Dataset Information

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam.

ABSTRACT:

Objectives

We investigated the genetic variations in the Alpha, Delta, and Omicron variants of SARS-CoV-2 and their association with clinical status and treatment outcomes in patients with COVID-19.

Methods

MiSeq was used to sequence the Alpha, Delta, and Omicron genomes, and MEGA 6.6 was used to define the nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants.

Results

The BA.1.1 and BA.2 lineages of the Omicron variant had 57-59 mutations, which is 2-2.7-fold higher than that of the B.1.1.7 (Alpha), B.1.617.2, and AY.57 (Delta) lineages. We found distinct mutations in SARS-CoV-2: five in Alpha (C26305T, G26558T, G7042T, C14120T, and C27509T); seven in Delta (C26408T, C1403T, C5184T, C9891T, T11418C, C11514T, and C22227T); and three in Omicron (C26408T, C8991T, and C25810T). Patients with the Delta variant had a severe rate of 23.8%, a critical rate of 53.7%, and a mortality rate of 38.9%, which were significantly higher than those with the Omicron and Alpha variants.

Conclusions

The Alpha, Delta, and Omicron variants in this study had genetic diversity and differed from the strains reported in other countries, with the Delta variant producing significantly more clinical severity and mortality than the Alpha and Omicron variants.

SUBMITTER: Van Nam L

PROVIDER: S-EPMC11004080 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature

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Publications

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam.

Van Nam Le L Dien Trinh Cong TC Bang Le Van Nguyen LVN Thach Pham Ngoc PN Van Duyet Le L

IJID regions 20240313

<h4>Objectives</h4>We investigated the genetic variations in the Alpha, Delta, and Omicron variants of SARS-CoV-2 and their association with clinical status and treatment outcomes in patients with COVID-19.<h4>Methods</h4>MiSeq was used to sequence the Alpha, Delta, and Omicron genomes, and MEGA 6.6 was used to define the nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants.<h4>Results</h4>The BA.1.1 and BA.2 lineages o ...[more]

PMID: 38601946

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Project description:BackgroundTaiwan was a coronavirus disease 2019 (COVID-19) outlier, with an extraordinarily long transmission-free record: 253 days without locally transmitted infections while the rest of the world battled wave after wave of infection. The appearance of the alpha variant in May 2021, closely followed by the delta variant, disrupted this transmission-free streak. However, despite low vaccination coverage (<1%), outbreaks were well-controlled.MethodsThis study analyzed the time to border closure and conducted one-sample t test to compare between Taiwan and Non-Taiwan countries prior to vaccine introduction. The study also collected case data to observe the dynamics of omicron transmission. Time-varying reproduction number,Rt, was calculated and was used to reflect infection impact at specified time points and model trends of future incidence.ResultsThe study analyzed and compare the time to border closure in Taiwan and non-Taiwan countries. The mean times to any border closure from the first domestic case within each country were -21 and 5.98 days, respectively (P < .0001). The Taiwanese government invested in quick and effective contact tracing with a precise quarantine strategy in lieu of a strict lockdown. Residents followed recommendations based on self-discipline and unity. The self-discipline in action is evidenced in Google mobility reports. The central and local governments worked together to enact non-pharmaceutical interventions (NPIs), including universal masking, social distancing, limited unnecessary gatherings, systematic contact tracing, and enhanced quarantine measures. The people cooperated actively with pandemic-prevention regulations, including vaccination and preventive NPIs.ConclusionsThis article describes four key factors underlying Taiwan's success in controlling COVID-19 transmission: quick responses; effective control measures with new technologies and rolling knowledge updates; unity and cooperation among Taiwanese government agencies, private companies and organizations, and individual citizens; and Taiwanese self-discipline.

Project description:New SARS-CoV-2 variants causing COVID-19 are a major risk to public health worldwide due to the potential for phenotypic change and increases in pathogenicity, transmissibility and/or vaccine escape. Recognising signatures of new variants in terms of replacing growth and severity are key to informing the public health response. To assess this, we aimed to investigate key time periods in the course of infection, hospitalisation and death, by variant. We linked datasets on contact tracing (Contact Tracing Advisory Service), testing (the Second-Generation Surveillance System) and hospitalisation (the Admitted Patient Care dataset) for the entire length of contact tracing in the England - from March 2020 to March 2022. We modelled, for England, time delay distributions using a Bayesian doubly interval censored modelling approach for the SARS-CoV-2 variants Alpha, Delta, Delta Plus (AY.4.2), Omicron BA.1 and Omicron BA.2. This was conducted for the incubation period, the time from infection to hospitalisation and hospitalisation to death. We further modelled the growth of novel variant replacement using a generalised additive model with a negative binomial error structure and the relationship between incubation period length and the risk of a fatality using a Bernoulli generalised linear model with a logit link. The mean incubation periods for each variant were: Alpha 4.19 (95% credible interval (CrI) 4.13-4.26) days; Delta 3.87 (95% CrI 3.82-3.93) days; Delta Plus 3.92 (95% CrI 3.87-3.98) days; Omicron BA.1 3.67 (95% CrI 3.61-3.72) days and Omicron BA.2 3.48 (95% CrI 3.43-3.53) days. The mean time from infection to hospitalisation was for Alpha 11.31 (95% CrI 11.20-11.41) days, Delta 10.36 (95% CrI 10.26-10.45) days and Omicron BA.1 11.54 (95% CrI 11.38-11.70) days. The mean time from hospitalisation to death was, for Alpha 14.31 (95% CrI 14.00-14.62) days; Delta 12.81 (95% CrI 12.62-13.00) days and Omicron BA.2 16.02 (95% CrI 15.46-16.60) days. The 95th percentile of the incubation periods were: Alpha 11.19 (95% CrI 10.92-11.48) days; Delta 9.97 (95% CrI 9.73-10.21) days; Delta Plus 9.99 (95% CrI 9.78-10.24) days; Omicron BA.1 9.45 (95% CrI 9.23-9.67) days and Omicron BA.2 8.83 (95% CrI 8.62-9.05) days. Shorter incubation periods were associated with greater fatality risk when adjusted for age, sex, variant, vaccination status, vaccination manufacturer and time since last dose with an odds ratio of 0.83 (95% confidence interval 0.82-0.83) (P value < 0.05). Variants of SARS-CoV-2 that have replaced previously dominant variants have had shorter incubation periods. Conversely co-existing variants have had very similar and non-distinct incubation period distributions. Shorter incubation periods reflect generation time advantage, with a reduction in the time to the peak infectious period, and may be a significant factor in novel variant replacing growth. Shorter times for admission to hospital and death were associated with variant severity - the most severe variant, Delta, led to significantly earlier hospitalisation, and death. These measures are likely important for future risk assessment of new variants, and their potential impact on population health.

Dataset Information

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam.

Objectives

Methods

Results

Conclusions

Publications

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam.

Similar Datasets

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