Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

Bui, Ngoc-Niem; Lin, Yu‐Hsien; Huang, Su-Hua; Lin, Cheng‐Wen

doi:10.1016/j.meegid.2021.105164

Cited by 11 publications

(14 citation statements)

References 46 publications

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“…We observed that most haplotypes are present in only one patient making any interpretation difficult. Moreover in previous studies only marginal differences in haplotype distributions have been observed between low and high vaccination rate countries [33]. As previously mentioned, we observed an increase in the prevalence of the Omicron variant over the previously predominant delta variant in the span of ~1 month.…”

Section: Haplotype Networksupporting

confidence: 67%

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Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

Cedro‐Tanda

Gómez-Romero

Anda-Jáuregui

et al. 2022

Preprint

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Background. Omicron is the most mutated SARS-CoV-2 variant that has emerged, resulting in viral phenotype alterations, which can affect transmissibility, disease severity, and immune evasiveness. Genomic surveillance of a highly transmissible variant is important in cities with millions of inhabitants and an economic center such as Mexico City. In this work, we describe the early effects of the Omicron variant in Mexico City, exploring its genomic profile and clinical description. Methodology. We sequenced SARS-CoV-2-positive samples in November and December 2021 using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database to explore the association with clinical information such as symptoms and vaccination status. Findings. The first case of Omicron was detected on November 16, 2022, and until December 31, 2021, we observed an increase from 88% in sequenced samples. Nineteen nonsynonymous mutations were found in the Omicron RBD, and we further explored the R346K substitution, which was prevalent in 42% of the samples and associated with immune escape by monoclonal antibodies. In the phylogenetic analysis, we found that there were several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. The haplotype analysis allowed us to observe that there was no association between haplotype and vaccination status. Of the patients with clinical data, 66% were vaccinated, none of the reported comorbidities were associated with Omicron, the presence of odynophagia and absence of dysgeusia were significant predictor symptoms for Omicron, and the Ct value on RT-qPCR was lower in Omicron. Conclusions. Genomic surveillance in highly populated and fast-moving urban regions such as Mexico City is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, to detect patterns that can inform public health decisions. It is also necessary to continue sequencing to detect the spread of any mutation that may affect the therapeutic efficacy or guide it.

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Section: Haplotype Networksupporting

confidence: 67%

Section: Resultsmentioning

confidence: 99%

Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

Cedro‐Tanda

Gómez-Romero

Anda-Jáuregui

et al. 2022

Preprint

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“…We observed that most haplotypes were present in only one patient, making any interpretation difficult. Moreover, in previous studies, only marginal differences in haplotype distributions have been observed between countries with low and high vaccination rates [ 27 ].…”

Section: Resultsmentioning

confidence: 99%

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

Cedro‐Tanda

Gómez-Romero

Anda-Jáuregui

et al. 2022

Viruses

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Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.

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“… 112 Following the Alpha, Beta, Gamma, and Delta variants, the most recently emerged VOC is the Omicron (B.1.1.529), which has evolved as a result of the accumulation of high numbers of mutations, particularly in the spike protein, raising concerns about its potential to dodge pre‐existing immunity obtained through vaccination or infection, and also outperforming antibodies‐based therapies. 113 The Omicron is extremely transmissible and spreads quicker than any prior version; however, it may cause milder symptoms than earlier forms. The Omicron can evade immune system defenses, and coronavirus disease 2019 vaccinations are less effective against the Omicron version.…”

Section: Variants Of the Sars‐cov‐2mentioning

confidence: 99%

“…The virus, which first arose in China, mutated multiple times before causing havoc and taking countless lives globally as part of the continuing COVID‐19 epidemic 112 . Following the Alpha, Beta, Gamma, and Delta variants, the most recently emerged VOC is the Omicron (B.1.1.529), which has evolved as a result of the accumulation of high numbers of mutations, particularly in the spike protein, raising concerns about its potential to dodge pre‐existing immunity obtained through vaccination or infection, and also outperforming antibodies‐based therapies 113 . The Omicron is extremely transmissible and spreads quicker than any prior version; however, it may cause milder symptoms than earlier forms.…”

Section: Variants Of the Sars‐cov‐2mentioning

confidence: 99%

SARS‐CoV‐2 variants and vulnerability at the global level

Chavda

Patel

Vaghasiya

2022

Journal of Medical Virology

103

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Numerous variants of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic have evolved. As viral variants may evolve with harmful susceptibility to the immunity established with the existing COVID‐19 vaccination, these variations are more transmissible, induce relatively extreme illness, have evasive immunological features, decrease neutralization using antibodies from vaccinated persons, and are more susceptible to re‐infection. The Centers for Disease Control and Prevention (CDC) has categorized SARS‐CoV‐2 mutations as variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC). At the moment, four VOC and many variants of interest have been defined and require constant observation. This review article summarizes various variants of SARS‐CoV‐2 surfaced with special emphasis on VOCs that are spreading across the world, as well as several viral mutational impacts and how these modifications alter the properties of the virus.

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Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

Cited by 11 publications

References 46 publications

Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

SARS‐CoV‐2 variants and vulnerability at the global level

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