Published on 08/20/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes
Interim Analysis of 2 Randomized Clinical Trials
S Xia et al, JAMA, August 13, 2020In this interim report of the phase 1 and phase 2 trials of an inactivated COVID-19 vaccine, patients had a low rate of adverse reactions and demonstrated immunogenicity; the study is ongoing. Efficacy and longer-term adverse event assessment will require phase 3 trials. -
Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space
J Kowalewski, et al, Helyon, (Cell) AUgust 2020We have developed a machine learning drug discovery pipeline to identify several drug candidates. First, we collect assay data for 65 human proteins known to interact SARS-CoV-2. We train machine learning models to predict inhibitory activity and use them to screen FDA registered chemicals and approved drugs and ~14 million purchasable chemicals. -
Geographic and Genomic Distribution of SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Frontiers in microbiology 2020 1800We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. -
SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance
CBF Vogels et al, MEDRXIV, August 2020Using saliva instead of respiratory swabs enables non-invasive frequent sampling and reduces the need for trained healthcare professionals during collection. Our test does not require nucleic acid preservatives at sample collection and replaces nucleic acid extraction with a simple proteinase K and heat treatment step. -
A dynamic COVID-19 immune signature includes associations with poor prognosis
AG Laing et al, Nature Medicine, August 17, 2020We have identified a core peripheral blood immune signature across 63 hospital-treated patients with COVID-19 who were otherwise highly heterogeneous. The signature includes discrete changes in B and myelomonocytic cell composition, profoundly altered T cell phenotypes, selective cytokine/chemokine upregulation and SARS-CoV-2-specific antibodies. -
Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study
Be Young et al, The Lancet, August 17, 2020Severe acute respiratory syndrome coronavirus 2 variants with a 382-nucleotide deletion (?382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. we found that the ?382 variant is associated with a milder infection. This could have implications for the development of treatments and vaccines. -
Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.
Ott Isabel M et al. medRxiv : the preprint server for health sciences 2020 AugWe investigated stability of SARS-CoV-2 RNA and infectious virus detection from saliva. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures. We found RNA in saliva is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods. -
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
MT Maurano et al, MEDRXIV, AUgust 19, 2020Analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area shows that the majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe.
Non-Genomics Precision Health Studies
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Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes
Interim Analysis of 2 Randomized Clinical Trials
S Xia et al, JAMA, August 13, 2020In this interim report of the phase 1 and phase 2 trials of an inactivated COVID-19 vaccine, patients had a low rate of adverse reactions and demonstrated immunogenicity; the study is ongoing. Efficacy and longer-term adverse event assessment will require phase 3 trials. -
Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space
J Kowalewski, et al, Helyon, (Cell) AUgust 2020We have developed a machine learning drug discovery pipeline to identify several drug candidates. First, we collect assay data for 65 human proteins known to interact SARS-CoV-2. We train machine learning models to predict inhibitory activity and use them to screen FDA registered chemicals and approved drugs and ~14 million purchasable chemicals. -
Geographic and Genomic Distribution of SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Frontiers in microbiology 2020 1800We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. -
SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance
CBF Vogels et al, MEDRXIV, August 2020Using saliva instead of respiratory swabs enables non-invasive frequent sampling and reduces the need for trained healthcare professionals during collection. Our test does not require nucleic acid preservatives at sample collection and replaces nucleic acid extraction with a simple proteinase K and heat treatment step. -
A dynamic COVID-19 immune signature includes associations with poor prognosis
AG Laing et al, Nature Medicine, August 17, 2020We have identified a core peripheral blood immune signature across 63 hospital-treated patients with COVID-19 who were otherwise highly heterogeneous. The signature includes discrete changes in B and myelomonocytic cell composition, profoundly altered T cell phenotypes, selective cytokine/chemokine upregulation and SARS-CoV-2-specific antibodies. -
Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study
Be Young et al, The Lancet, August 17, 2020Severe acute respiratory syndrome coronavirus 2 variants with a 382-nucleotide deletion (?382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. we found that the ?382 variant is associated with a milder infection. This could have implications for the development of treatments and vaccines. -
Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.
Ott Isabel M et al. medRxiv : the preprint server for health sciences 2020 AugWe investigated stability of SARS-CoV-2 RNA and infectious virus detection from saliva. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures. We found RNA in saliva is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods. -
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
MT Maurano et al, MEDRXIV, AUgust 19, 2020Analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area shows that the majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe.
News, Reviews and Commentaries
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Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes
Interim Analysis of 2 Randomized Clinical Trials
S Xia et al, JAMA, August 13, 2020In this interim report of the phase 1 and phase 2 trials of an inactivated COVID-19 vaccine, patients had a low rate of adverse reactions and demonstrated immunogenicity; the study is ongoing. Efficacy and longer-term adverse event assessment will require phase 3 trials. -
Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space
J Kowalewski, et al, Helyon, (Cell) AUgust 2020We have developed a machine learning drug discovery pipeline to identify several drug candidates. First, we collect assay data for 65 human proteins known to interact SARS-CoV-2. We train machine learning models to predict inhibitory activity and use them to screen FDA registered chemicals and approved drugs and ~14 million purchasable chemicals. -
Geographic and Genomic Distribution of SARS-CoV-2 Mutations.
Mercatelli Daniele et al. Frontiers in microbiology 2020 1800We analyzed and annotated all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. -
SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance
CBF Vogels et al, MEDRXIV, August 2020Using saliva instead of respiratory swabs enables non-invasive frequent sampling and reduces the need for trained healthcare professionals during collection. Our test does not require nucleic acid preservatives at sample collection and replaces nucleic acid extraction with a simple proteinase K and heat treatment step. -
A dynamic COVID-19 immune signature includes associations with poor prognosis
AG Laing et al, Nature Medicine, August 17, 2020We have identified a core peripheral blood immune signature across 63 hospital-treated patients with COVID-19 who were otherwise highly heterogeneous. The signature includes discrete changes in B and myelomonocytic cell composition, profoundly altered T cell phenotypes, selective cytokine/chemokine upregulation and SARS-CoV-2-specific antibodies. -
Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study
Be Young et al, The Lancet, August 17, 2020Severe acute respiratory syndrome coronavirus 2 variants with a 382-nucleotide deletion (?382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. we found that the ?382 variant is associated with a milder infection. This could have implications for the development of treatments and vaccines. -
Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.
Ott Isabel M et al. medRxiv : the preprint server for health sciences 2020 AugWe investigated stability of SARS-CoV-2 RNA and infectious virus detection from saliva. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures. We found RNA in saliva is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods. -
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
MT Maurano et al, MEDRXIV, AUgust 19, 2020Analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area shows that the majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe.
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- Page last updated:Apr 18, 2024
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