Autochthonous Outbreak of SARS-CoV-2 Omicron Variant in Booster-Vaccinated (3 Doses) Healthcare Workers in Southern Italy: Just the Tip of the Iceberg?

Loconsole, Daniela; Bisceglia, Lucia; Centrone, Francesca; Sallustio, Anna; Accogli, Marisa; Dalfino, Lidia; Brienza, Nicola; Chironna, Maria

doi:10.3390/vaccines10020283

Cited by 14 publications

(17 citation statements)

References 18 publications

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“…However, with the emergence of the newest VOC, Omicron, the efficacy of the booster vaccination doses have again been challenged. While the cross-reactive cellular response is maintained in the majority of individuals, the functionality of the cross-reactive antibody response declines dramatically [ 45 , 46 , 47 , 48 ]. We have previously demonstrated vaccine efficacy similar to the results presented here, inhibiting infection of the lungs and no effect on oral viral shedding [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

VSV-Based Vaccines Reduce Virus Shedding and Viral Load in Hamsters Infected with SARS-CoV-2 Variants of Concern

et al. 2022

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The continued progression of the COVID-19 pandemic can partly be attributed to the ability of SARS-CoV-2 to mutate and introduce new viral variants. Some of these variants with the potential to spread quickly and conquer the globe are termed variants of concern (VOC). The existing vaccines implemented on a global scale are based on the ancestral strain, which has resulted in increased numbers of breakthrough infections as these VOC have emerged. It is imperative to show protection against VOC infection with newly developed vaccines. Previously, we evaluated two vesicular stomatitis virus (VSV)-based vaccines expressing the SARS-CoV-2 spike protein alone (VSV-SARS2) or in combination with the Ebola virus glycoprotein (VSV-SARS2-EBOV) and demonstrated their fast-acting potential. Here, we prolonged the time to challenge; we vaccinated hamsters intranasally (IN) or intramuscularly 28 days prior to infection with three SARS-CoV-2 VOC—the Alpha, Beta, and Delta variants. IN vaccination with either the VSV-SARS2 or VSV-SARS2-EBOV resulted in the highest protective efficacy as demonstrated by decreased virus shedding and lung viral load of vaccinated hamsters. Histopathologic analysis of the lungs revealed the least amount of lung damage in the IN-vaccinated animals regardless of the challenge virus. This data demonstrates the ability of a VSV-based vaccine to not only protect from disease caused by SARS-CoV-2 VOC but also reduce viral shedding.

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Section: Discussionmentioning

confidence: 99%

VSV-Based Vaccines Reduce Virus Shedding and Viral Load in Hamsters Infected with SARS-CoV-2 Variants of Concern

et al. 2022

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“…In addition to this, density of the population, vaccination status of the hosts, would also further determine the evolution of sub-sub lineages within the sub lineages into novel variants of concern. A study published by [16] Loconsole et al (2022), reveals an outbreak of SARS-CoV-2 omicron infection and successful immune escape in 15 booster vaccinated healthcare workers in Italy. While study by [15] Liu et al (2022) demonstrated chimerism in omicron variants, as a result of genomic recombination between two SARS-CoV-2 lineages involving the spike protein gene.…”

Section: Discussionmentioning

confidence: 99%

Analyses of Omicron genomes from India reveal BA.2 as a more transmissible variant

Atkulwar¹,

Rehman²,

Yashal

et al. 2022

Preprint

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This is the first study on omicron genomes from India to focus on phylodynamics and phylogenomics trait to provide an insight into the evolution of omicron variants. We analyzed 564 genomes deposited to GISAID database from various states of India. Pangolin COVID-19 Lineage Assigner tool was used to determine lineage assignment of all retrieved genomes. A Maximum likelihood (MLE) tree construction further confirms the separation of genomes into two distinct clades, BA. 1. and BA. 2. A very high reproduction number (R0) of 2.445 was estimated for the lineage BA.2. The highest R0 value in Telangana confirms the prevalence of lineage BA.2 in the state. Construction of the Reduced Median (RM) network shows evolution of some autochthonous haplogroups and haplotypes, which further supports the rapid evolution of omicron as compared to its previous variants. Phylogenomic analyses using maximum likelihood (ML) and RM show the potential for the emergence of sub-sublineages and novel haplogroups respectively. Due to the recombinant property and high transmissibility of omicron virus, we suggest continuous and more widespread genome sequencing in all states of India to track evolution of SARS-CoV-2 in real time.

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“…In particular, the BA.2 lineage does not harbor the 69/70 deletion in the spike protein. This mutation impairs the detection of the S gene by common commercial real-time PCR kits, a phenomenon called S gene target failure (SGTF), and was used as a proxy for early identification of the Alpha and Omicron VOCs [ 6 , 7 , 8 , 9 ]. BA.2 is thought to originate from overlooked virus evolution in individuals with low access to viral diagnosis and sequencing, in immunocompromised, chronically-infected patients, or in animals [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

“…During a 2-week period in January 2022, the prevalence of BA.2 in sequenced samples of patients infected with the Omicron VOC increased from 1% to 3% [ 15 ]. In the Apulia region of Italy, the prevalence of the Omicron VOC was 100% within a few weeks of its first identification in December 2021, with this virus inducing autochthonous outbreaks in booster-vaccinated subjects [ 9 ]. The first Omicron BA.2 subvariant in Apulia was identified in a sample collected on 31 January 2022 [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

Characteristics of the First 284 Patients Infected with the SARS-CoV-2 Omicron BA.2 Subvariant at a Single Center in the Apulia Region of Italy, January–March 2022

et al. 2022

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Since its initial detection, the SARS-CoV-2 Omicron sublineage BA.2 has been spreading rapidly worldwide. The aims of this study were to describe the first 284 patients infected with the Omicron BA.2 variant of concern (VOC) in the Apulia region of southern Italy and to assess the differences in the demographic and clinical characteristics of patients infected with the SARS-CoV-2 BA.1 and BA.2 variants. The demographic characteristics of patients, as well as information about symptoms, vaccinations and hospitalizations for COVID-19, were collected. A subset of samples from patients infected with the BA.2 variant was subjected to whole-genome sequencing. The characteristics of the first 284 patients infected with Omicron BA.2 and the first 175 patients infected with Omicron BA.1 were compared. The proportion of patients infected with the BA.2 variant rapidly increased, from 0.5% during the third week of 2022 to 29.6% during the tenth week of 2022. Ten isolates (out of 34 BA.2 isolates) contain the substitutional mutation, H78K in ORF3a, and four isolates include two mutations, A2909V in ORF1a and L140F in ORDF3a. Compared with patients infected with BA.1, those infected with BA.2 were more likely to be symptomatic and booster-vaccinated, and showed a shorter time from the last dose of vaccine to infection. The high transmissibility and immune-evasive properties of Omicron BA.2, which will become the leading SARS-CoV-2 VOC, suggest that short-term public health measures should not be discontinued in Italy.

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Autochthonous Outbreak of SARS-CoV-2 Omicron Variant in Booster-Vaccinated (3 Doses) Healthcare Workers in Southern Italy: Just the Tip of the Iceberg?

Cited by 14 publications

References 18 publications

VSV-Based Vaccines Reduce Virus Shedding and Viral Load in Hamsters Infected with SARS-CoV-2 Variants of Concern

VSV-Based Vaccines Reduce Virus Shedding and Viral Load in Hamsters Infected with SARS-CoV-2 Variants of Concern

Analyses of Omicron genomes from India reveal BA.2 as a more transmissible variant

Characteristics of the First 284 Patients Infected with the SARS-CoV-2 Omicron BA.2 Subvariant at a Single Center in the Apulia Region of Italy, January–March 2022

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