Secondary Attack Rate, Transmission and Incubation Periods, and Serial Interval of SARS-CoV-2 Omicron Variant, Spain

Del-Águila-Mejía, Javier; Wallmann, Reinhard; Calvo-Montes, Jorge; Rodrı́guez-Lozano, Jesús; Valle-Madrazo, Trinidad; Llorente, Adrián Hugo Aginagalde

doi:10.3201/eid2806.220158

Cited by 76 publications

(64 citation statements)

References 6 publications

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“…The HSAR of COVID-19 was 31.8% (95% CI 27.7-36.2) during the omicron variantdominant period in Itako, Japan. The HSAR for the omicron variant was 25% in Norway [8], 49% in Spain [9], 53% in the USA [10], and 65% in Korea [11]. The HSAR in the present study was in the range of those reported previously.…”

Section: Discussionsupporting

confidence: 73%

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Increased Secondary Attack Rates among the Household Contacts of Patients with the Omicron Variant of the Coronavirus Disease 2019 in Japan

Ogata

Tanaka²,

Tanaka

et al. 2022

IJERPH

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This study investigated the household secondary attack rate (HSAR) of patients with coronavirus disease (COVID-19) during the omicron variant-dominant period. The HSAR of COVID-19 cases during the omicron variant-dominant period (4–20 January 2022) was calculated and compared with the delta variant-dominant period (20 August to 7 November 2021) in Itako, Japan. In Itako, all 47 and 119 samples tested during the omicron and delta variant-dominant periods were negative and positive, respectively, for the L452R mutation. We used a generalized estimating equation regression model. The HSAR was 31.8% (95% confidence interval (CI) 27.7–36.2) for 456 household contacts during the omicron variant-dominant period; it was higher than that during the delta variant-dominant period (25.2%) (adjusted risk ratio [aRR] 1.61, CI 1.13–2.28). During the omicron variant-dominant period, HSAR was lower for the household contacts of completely vaccinated index patients (27.3%) than for contacts of other index patients (41.2%) (vaccine effectiveness for infectee 0.43, 95% CI 0.16–0.62) and was significantly higher for female contacts than for male contacts (36.2% vs. 26.1%; aRR 1.29, 95% CI 1.01–1.65). The HSAR was significantly higher during the omicron variant-dominant period than the delta variant-dominant period. The vaccination of index patients might protect household contacts.

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Section: Discussionsupporting

confidence: 73%

“…Studying the transmissibility of the Omicron variant and comparing it with that of the Delta variant is useful. However, few studies have reported the HSAR of the omicron SARS-CoV-2 variant [8][9][10][11][12]. The effective reproduction number of omicron is greater than that of delta in several countries [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Increased Secondary Attack Rates among the Household Contacts of Patients with the Omicron Variant of the Coronavirus Disease 2019 in Japan

Ogata

Tanaka²,

Tanaka

et al. 2022

IJERPH

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“…Of these, 541 studies underwent full-text review. Eight studies [ 19 , 21 , 32 , 33 , 34 , 41 , 42 , 43 ] with information concerning the percentage of asymptomatic infections among SARS-CoV-2 Omicron variant-positive individuals were included in the final analysis ( Figure 1 ). The characteristics of the studies included in this systematic review and meta-analysis are shown in Table 1 .…”

Section: Resultsmentioning

confidence: 99%

“… The Percentage of Asymptomatic Infections Among SARS-CoV-2 Omicron Variant-Positive Individuals [ 19 , 21 , 32 , 33 , 34 , 41 , 42 , 43 ]. …”

Section: Figurementioning

confidence: 99%

Percentage of Asymptomatic Infections among SARS-CoV-2 Omicron Variant-Positive Individuals: A Systematic Review and Meta-Analysis

et al. 2022

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Background: Asymptomatic infections are potential sources of transmission for coronavirus disease 2019, especially during the epidemic of the SARS-CoV-2 Omicron variant. We aimed to assess the percentage of asymptomatic infections among SARS-CoV-2 Omicron variant-positive individuals detected by gene sequencing or specific polymerase chain reaction (PCR). Methods: We searched PubMed, EMBASE, and Web of Science from 26 November 2021 to 13 April 2022. This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and was registered with PROSPERO (CRD42022327894). Three researchers independently extracted data and two researchers assessed quality using pre-specified criteria. The pooled percentage with 95% confidence interval (CI) of asymptomatic infections of SARS-CoV-2 Omicron was estimated using random-effects models. Results: Our meta-analysis included eight eligible studies, covering 7640 Omicron variant-positive individuals with 2190 asymptomatic infections. The pooled percentage of asymptomatic infections was 32.40% (95% CI: 25.30–39.51%) among SARS-CoV-2 Omicron variant-positive individuals, which was higher in the population in developing countries (38.93%; 95% CI: 19.75–58.11%), with vaccine coverage ≥ 80% (35.93%; 95% CI: 25.36–46.51%), with a travel history (40.05%; 95% CI: 7.59–72.51%), community infection (37.97%; 95% CI: 10.07–65.87%), and with a median age < 20 years (43.75%; 95% CI: 38.45–49.05%). Conclusion: In this systematic review and meta-analysis, the pooled percentage of asymptomatic infections was 32.40% among SARS-CoV-2 Omicron variant-positive individuals. The people who were vaccinated, young (median age < 20 years), had a travel history, and were infected outside of a clinical setting (community infection) had higher percentages of asymptomatic infections. Screening is required to prevent clustered epidemics or sustained community transmission caused by asymptomatic infections of Omicron variants, especially for countries and regions that have successfully controlled SARS-CoV-2.

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“…Spain has been one of the European countries with the highest number of COVID-19 cases, according to the European Centre for Disease Prevention and Control (ECDC, (accessed on 22 January 2022)). Previous studies have analyzed the epidemiology of SARS-CoV-2 in Spain [ 5 , 112 ], certain Spanish cities or AC [ 113 , 114 , 115 , 116 , 117 , 118 ], and variants [ 119 , 120 ]. However, as far as we know, this is the first study including all SARS-CoV-2 GISAID available sequences from the 17 AC and 2 Autonomous Cities since the beginning of the pandemic until the sixth epidemiologic wave, including the most prevalent mutations.…”

Section: Discussionmentioning

confidence: 99%

Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins

Troyano-Hernáez

Reinosa

Holguín

2022

IJMS

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Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.

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Secondary Attack Rate, Transmission and Incubation Periods, and Serial Interval of SARS-CoV-2 Omicron Variant, Spain

Cited by 76 publications

References 6 publications

Increased Secondary Attack Rates among the Household Contacts of Patients with the Omicron Variant of the Coronavirus Disease 2019 in Japan

Increased Secondary Attack Rates among the Household Contacts of Patients with the Omicron Variant of the Coronavirus Disease 2019 in Japan

Percentage of Asymptomatic Infections among SARS-CoV-2 Omicron Variant-Positive Individuals: A Systematic Review and Meta-Analysis

Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins

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