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Two cases of breakthrough SARS-CoV-2 infections caused by the Omicron variant (B.1.1.529 lineage) in international travelers to Japan.

ABSTRACT: In November 2021, the World Health Organization designated a new SARS-CoV-2 variant of concern, Omicron (PANGO lineage B.1.1.529). We report on first two cases of breakthrough COVID-19 caused by Omicron in Japan among international travelers returning from the country with undetected infection. The spread of infection by Omicron were considered.

SUBMITTER: Maruki T

PROVIDER: S-EPMC8755371 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Two Cases of Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections Caused by the Omicron Variant (B.1.1.529 Lineage) in International Travelers to Japan.

Maruki Taketomo T Iwamoto Noriko N Kanda Kohei K Okumura Nobumasa N Yamada Gen G Ishikane Masahiro M Ujiie Mugen M Saito Masumichi M Fujimoto Tsuguto T Kageyama Tsutomu T Saito Tomoya T Saito Shinji S Suzuki Tadaki T Ohmagari Norio N

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20220801 1

In November 2021, the World Health Organization designated a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern, Omicron (PANGO lineage B.1.1.529). We report on the first 2 cases of breakthrough coronavirus disease 2019 (COVID-19) caused by Omicron in Japan among international travelers returning from the country with undetected infection. The spread of infection by Omicron were considered. ...[more]

PMID: 34979547

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Project description:ObjectivesTo compare the RNA loads of severe acute respiratory syndrome coronavirus 2 in nasopharyngeal specimens collected from patients with breakthrough coronavirus disease 2019 (COVID-19) caused by the Delta variant with those in specimens collected from patients with breakthrough COVID-19 caused by the Omicron variant.MethodsA retrospective, observational study was conducted, including 240 consecutive adult out-patients, of whom 121 (74 females; median age, 40 years) had COVID-19 due to the Omicron variant and 119 (65 females; median age, 48 years) had COVID-19 caused by the Delta variant. The viral RNA load was quantitated using the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, Waltham, MS, USA). The viability platinum chloride reverse transcription-PCR assay was used to discriminate between potentially infectious viral particles and free (encapsidated) viral RNA.ResultsOverall, the viral RNA loads were significantly higher (p 0.003) for the Omicron variant (median, 8.1 log10 copies/mL; range, 4.0-10.9 log10 copies/mL) than for the Delta variant (median, 7.5 log10 copies/mL; range, 3.0-11.6 log10 copies/mL). A trend towards higher viral loads was noticed for Omicron compared with that for Delta across the following time frames since vaccination: 16-90 days (median, 6.83 vs. 5.88 log10 copies/mL, respectively; range, 3.91-10.68 vs. 3.67-9.66 log10 copies/mL, respectively; p 0.10), 91-180 days (median, 8.09 vs. 7.46 log10 copies/mL, respectively; range, 4.30-10.92 vs. 3.03-11.56 log10 copies/mL, respectively; p 0.003) and 181-330 days (median, 8.56 vs. 8.10 log10 copies/mL, respectively; range, 6.51-10.29 vs. 3.03-10.61 log10 copies/mL, respectively; p 0.11). The platinum chloride treated or untreated reverse transcription-PCR cycle threshold ratio for the nucleocapsid gene as the target was slightly higher for Omicron than for Delta (median, 0.62 vs. 0.57, respectively; range, 0.57-0.98 vs. 0.61-0.87, respectively), although statistical significance was not reached (p 0.10).ConclusionThe time elapsed since vaccination has a major impact on the RNA loads of severe acute respiratory syndrome coronavirus 2 in nasopharyngeal specimens, particularly for the Omicron variant. The Omicron variant may be better adapted for replication in the upper respiratory tract than the Delta variant, in which this is unlikely given its more efficient generation of viral particles.

Project description:BackgroundRecent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.MethodsWhole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.ResultsThe mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.ConclusionThe current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.

Project description:Background Omicron subvariants have led to millions of coronavirus disease 2019 (COVID-19) cases worldwide. Although Omicron breakthrough infections (BTIs) exhibit lower hospitalization rates than previous variants, post-COVID conditions persist. However, the immune response dynamics, lymphocyte subsets, and immune repertoire features following BA.5 sublineage BTI remain poorly understood. Methods In a longitudinal cohort, we monitored the recovery dynamics in patients with BTI at various time points. We employed single-cell transcriptomics, T cell receptor (TCR)/BCR sequencing, and antibody mass spectrometry to sequentially assess the immune response following BA.5.2 or BF.7 BTI. Findings Serological analysis revealed active cellular and humoral immunity 2 weeks post-BTI, with significant increases in cytokines (CKs) like IFN-γ, TNFβ, IL-2, and neutralizing antibodies. CK levels reverted to pre-infection levels, while broadly neutralizing antibodies remained high 1 month post-infection. Single-cell sequencing demonstrated robust immune activation and antiviral responses in NK, T, and B lymphocytes within 1 month post-BTI. Interestingly, the immune system maintained its strength to combat viral infection at 2 weeks post-BTI, transitioning toward repair and tissue damage elimination at 1 month. TCR/BCR library analysis revealed a higher clonal type in the BTI_2w group, mainly in NKT, memory T or B, and plasma cells, crucial for immune memory and antigen clearance. The BTI_1m group exhibited more IgG and IgA BCR subtypes, with somatic hypermutation indicating mature antibodies. Biological function verification of IgG and IgA-type monoclonal antibodies corresponding to expanded BCRs revealed antigen-specific and broad-spectrum antibodies. Interpretation Our study elucidated the dynamic immune profiling of individuals 2 weeks and 1 month after Omicron BA.5 sublineage BTI. This provided essential insights into pathogenicity, sequential immune status, recovery mechanisms of Omicron subvariant BTI, and novel concepts for broad-spectrum antibody development.

Dataset Information

Two cases of breakthrough SARS-CoV-2 infections caused by the Omicron variant (B.1.1.529 lineage) in international travelers to Japan.

Publications

Two Cases of Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections Caused by the Omicron Variant (B.1.1.529 Lineage) in International Travelers to Japan.

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