020 (the epicenter of 43 COVID-19 patients), and a patient's apartment were included as room-temperature environments after being blocked for 57 days and 48 days, respectively. Seven cold storages and imported frozen foods inside were included as low-temperature environments (under -18 °C). Twenty food markets with potential contamination of imported frozen foods were also included to study the consecutive contamination. Information about temperature, relative humidity, and the number of days of environmental samples since the last exposure was collected and analyzed. In sum, 11,808 swab samples were collected before disinfection, of which 35 samples were positive. Persistent contamination of SARS-CoV-2 RNA was identified in the apartment (6/19), the department store (3/50), food packages in cold storages (23/1360), environmental surfaces of cold storages (2/345), and a package in the food market (1/10,034). Two positive samples were isolated from the bathroom of the apartment (66.7 %, 2/3), and doorknobs were proved with contamination in the apartment (40 %, 2/5) and cold storage (33.3 %, 1/3). The epidemiology information and environmental contamination results of an imported frozen food related COVID-19 case (138th COVID-19 patient in Tianjin) were analyzed. Based on the Ct values, the number of copies of two target genes was calculated by standard curves and linear regressions. In conclusion, SARS-CoV-2 RNA can be detected in room-temperature environments at least 57 days after the last exposure, much longer than previous reports. Based on the results of this study and previous studies, infectious SARS-CoV-2 could exist for at least 60 days on the surface of cold-chain food packages. Doorknobs and toilets (bathrooms) were important positions in COVID-19 control. High-risk populations of cold-chain-related logistic operations, such as porters, require strict prevention and high-level personal protection.

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Persistent minimal sequences of SARS-CoV-2.

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Persistent minimal sequences of SARS-CoV-2.

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