Epidemiology of SARS-CoV-2 Omicron BA.5 Infections, Macau, June–July 2022

Xiong, Weijia; Peng, Liping; Tsang, Tim K.; Cowling, Benjamin J.

doi:10.3201/eid2902.221243

Cited by 9 publications

(12 citation statements)

References 6 publications

(6 reference statements)

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“…Quality assessment (Additional file 1 : Table S4 [ 9 , 10 , 12 , 13 , 21 , 22 , 26 – 32 , 34 , 37 – 40 , 42 – 60 , 62 – 65 , 67 – 71 , 73 , 74 , 76 , 78 – 86 , 89 , 90 , 92 – 94 , 97 – 99 , 101 – 107 , 109 – 115 , 117 – 121 , 123 – 128 , 130 , 131 , 133 , 136 – 139 , 141 – 153 , 155 – 161 , 164 – 166 ]) indicated that 1 study provided a precise exposure window for cases and identification of the potential infector(s). Sixty-eight studies included a well-characterized cohort of individuals that were comparable with the population and provided precise estimates for the symptom onset window for themselves and their potential infector(s).…”

Section: Resultsmentioning

confidence: 99%

Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis

Xu,

Wu,

Kummer

et al. 2023

BMC Med

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Background After the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern. Methods We conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2. Results Our study included 280 records obtained from 147 household studies, contact tracing studies, or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods, although we did not find statistically significant differences between the Omicron subvariants. We found that Omicron BA.1 had the shortest pooled estimates for the incubation period (3.49 days, 95% CI: 3.13–4.86 days), Omicron BA.5 for the serial interval (2.37 days, 95% CI: 1.71–3.04 days), and Omicron BA.1 for the realized generation time (2.99 days, 95% CI: 2.48–3.49 days). Only one estimate for the intrinsic generation time was available for Omicron subvariants: 6.84 days (95% CrI: 5.72–8.60 days) for Omicron BA.1. The ancestral lineage had the highest pooled estimates for each investigated key time-to-event period. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. When pooling the estimates across different virus lineages, we found considerable heterogeneities (I2 > 80%; I2 refers to the percentage of total variation across studies that is due to heterogeneity rather than chance), possibly resulting from heterogeneities between the different study populations (e.g., deployed interventions, social behavior, demographic characteristics). Conclusions Our study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.

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Section: Resultsmentioning

confidence: 99%

Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis

Xu,

Wu,

Kummer

et al. 2023

BMC Med

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“…For this study specifically, we chose individuals within each of the groups who had an HAI titer of <10 against the A/Hawaii/70/2019 (H1N1) vaccine strain prior to vaccination in year 1 (2020-2021); this criterion means that the study focuses on individuals with relatively low initial titers. None of the participants were infected with influenza during the study time frame because there was minimal influenza circulation at the study site in Hong Kong between the initial 2020-2021 blood draw and the 2021-2022 blood draws due to COVID-19 mitigation measures (27,28). We analyzed sera collected immediately before (day 0) and approximately 30 days after the participants were given the 2021-2022 vaccine (Fig.…”

Section: Resultsmentioning

confidence: 99%

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

Loes,

Tarabi,

Huddleston

et al. 2024

Preprint

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The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year--although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.

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“…Meanwhile, the parameter values of the SEIHR model were set by steps. Firstly, the awareness delay was assumed to be 2 days for Fuzhou COVID-19 large wave, because Omicron BA.5.2 variant was a highly infectious variant as studied in ( Duan & Jin, 2022 ; Huang et al., 2020 ; Huo et al., 2023 ; Nguyen et al., 2021 ; Xiong et al., 2023 ; Fuzhou Statistics Bureau, 2020 ). Then, the average lengths of hospitalization 1/ γ 2 k were calculated using the surveillance data from Fujian CDC.…”

Section: Methodsmentioning

confidence: 99%

An SEIHR model with age group and social contact for analysis of Fuzhou COVID-19 large wave

Lan,

Chen,

Zhou

et al. 2024

Infectious Disease Modelling

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Epidemiology of SARS-CoV-2 Omicron BA.5 Infections, Macau, June–July 2022

Cited by 9 publications

References 6 publications

Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis

Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

An SEIHR model with age group and social contact for analysis of Fuzhou COVID-19 large wave

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