Increased household secondary attacks rates with Variant of Concern SARS-CoV-2 index cases.
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ABSTRACT:
SUBMITTER: Buchan SA
PROVIDER: S-EPMC8384411 | biostudies-literature | 2021 Jun
REPOSITORIES: biostudies-literature
Publications
Increased Household Secondary Attacks Rates With Variant of Concern Severe Acute Respiratory Syndrome Coronavirus 2 Index Cases.
Buchan Sarah A SA Tibebu Semra S Daneman Nick N Whelan Michael M Vanniyasingam Thuva T Murti Michelle M Brown Kevin A KA
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20220301 4
We compared secondary attack rates in households with B.1.1.7 variant of concern (VOC) versus non-VOC index cases in a matched cohort in Ontario, Canada. The secondary attack rate for VOC index cases was 1.31 times higher than non-VOC index cases. This increase was particularly accentuated for asymptomatic or presymptomatic index cases. ...[more]
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Project description:BackgroundThe emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 variant in England in 2020 and subsequent global spread emphasized the need to understand epidemiologic characteristics of SARS-CoV-2 variants. A diagnostic proxy for this variant, referred to as S-gene target failure, provided a rich dataset to assess transmissibility of the variant in an analysis of clustering in residential settings.MethodsWe used a pair-matched case-control study design to estimate odds of onward transmission within households with S-gene target failure index cases versus nontarget failure index cases. We defined cases as the index in a household cluster (clustered case) and controls as a case with no subsequent household cluster (sporadic). We matched clustered and sporadic cases one-to-one on specimen week, geography, and property type. We used conditional logistic regression, adjusting for age, sex, ethnicity, and symptom status, to assess odds of residential clustering.ResultsOur study population comprised 57,244 individuals with specimen dates from 23 November 2020 to 4 January 2021. Crude analysis yielded 54% increased odds (odds ratio [OR] = 1.5; 95% confidence interval [CI] = 1.5, 1.6) of residential clustering associated with S-gene target failure; the association remained in the fully adjusted model (OR = 1.6, 95% CI = 1.5, 1.6). Stratified analyses by region showed increased odds of residential clustering associated with target failure in all regions apart from the Southwest, where we observed lower precision. Similar adjusted odds ratios with precise confidence intervals remained in stratified analyses by property category.ConclusionWe observed increased odds in all property types, consistent with greater transmissibility of the B.1.1.7 variant in this high-risk setting.
| S-EPMC9148639 | biostudies-literature
Project description:ImportanceAn overall household secondary attack rate (SAR) of 18.9% (95% CI, 16.2%-22.0%) through June 17, 2021 was previously reported for SARS-CoV-2. Emerging variants of concern and increased vaccination have affected transmission rates.ObjectiveTo evaluate how reported household SARs changed over time and whether SARs varied by viral variant and index case and contact vaccination status.Data sourcesPubMed and medRxiv from June 18, 2021, through March 8, 2022, and reference lists of eligible articles. Preprints were included.Study selectionArticles with original data reporting the number of infected and total number of household contacts. Search terms included SARS-CoV-2, COVID-19, variant, vaccination, secondary attack rate, secondary infection rate, household, index case, family contacts, close contacts, and family transmission.Data extraction and synthesisThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guideline was followed. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95% CIs.Main outcomes and measuresSAR stratified by covariates according to variant, index case and contact vaccination status, and index case identification period. SARs were used to estimate vaccine effectiveness on the basis of the transmission probability for susceptibility to infection (VES,p), infectiousness given infection (VEI,p), and total vaccine effectiveness (VET,p).ResultsHousehold SARs were higher for 33 studies with midpoints in 2021 to 2022 (37.3%; 95% CI, 32.7% to 42.1%) compared with 63 studies with midpoints through April 2020 (15.5%; 95% CI, 13.2% to 18.2%). Household SARs were 42.7% (95% CI, 35.4% to 50.4%) for Omicron (7 studies), 36.4% (95% CI, 33.4% to 39.5%) for Alpha (11 studies), 29.7% (95% CI, 23.0% to 37.3%) for Delta (16 studies), and 22.5% (95% CI, 18.6% to 26.8%) for Beta (3 studies). For full vaccination, VES,p was 78.6% (95% CI, 76.0% to 80.9%) for Alpha, 56.4% (95% CI, 54.6% to 58.1%) for Delta, and 18.1% (95% CI, -18.3% to 43.3%) for Omicron; VEI,p was 75.3% (95% CI, 69.9% to 79.8%) for Alpha, 21.9% (95% CI, 11.0% to 31.5%) for Delta, and 18.2% (95% CI, 0.6% to 32.6%) for Omicron; and VET,p was 94.7% (95% CI, 93.3% to 95.8%) for Alpha, 64.4% (95% CI, 58.0% to 69.8%) for Delta, and 35.8% (95% CI, 13.0% to 52.6%) for Omicron.Conclusions and relevanceThese results suggest that emerging SARS-CoV-2 variants of concern have increased transmissibility. Full vaccination was associated with reductions in susceptibility and infectiousness, but more so for Alpha than Delta and Omicron. The changes in estimated vaccine effectiveness underscore the challenges of developing effective vaccines concomitant with viral evolution.
| S-EPMC9051991 | biostudies-literature
Project description:We performed a prospective, cross-sectional study of household contacts of symptomatic index case-patients with SARS-CoV-2 infection during the shift from Delta- to Omicron-dominant variants in Spain. We included 466 household contacts from 227 index cases. The secondary attack rate was 58.2% (95% CI 49.1%-62.6%) during the Delta-dominant period and 80.9% (95% CI 75.0%-86.9%) during the Omicron-dominant period. During the Delta-dominant period, unvaccinated contacts had higher probability of infection than vaccinated contacts (odds ratio 5.42, 95% CI 1.6-18.6), but this effect disappeared at ≈20 weeks after vaccination. Contacts showed a higher relative risk of infection (9.16, 95% CI 3.4-25.0) in the Omicron-dominant than Delta-dominant period when vaccinated within the previous 20 weeks. Our data suggest vaccine evasion might be a cause of rapid spread of the Omicron variant. We recommend a focus on developing vaccines with long-lasting protection against severe disease, rather than only against infectivity.
| S-EPMC9514368 | biostudies-literature
Project description:We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility ( VE S,p ), infectiousness ( VE I,p ), and total vaccine effectiveness ( VE T,p ). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VE I,p , VE S,p , and VE T,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others.SummaryHousehold secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.
| S-EPMC8764734 | biostudies-literature
Project description:Effective vaccines protect individuals by not only reducing the susceptibility to infection, but also reducing the infectiousness of breakthrough infections in vaccinated cases. To disentangle the vaccine effectiveness against susceptibility to infection (VES) and vaccine effectiveness against infectiousness (VEI), we took advantage of Danish national data comprising 24,693 households with a primary case of SARS-CoV-2 infection (Delta Variant of Concern, 2021) including 53,584 household contacts. In this setting, we estimated VES as 61% (95%-CI: 59-63), when the primary case was unvaccinated, and VEI as 31% (95%-CI: 26-36), when the household contact was unvaccinated. Furthermore, unvaccinated secondary cases with an infection exhibited a three-fold higher viral load compared to fully vaccinated secondary cases with a breakthrough infection. Our results demonstrate that vaccinations reduce susceptibility to infection as well as infectiousness, which should be considered by policy makers when seeking to understand the public health impact of vaccination against transmission of SARS-CoV-2.
| S-EPMC9244879 | biostudies-literature
Project description:Identification of blood transcriptional biomarkers linked to different phases of tuberculosis. The discovery of a transcriptional signature that distinguishes subclinical TB from incipient TB at baseline could lead to tuberculosis interventions that combat the tuberculosis epidemic in the context of household contacts.
2023-01-10 | GSE193777 | GEO
Project description:BackgroundSpread of variants of concerns (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an increase in children with coronavirus disease 2019 (COVID-19). In February 2021, clusters of the Alpha variant of SARS-CoV-2 started to be reported in Niigata, Japan, including a large nursery cluster. We investigated the transmission routes and household secondary attack rates (SARs) in this cluster.MethodsEpidemiologic data related to a nursery cluster in Niigata, Japan, particularly child-origin and adult-origin SARs, were analyzed. VOCs were confirmed by whole-genome sequencing of virus from patients.ResultsIn total, 42 persons (22 children and 20 adults) in the cluster were infected with the Alpha variant. In the nursery, 13 of 81 children (16.0%) and 4 of 24 teachers (16.7%) were infected. SARS-CoV-2 later spread to 25 persons (10 children and 15 adults) outside the nursery. Child-origin and adult-origin household SARs were 27.7% (13/47) and 47.0% (8/17) ( P = 0.11), respectively, which were higher than rates attributable to non-VOCs in previous studies.ConclusionsAs compared with non-VOCs, the Alpha variant of SARS-CoV-2 exhibited high transmissibility among children and adults and may pose a high risk for household secondary transmission from SARS-CoV-2-infected children. Increased transmissibility of current or future VOCs could lead to greater transmission from children to adults or other children.
| S-EPMC9359683 | biostudies-literature
Project description:ObjectiveWe compared the rates of hospital-onset secondary bacterial infections in patients with coronavirus disease 2019 (COVID-19) with rates in patients with influenza and controls, and we investigated reports of increased incidence of Enterococcus infections in patients with COVID-19.DesignRetrospective cohort study.SettingAn academic quaternary-care hospital in San Francisco, California.PatientsPatients admitted between October 1, 2019, and October 1, 2020, with a positive SARS-CoV-2 PCR (N = 314) or influenza PCR (N = 82) within 2 weeks of admission were compared with inpatients without positive SARS-CoV-2 or influenza tests during the study period (N = 14,332).MethodsNational Healthcare Safety Network definitions were used to identify infection-related ventilator-associated complications (IVACs), probable ventilator-associated pneumonia (PVAP), bloodstream infections (BSIs), and catheter-associated urinary tract infections (CAUTIs). A multiple logistic regression model was used to control for likely confounders.ResultsCOVID-19 patients had significantly higher rates of IVAC and PVAP compared to controls, with adjusted odds ratios of 4.7 (95% confidence interval [CI], 1.7-13.9) and 10.4 (95 % CI, 2.1-52.1), respectively. COVID-19 patients had higher incidence of BSI due to Enterococcus but not BSI generally, and whole-genome sequencing of Enterococcus isolates demonstrated that nosocomial transmission did not explain the increased rate. Subanalyses of patients admitted to the intensive care unit and patients who required mechanical ventilation revealed similar findings.ConclusionsCOVID-19 is associated with an increased risk of IVAC, PVAP, and Enterococcus BSI compared with hospitalized controls, which is not fully explained by factors such as immunosuppressive treatments and duration of mechanical ventilation. The mechanism underlying increased rates of Enterococcus BSI in COVID-19 patients requires further investigation.
| S-EPMC8458844 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that belongs to the family Coronaviridae. This virus produces a respiratory illness known as coronavirus disease 2019 (COVID-19) and is to blame for the pandemic of COVID-19. Due to its massive circulation around the world and the capacity of mutation of this virus, genomic studies are much needed in to order to reveal new variants of concern (VOCs). On November 26th, 2021, the WHO announced that a new SARS-CoV-2 VOC, named Omicron, had emerged. In order to get insight into the emergence, spread and evolution of Omicron SARS-CoV-2 variants, a comprehensive phylogenetic study was performed. The results of these studies revealed significant differences in codon usage among the S genes of SARS-CoV-2 VOCs Alfa, Beta, Gamma, Delta and Omicron, which can be linked to SARS-CoV-2 genotypes. Omicron variant did not evolve out of one of the early VOCs, but instead it belongs to a complete different genetic lineage from previous ones. Strains classified as Omicron variants evolved from ancestors that existed around May 15th, 2020, suggesting that this VOC may have been circulating undetected for a period of time until its emergence was observed in South Africa. A rate of evolution of 5.61 × 10-4 substitutions/site/year was found for Omicron strains enrolled in these analyses. The results of these studies demonstrate that S genes have suitable genetic information for clear assignment of emerging VOCs to its specific genotypes.
| S-EPMC8937608 | biostudies-literature
Project description:BackgroundIn South Africa, 19% of adults are living with human immunodeficiency virus (HIV; LWH). Few data on the influence of HIV on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission are available.MethodsWe performed a case-ascertained, prospective household transmission study of symptomatic adult index SARS-CoV-2 cases LWH and not living with HIV (NLWH) and their contacts from October 2020 to September 2021. Households were followed up 3 times a week for 6 weeks to collect nasal swabs for SARS-CoV-2 testing. We estimated household cumulative infection risk (HCIR) and duration of SARS-CoV-2 positivity (at a cycle threshold value <30 as proxy for high viral load).ResultsHCIR was 59% (220 of 373), not differing by index HIV status (60% LWH vs 58% NLWH). HCIR increased with index case age (35-59 years: adjusted OR [aOR], 3.4; 95% CI, 1.5-7.8 and ≥60 years: aOR, 3.1; 95% CI, 1.0-10.1) compared with 18-34 years and with contacts' age, 13-17 years (aOR, 7.1; 95% CI, 1.5-33.9) and 18-34 years (aOR, 4.4; 95% CI, 1.0-18.4) compared with <5 years. Mean positivity was longer in cases LWH (adjusted hazard ratio, 0.4; 95% CI, .1-.9).ConclusionsIndex HIV status was not associated with higher HCIR, but cases LWH had longer positivity duration. Adults aged >35 years were more likely to transmit and individuals aged 13-34 to be infected SARS-CoV-2 in the household. As HIV infection may increase transmission, health services must maintain HIV testing and antiretroviral therapy initiation.
| S-EPMC9384657 | biostudies-literature