Skip directly to search Skip directly to A to Z list Skip directly to navigation Skip directly to page options Skip directly to site content

Published on 10/07/2021

COVID-19 Genomics and Precision Public Health Weekly Update Content

Pathogen and Human Genomics Studies

  • The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission
    DW Eyre et al, MEDRXIV, September 29, 2021
    51,798/139,164(37.2%) contacts tested were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha variant index cases independently reduced PCR-positivity in contacts (aOR, adjusted odds ratio vs. unvaccinated=0.18[95%CI 0.12-0.29] and 0.37[0.22-0.63] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aOR=0.35[0.26-0.48]), more than ChAdOx1 (aOR=0.64[0.57-0.72].
  • Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study
    MI Paredes et al, MEDRXIV, September 30, 2021
    Of the 27,814 cases, 23,170 (83.3%) were sequenced through sentinel surveillance, of which 726 (3.1%) were hospitalized due to COVID–19. Higher hospitalization risk was found for infections with Gamma (HR 3.17, 95% CI 2.15–4.67), Beta (HR: 2.97, 95% CI 1.65–5.35), Delta (HR: 2.30, 95% CI 1.69–3.15), and Alpha (HR 1.59, 95% CI 1.26–1.99) compared to infections with an ancestral lineage. Following VOC infection, unvaccinated patients show a similar higher hospitalization risk, while vaccinated patients show no significant difference in risk, both when compared to unvaccinated, ancestral lineage cases.
  • Immune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors
    RT Shroff et al, Nature Medicine, September 30, 2021
    We initiated a phase 1 trial for 20 cancer cohort participants of a third vaccine dose of BNT162b2 ; primary outcomes were immune responses, with a secondary outcome of safety. At 1 week after a third immunization, 16 participants demonstrated a median threefold increase in neutralizing antibody responses, but no improvement was observed in T cell responses. Adverse events were mild. These results suggest that a third dose of BNT162b2 is safe, improves humoral immunity against SARS-CoV-2 and could be immunologically beneficial for patients with cancer on active chemotherapy.
  • The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA
    B Blaiszik et al, MEDRXIV, September 30, 2021
    We accessed openly available data sources from the public health authorities of seven U.S. states, five U.S. counties, and the District of Columbia on RT-PCR COVID-19 tests split by the COVID-19 vaccination status of individuals tested during this period. Together, these time series enable estimation and tracking of COVID-19 vaccine effectiveness (VE*) (against RT-PCR diagnosed infection) concurrently with the growth of Delta variant prevalence in those locations. Our analyses reveal that in each locality the VE* for the combined set of all three US vaccines remained relatively stable and quite well-performing, despite the dramatic concurrent rise of Delta variant prevalence.
  • Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants
    K Broxvoort et al, MEDRXIV, October 1, 2021
    We conducted a test-negative case-control study at Kaiser Permanente Southern California. The study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged =65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]).
  • Nosocomial outbreak caused by the SARS-CoV-2 Delta variant in a highly vaccinated population, Israel, July 2021 separator
    P Shitrit et al, Eurosurveillance, September 2021
    We present an investigation of a coronavirus disease (COVID-19) outbreak that started from one unidentified COVID-19 patient, with extensive, rapid nosocomial spread among vaccinated, including individuals wearing surgical masks.
  • The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.
    López Mariana G et al. Nature genetics 2021 10
    As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020
  • Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.
    Mutnal Manohar B et al. Journal of medical virology 2021 10
    We analyzed virus sequencing results of specimens collected across Central Texas and found dramatic changes in variant distribution in the first half of 2021. The alpha variant (B 1.1.7) became predominant at week 13 and continued dominance until week 25. A growth rate of 1.20 (R2 = 0.92) for the first 15 weeks was noted and this growth gradually declined to -0.55 (R2 = 0.99) for the final 13 weeks. Currently, B.1.1.7 is being displaced with B.1.617.2 at 0.58 growth rate (R2 = 0.97). We also investigated vaccine breakthrough cases (VBCs) within our healthcare system and present clinical data on 28 symptomatic patients.
  • Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality.
    Nakanishi Tomoko et al. The Journal of clinical investigation 2021 10
    We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (HR 1.4, 95%CI 1.2-1.7). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (OR 2.1, 95%CI 1.6-2.6), venous thromboembolism (OR 1.7, 95%CI 1.2-2.4), and hepatic injury (OR 1.5, 95%CI 1.2-2.0). Risk allele carriers =60 years had higher odds of death or severe respiratory failure (OR 2.7, 95%CI 1.8-3.9) compared to those >60 years (OR 1.5, 95%CI 1.2-1.8, interaction-p=0.038). Amongst individuals =60 years who died or experienced severe respiratory failure, 32.3% were risk variant carriers, compared to 13.9% of those not experiencing these outcomes.
  • Acute Myocarditis Following COVID-19 mRNA Vaccination in Adults Aged 18 Years or Older
    A Simone et al, JAMA Internal Medicine, October 4, 2021
    In this population-based cohort study of 2?392?924 individuals who received at least 1 dose of COVID-19 mRNA vaccines, acute myocarditis was rare, at an incidence of 5.8 cases per 1 million individuals after the second dose (1 case per 172?414 fully vaccinated individuals). The signal of increased myocarditis in young men warrants further investigation.
  • COVID vaccines cut the risk of transmitting Delta — but not for long
    S Mallapaty, Nature, October 5, 2021
    The study shows that people who become infected with the Delta variant are less likely to pass the virus to their close contacts if they have already had a COVID-19 vaccine than if they haven’t1. But that protective effect is relatively small, and dwindles alarmingly at three months after the receipt of the second shot.
  • Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study
    SY Tartoff et al, The Lancet, October 4, 2021
    Effectiveness against infections declined from 88% (95% CI 86–89) during the first month after full vaccination to 47% (43–51) after 5 months. Among sequenced infections, vaccine effectiveness against infections of the delta variant was high during the first month after full vaccination (93% [95% CI 85–97]) but declined to 53% [39–65] after 4 months. Effectiveness against other (non-delta) variants the first month after full vaccination was also high at 97% (95% CI 95–99), but waned to 67% (45–80) at 4–5 months. Vaccine effectiveness against hospital admissions for infections with the delta variant for all ages was high overall (93% [95% CI 84–96]) up to 6 months.
  • Waning of BNT162b2 Vaccine Protection against SARS-CoV-2 Infection in Qatar
    H Chemaitelly et al, NEJM, October 6, 2021
    Estimated BNT162b2 effectiveness against any SARS-CoV-2 infection was negligible in the first 2 weeks after the first dose. It increased to 36.8% (95% confidence interval [CI], 33.2 to 40.2) in the third week after the first dose and reached its peak at 77.5% (95% CI, 76.4 to 78.6) in the first month after the second dose. Effectiveness declined gradually thereafter, with the decline accelerating after the fourth month to reach approximately 20% in months 5 through 7 after the second dose. Effectiveness against symptomatic infection was higher than effectiveness against asymptomatic infection but waned similarly. Variant-specific effectiveness waned in the same pattern
  • Waning Immune Humoral Response to BNT162b2 Covid-19 Vaccine over 6 Months
    EG Levin et al, NEJM October 6, 2021
    The level of IgG antibodies decreased at a consistent rate, whereas the neutralizing antibody level decreased rapidly for the first 3 months with a relatively slow decrease thereafter.Six months after receipt of the second dose, neutralizing antibody titers were substantially lower among men than among women (ratio of means, 0.64; 95% confidence interval [CI], 0.55 to 0.75), lower among persons 65 years of age or older than among those 18 to less than 45 years of age (ratio of means, 0.58; 95% CI, 0.48 to 0.70), and lower among participants with immunosuppression than among those without immunosuppression (ratio of means, 0.30; 95% CI, 0.20 to 0.46).
  • Myocarditis after BNT162b2 mRNA Vaccine against Covid-19 in Israel
    D Mevorach et al, NEJM, October 6, 2021
    The overall risk difference between the first and second doses was 1.76 per 100,000 persons (95% confidence interval [CI], 1.33 to 2.19), with the largest difference among male recipients between the ages of 16 and 19 years (difference, 13.73 per 100,000 persons; 95% CI, 8.11 to 19.46). As compared with the expected incidence based on historical data, the standardized incidence ratio was 5.34 (95% CI, 4.48 to 6.40) and was highest after the second dose in male recipients between the ages of 16 and 19 years (13.60; 95% CI, 9.30 to 19.20).
  • Effectiveness of Covid-19 Vaccines in Ambulatory and Inpatient Care Settings
    MG Thomson et al, NEJM, October 7, 2021
    The effectiveness of full messenger RNA (mRNA) vaccination (=14 days after the second dose) was 89% (95% confidence interval [CI], 87 to 91) against laboratory-confirmed SARS-CoV-2 infection leading to hospitalization, 90% (95% CI, 86 to 93) against infection leading to an ICU admission, and 91% (95% CI, 89 to 93) against infection leading to an emergency department or urgent care clinic visit. The effectiveness of full vaccination with respect to a Covid-19–associated hospitalization or emergency department or urgent care clinic visit was similar with the BNT162b2 and mRNA-1273 vaccines.

Non-Genomics Precision Health Studies

  • The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission
    DW Eyre et al, MEDRXIV, September 29, 2021
    51,798/139,164(37.2%) contacts tested were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha variant index cases independently reduced PCR-positivity in contacts (aOR, adjusted odds ratio vs. unvaccinated=0.18[95%CI 0.12-0.29] and 0.37[0.22-0.63] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aOR=0.35[0.26-0.48]), more than ChAdOx1 (aOR=0.64[0.57-0.72].
  • Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study
    MI Paredes et al, MEDRXIV, September 30, 2021
    Of the 27,814 cases, 23,170 (83.3%) were sequenced through sentinel surveillance, of which 726 (3.1%) were hospitalized due to COVID–19. Higher hospitalization risk was found for infections with Gamma (HR 3.17, 95% CI 2.15–4.67), Beta (HR: 2.97, 95% CI 1.65–5.35), Delta (HR: 2.30, 95% CI 1.69–3.15), and Alpha (HR 1.59, 95% CI 1.26–1.99) compared to infections with an ancestral lineage. Following VOC infection, unvaccinated patients show a similar higher hospitalization risk, while vaccinated patients show no significant difference in risk, both when compared to unvaccinated, ancestral lineage cases.
  • Immune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors
    RT Shroff et al, Nature Medicine, September 30, 2021
    We initiated a phase 1 trial for 20 cancer cohort participants of a third vaccine dose of BNT162b2 ; primary outcomes were immune responses, with a secondary outcome of safety. At 1 week after a third immunization, 16 participants demonstrated a median threefold increase in neutralizing antibody responses, but no improvement was observed in T cell responses. Adverse events were mild. These results suggest that a third dose of BNT162b2 is safe, improves humoral immunity against SARS-CoV-2 and could be immunologically beneficial for patients with cancer on active chemotherapy.
  • The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA
    B Blaiszik et al, MEDRXIV, September 30, 2021
    We accessed openly available data sources from the public health authorities of seven U.S. states, five U.S. counties, and the District of Columbia on RT-PCR COVID-19 tests split by the COVID-19 vaccination status of individuals tested during this period. Together, these time series enable estimation and tracking of COVID-19 vaccine effectiveness (VE*) (against RT-PCR diagnosed infection) concurrently with the growth of Delta variant prevalence in those locations. Our analyses reveal that in each locality the VE* for the combined set of all three US vaccines remained relatively stable and quite well-performing, despite the dramatic concurrent rise of Delta variant prevalence.
  • Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants
    K Broxvoort et al, MEDRXIV, October 1, 2021
    We conducted a test-negative case-control study at Kaiser Permanente Southern California. The study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged =65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]).
  • Nosocomial outbreak caused by the SARS-CoV-2 Delta variant in a highly vaccinated population, Israel, July 2021 separator
    P Shitrit et al, Eurosurveillance, September 2021
    We present an investigation of a coronavirus disease (COVID-19) outbreak that started from one unidentified COVID-19 patient, with extensive, rapid nosocomial spread among vaccinated, including individuals wearing surgical masks.
  • The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.
    López Mariana G et al. Nature genetics 2021 10
    As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020
  • Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.
    Mutnal Manohar B et al. Journal of medical virology 2021 10
    We analyzed virus sequencing results of specimens collected across Central Texas and found dramatic changes in variant distribution in the first half of 2021. The alpha variant (B 1.1.7) became predominant at week 13 and continued dominance until week 25. A growth rate of 1.20 (R2 = 0.92) for the first 15 weeks was noted and this growth gradually declined to -0.55 (R2 = 0.99) for the final 13 weeks. Currently, B.1.1.7 is being displaced with B.1.617.2 at 0.58 growth rate (R2 = 0.97). We also investigated vaccine breakthrough cases (VBCs) within our healthcare system and present clinical data on 28 symptomatic patients.
  • Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality.
    Nakanishi Tomoko et al. The Journal of clinical investigation 2021 10
    We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (HR 1.4, 95%CI 1.2-1.7). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (OR 2.1, 95%CI 1.6-2.6), venous thromboembolism (OR 1.7, 95%CI 1.2-2.4), and hepatic injury (OR 1.5, 95%CI 1.2-2.0). Risk allele carriers =60 years had higher odds of death or severe respiratory failure (OR 2.7, 95%CI 1.8-3.9) compared to those >60 years (OR 1.5, 95%CI 1.2-1.8, interaction-p=0.038). Amongst individuals =60 years who died or experienced severe respiratory failure, 32.3% were risk variant carriers, compared to 13.9% of those not experiencing these outcomes.
  • Acute Myocarditis Following COVID-19 mRNA Vaccination in Adults Aged 18 Years or Older
    A Simone et al, JAMA Internal Medicine, October 4, 2021
    In this population-based cohort study of 2?392?924 individuals who received at least 1 dose of COVID-19 mRNA vaccines, acute myocarditis was rare, at an incidence of 5.8 cases per 1 million individuals after the second dose (1 case per 172?414 fully vaccinated individuals). The signal of increased myocarditis in young men warrants further investigation.
  • COVID vaccines cut the risk of transmitting Delta — but not for long
    S Mallapaty, Nature, October 5, 2021
    The study shows that people who become infected with the Delta variant are less likely to pass the virus to their close contacts if they have already had a COVID-19 vaccine than if they haven’t1. But that protective effect is relatively small, and dwindles alarmingly at three months after the receipt of the second shot.
  • Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study
    SY Tartoff et al, The Lancet, October 4, 2021
    Effectiveness against infections declined from 88% (95% CI 86–89) during the first month after full vaccination to 47% (43–51) after 5 months. Among sequenced infections, vaccine effectiveness against infections of the delta variant was high during the first month after full vaccination (93% [95% CI 85–97]) but declined to 53% [39–65] after 4 months. Effectiveness against other (non-delta) variants the first month after full vaccination was also high at 97% (95% CI 95–99), but waned to 67% (45–80) at 4–5 months. Vaccine effectiveness against hospital admissions for infections with the delta variant for all ages was high overall (93% [95% CI 84–96]) up to 6 months.
  • Waning of BNT162b2 Vaccine Protection against SARS-CoV-2 Infection in Qatar
    H Chemaitelly et al, NEJM, October 6, 2021
    Estimated BNT162b2 effectiveness against any SARS-CoV-2 infection was negligible in the first 2 weeks after the first dose. It increased to 36.8% (95% confidence interval [CI], 33.2 to 40.2) in the third week after the first dose and reached its peak at 77.5% (95% CI, 76.4 to 78.6) in the first month after the second dose. Effectiveness declined gradually thereafter, with the decline accelerating after the fourth month to reach approximately 20% in months 5 through 7 after the second dose. Effectiveness against symptomatic infection was higher than effectiveness against asymptomatic infection but waned similarly. Variant-specific effectiveness waned in the same pattern
  • Waning Immune Humoral Response to BNT162b2 Covid-19 Vaccine over 6 Months
    EG Levin et al, NEJM October 6, 2021
    The level of IgG antibodies decreased at a consistent rate, whereas the neutralizing antibody level decreased rapidly for the first 3 months with a relatively slow decrease thereafter.Six months after receipt of the second dose, neutralizing antibody titers were substantially lower among men than among women (ratio of means, 0.64; 95% confidence interval [CI], 0.55 to 0.75), lower among persons 65 years of age or older than among those 18 to less than 45 years of age (ratio of means, 0.58; 95% CI, 0.48 to 0.70), and lower among participants with immunosuppression than among those without immunosuppression (ratio of means, 0.30; 95% CI, 0.20 to 0.46).
  • Myocarditis after BNT162b2 mRNA Vaccine against Covid-19 in Israel
    D Mevorach et al, NEJM, October 6, 2021
    The overall risk difference between the first and second doses was 1.76 per 100,000 persons (95% confidence interval [CI], 1.33 to 2.19), with the largest difference among male recipients between the ages of 16 and 19 years (difference, 13.73 per 100,000 persons; 95% CI, 8.11 to 19.46). As compared with the expected incidence based on historical data, the standardized incidence ratio was 5.34 (95% CI, 4.48 to 6.40) and was highest after the second dose in male recipients between the ages of 16 and 19 years (13.60; 95% CI, 9.30 to 19.20).
  • Effectiveness of Covid-19 Vaccines in Ambulatory and Inpatient Care Settings
    MG Thomson et al, NEJM, October 7, 2021
    The effectiveness of full messenger RNA (mRNA) vaccination (=14 days after the second dose) was 89% (95% confidence interval [CI], 87 to 91) against laboratory-confirmed SARS-CoV-2 infection leading to hospitalization, 90% (95% CI, 86 to 93) against infection leading to an ICU admission, and 91% (95% CI, 89 to 93) against infection leading to an emergency department or urgent care clinic visit. The effectiveness of full vaccination with respect to a Covid-19–associated hospitalization or emergency department or urgent care clinic visit was similar with the BNT162b2 and mRNA-1273 vaccines.

News, Reviews and Commentaries

  • The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission
    DW Eyre et al, MEDRXIV, September 29, 2021
    51,798/139,164(37.2%) contacts tested were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha variant index cases independently reduced PCR-positivity in contacts (aOR, adjusted odds ratio vs. unvaccinated=0.18[95%CI 0.12-0.29] and 0.37[0.22-0.63] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aOR=0.35[0.26-0.48]), more than ChAdOx1 (aOR=0.64[0.57-0.72].
  • Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study
    MI Paredes et al, MEDRXIV, September 30, 2021
    Of the 27,814 cases, 23,170 (83.3%) were sequenced through sentinel surveillance, of which 726 (3.1%) were hospitalized due to COVID–19. Higher hospitalization risk was found for infections with Gamma (HR 3.17, 95% CI 2.15–4.67), Beta (HR: 2.97, 95% CI 1.65–5.35), Delta (HR: 2.30, 95% CI 1.69–3.15), and Alpha (HR 1.59, 95% CI 1.26–1.99) compared to infections with an ancestral lineage. Following VOC infection, unvaccinated patients show a similar higher hospitalization risk, while vaccinated patients show no significant difference in risk, both when compared to unvaccinated, ancestral lineage cases.
  • Immune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors
    RT Shroff et al, Nature Medicine, September 30, 2021
    We initiated a phase 1 trial for 20 cancer cohort participants of a third vaccine dose of BNT162b2 ; primary outcomes were immune responses, with a secondary outcome of safety. At 1 week after a third immunization, 16 participants demonstrated a median threefold increase in neutralizing antibody responses, but no improvement was observed in T cell responses. Adverse events were mild. These results suggest that a third dose of BNT162b2 is safe, improves humoral immunity against SARS-CoV-2 and could be immunologically beneficial for patients with cancer on active chemotherapy.
  • The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA
    B Blaiszik et al, MEDRXIV, September 30, 2021
    We accessed openly available data sources from the public health authorities of seven U.S. states, five U.S. counties, and the District of Columbia on RT-PCR COVID-19 tests split by the COVID-19 vaccination status of individuals tested during this period. Together, these time series enable estimation and tracking of COVID-19 vaccine effectiveness (VE*) (against RT-PCR diagnosed infection) concurrently with the growth of Delta variant prevalence in those locations. Our analyses reveal that in each locality the VE* for the combined set of all three US vaccines remained relatively stable and quite well-performing, despite the dramatic concurrent rise of Delta variant prevalence.
  • Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants
    K Broxvoort et al, MEDRXIV, October 1, 2021
    We conducted a test-negative case-control study at Kaiser Permanente Southern California. The study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged =65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]).
  • Nosocomial outbreak caused by the SARS-CoV-2 Delta variant in a highly vaccinated population, Israel, July 2021 separator
    P Shitrit et al, Eurosurveillance, September 2021
    We present an investigation of a coronavirus disease (COVID-19) outbreak that started from one unidentified COVID-19 patient, with extensive, rapid nosocomial spread among vaccinated, including individuals wearing surgical masks.
  • The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.
    López Mariana G et al. Nature genetics 2021 10
    As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020
  • Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.
    Mutnal Manohar B et al. Journal of medical virology 2021 10
    We analyzed virus sequencing results of specimens collected across Central Texas and found dramatic changes in variant distribution in the first half of 2021. The alpha variant (B 1.1.7) became predominant at week 13 and continued dominance until week 25. A growth rate of 1.20 (R2 = 0.92) for the first 15 weeks was noted and this growth gradually declined to -0.55 (R2 = 0.99) for the final 13 weeks. Currently, B.1.1.7 is being displaced with B.1.617.2 at 0.58 growth rate (R2 = 0.97). We also investigated vaccine breakthrough cases (VBCs) within our healthcare system and present clinical data on 28 symptomatic patients.
  • Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality.
    Nakanishi Tomoko et al. The Journal of clinical investigation 2021 10
    We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (HR 1.4, 95%CI 1.2-1.7). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (OR 2.1, 95%CI 1.6-2.6), venous thromboembolism (OR 1.7, 95%CI 1.2-2.4), and hepatic injury (OR 1.5, 95%CI 1.2-2.0). Risk allele carriers =60 years had higher odds of death or severe respiratory failure (OR 2.7, 95%CI 1.8-3.9) compared to those >60 years (OR 1.5, 95%CI 1.2-1.8, interaction-p=0.038). Amongst individuals =60 years who died or experienced severe respiratory failure, 32.3% were risk variant carriers, compared to 13.9% of those not experiencing these outcomes.
  • Acute Myocarditis Following COVID-19 mRNA Vaccination in Adults Aged 18 Years or Older
    A Simone et al, JAMA Internal Medicine, October 4, 2021
    In this population-based cohort study of 2?392?924 individuals who received at least 1 dose of COVID-19 mRNA vaccines, acute myocarditis was rare, at an incidence of 5.8 cases per 1 million individuals after the second dose (1 case per 172?414 fully vaccinated individuals). The signal of increased myocarditis in young men warrants further investigation.
  • COVID vaccines cut the risk of transmitting Delta — but not for long
    S Mallapaty, Nature, October 5, 2021
    The study shows that people who become infected with the Delta variant are less likely to pass the virus to their close contacts if they have already had a COVID-19 vaccine than if they haven’t1. But that protective effect is relatively small, and dwindles alarmingly at three months after the receipt of the second shot.
  • Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study
    SY Tartoff et al, The Lancet, October 4, 2021
    Effectiveness against infections declined from 88% (95% CI 86–89) during the first month after full vaccination to 47% (43–51) after 5 months. Among sequenced infections, vaccine effectiveness against infections of the delta variant was high during the first month after full vaccination (93% [95% CI 85–97]) but declined to 53% [39–65] after 4 months. Effectiveness against other (non-delta) variants the first month after full vaccination was also high at 97% (95% CI 95–99), but waned to 67% (45–80) at 4–5 months. Vaccine effectiveness against hospital admissions for infections with the delta variant for all ages was high overall (93% [95% CI 84–96]) up to 6 months.
  • Waning of BNT162b2 Vaccine Protection against SARS-CoV-2 Infection in Qatar
    H Chemaitelly et al, NEJM, October 6, 2021
    Estimated BNT162b2 effectiveness against any SARS-CoV-2 infection was negligible in the first 2 weeks after the first dose. It increased to 36.8% (95% confidence interval [CI], 33.2 to 40.2) in the third week after the first dose and reached its peak at 77.5% (95% CI, 76.4 to 78.6) in the first month after the second dose. Effectiveness declined gradually thereafter, with the decline accelerating after the fourth month to reach approximately 20% in months 5 through 7 after the second dose. Effectiveness against symptomatic infection was higher than effectiveness against asymptomatic infection but waned similarly. Variant-specific effectiveness waned in the same pattern
  • Waning Immune Humoral Response to BNT162b2 Covid-19 Vaccine over 6 Months
    EG Levin et al, NEJM October 6, 2021
    The level of IgG antibodies decreased at a consistent rate, whereas the neutralizing antibody level decreased rapidly for the first 3 months with a relatively slow decrease thereafter.Six months after receipt of the second dose, neutralizing antibody titers were substantially lower among men than among women (ratio of means, 0.64; 95% confidence interval [CI], 0.55 to 0.75), lower among persons 65 years of age or older than among those 18 to less than 45 years of age (ratio of means, 0.58; 95% CI, 0.48 to 0.70), and lower among participants with immunosuppression than among those without immunosuppression (ratio of means, 0.30; 95% CI, 0.20 to 0.46).
  • Myocarditis after BNT162b2 mRNA Vaccine against Covid-19 in Israel
    D Mevorach et al, NEJM, October 6, 2021
    The overall risk difference between the first and second doses was 1.76 per 100,000 persons (95% confidence interval [CI], 1.33 to 2.19), with the largest difference among male recipients between the ages of 16 and 19 years (difference, 13.73 per 100,000 persons; 95% CI, 8.11 to 19.46). As compared with the expected incidence based on historical data, the standardized incidence ratio was 5.34 (95% CI, 4.48 to 6.40) and was highest after the second dose in male recipients between the ages of 16 and 19 years (13.60; 95% CI, 9.30 to 19.20).
  • Effectiveness of Covid-19 Vaccines in Ambulatory and Inpatient Care Settings
    MG Thomson et al, NEJM, October 7, 2021
    The effectiveness of full messenger RNA (mRNA) vaccination (=14 days after the second dose) was 89% (95% confidence interval [CI], 87 to 91) against laboratory-confirmed SARS-CoV-2 infection leading to hospitalization, 90% (95% CI, 86 to 93) against infection leading to an ICU admission, and 91% (95% CI, 89 to 93) against infection leading to an emergency department or urgent care clinic visit. The effectiveness of full vaccination with respect to a Covid-19–associated hospitalization or emergency department or urgent care clinic visit was similar with the BNT162b2 and mRNA-1273 vaccines.
Disclaimer: Articles listed in COVID-19 Genomics and Precision Public Health Weekly Update are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
TOP