Published on 10/01/2020
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Auto-antibodies against type I IFNs in patients with life-threatening COVID-19
P Bastard et al, Science, September 24, 2020101 of 987 patients with life-threatening COVID-19 pneumonia had neutralizing IgG auto-Abs against IFN-? (13 patients), the 13 types of IFN-a (36), or both (52). These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1,227 healthy individuals. -
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Q Zhang et al, Science, September 24, 2020We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. -
Genetic variants mimicking therapeutic inhibition of IL-6 receptor signaling and risk of COVID-19
J Bovijn et al, Lancet Rheumatology, September 25, 2020Our findings show that IL6R variants mimicking therapeutic inhibition of IL-6 receptor are associated with a lower risk of hospitalization for COVID-19, a phenotype that is associated with disease severity (eg, requiring supplemental oxygen is a typical reason for hospitalization). -
Mass screening of asymptomatic persons for SARS-CoV-2 using saliva.
Yokota Isao et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 SepIn this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing
https://wwwnc.cdc.gov/eid/article/26/12/20-3910_articleTo investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified SARS-CoV-2 outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had primary, culture-positive, A2-RP cases. This investigation provides evidence of flight-associated SARS-CoV-2 transmission. -
Rethinking Covid-19 Test Sensitivity - A Strategy for Containment.
Mina Michael J et al. The New England journal of medicine 2020 SepIt’s time to change how we think about the sensitivity of testing for Covid-19. The Food and Drug Administration (FDA) and the scientific community are currently almost exclusively focused on test sensitivity. Critically, this measure neglects the context of how the test is being used. Yet when it comes to broad screening, context is fundamental. -
Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia.
Logunov Denis Y et al. Lancet (London, England) 2020 09 (10255) 887-897In this small study involving older adults, adverse events associated with the mRNA-1273 vaccine were mainly mild or moderate. The 100-µg dose induced higher binding- and neutralizing-antibody titers than the 25-µg dose, which supports the use of the 100-µg dose in a phase 3 vaccine trial
Non-Genomics Precision Health Studies
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Auto-antibodies against type I IFNs in patients with life-threatening COVID-19
P Bastard et al, Science, September 24, 2020101 of 987 patients with life-threatening COVID-19 pneumonia had neutralizing IgG auto-Abs against IFN-? (13 patients), the 13 types of IFN-a (36), or both (52). These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1,227 healthy individuals. -
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Q Zhang et al, Science, September 24, 2020We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. -
Genetic variants mimicking therapeutic inhibition of IL-6 receptor signaling and risk of COVID-19
J Bovijn et al, Lancet Rheumatology, September 25, 2020Our findings show that IL6R variants mimicking therapeutic inhibition of IL-6 receptor are associated with a lower risk of hospitalization for COVID-19, a phenotype that is associated with disease severity (eg, requiring supplemental oxygen is a typical reason for hospitalization). -
Mass screening of asymptomatic persons for SARS-CoV-2 using saliva.
Yokota Isao et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 SepIn this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing
https://wwwnc.cdc.gov/eid/article/26/12/20-3910_articleTo investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified SARS-CoV-2 outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had primary, culture-positive, A2-RP cases. This investigation provides evidence of flight-associated SARS-CoV-2 transmission. -
Rethinking Covid-19 Test Sensitivity - A Strategy for Containment.
Mina Michael J et al. The New England journal of medicine 2020 SepIt’s time to change how we think about the sensitivity of testing for Covid-19. The Food and Drug Administration (FDA) and the scientific community are currently almost exclusively focused on test sensitivity. Critically, this measure neglects the context of how the test is being used. Yet when it comes to broad screening, context is fundamental. -
Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia.
Logunov Denis Y et al. Lancet (London, England) 2020 09 (10255) 887-897In this small study involving older adults, adverse events associated with the mRNA-1273 vaccine were mainly mild or moderate. The 100-µg dose induced higher binding- and neutralizing-antibody titers than the 25-µg dose, which supports the use of the 100-µg dose in a phase 3 vaccine trial
News, Reviews and Commentaries
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Auto-antibodies against type I IFNs in patients with life-threatening COVID-19
P Bastard et al, Science, September 24, 2020101 of 987 patients with life-threatening COVID-19 pneumonia had neutralizing IgG auto-Abs against IFN-? (13 patients), the 13 types of IFN-a (36), or both (52). These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1,227 healthy individuals. -
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Q Zhang et al, Science, September 24, 2020We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. -
Genetic variants mimicking therapeutic inhibition of IL-6 receptor signaling and risk of COVID-19
J Bovijn et al, Lancet Rheumatology, September 25, 2020Our findings show that IL6R variants mimicking therapeutic inhibition of IL-6 receptor are associated with a lower risk of hospitalization for COVID-19, a phenotype that is associated with disease severity (eg, requiring supplemental oxygen is a typical reason for hospitalization). -
Mass screening of asymptomatic persons for SARS-CoV-2 using saliva.
Yokota Isao et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 SepIn this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. -
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing
https://wwwnc.cdc.gov/eid/article/26/12/20-3910_articleTo investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified SARS-CoV-2 outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had primary, culture-positive, A2-RP cases. This investigation provides evidence of flight-associated SARS-CoV-2 transmission. -
Rethinking Covid-19 Test Sensitivity - A Strategy for Containment.
Mina Michael J et al. The New England journal of medicine 2020 SepIt’s time to change how we think about the sensitivity of testing for Covid-19. The Food and Drug Administration (FDA) and the scientific community are currently almost exclusively focused on test sensitivity. Critically, this measure neglects the context of how the test is being used. Yet when it comes to broad screening, context is fundamental. -
Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia.
Logunov Denis Y et al. Lancet (London, England) 2020 09 (10255) 887-897In this small study involving older adults, adverse events associated with the mRNA-1273 vaccine were mainly mild or moderate. The 100-µg dose induced higher binding- and neutralizing-antibody titers than the 25-µg dose, which supports the use of the 100-µg dose in a phase 3 vaccine trial
- Page last reviewed:Feb 1, 2024
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