SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021

Nagano, Katsutoshi; Tani‐Sassa, Chihiro; Iwasaki, Yumi; Takatsuki, Yuna; Yuasa, Sonoka; Takahashi, Yuta; Nakajima, Jun; Sonobe, Kazunari; Ichimura, Naoya; Nukui, Yoko; Takeuchi, Hiroaki; Tanimoto, Kousuke; Tanaka, Yukië; Kimura, Akinori; Tohda, Shuji

doi:10.1101/2021.05.11.21257004

Cited by 9 publications

(3 citation statements)

References 6 publications

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“…We previously reported that the R.1 variant (the sublineage of B.1.1.316) spread rapidly in Tokyo in March 2021 3 and that the copy numbers of SARS‐CoV‐2 in patients infected with the Delta variant were no higher than those of the R.1 and Alpha variants 4 …”

Section: Introductionmentioning

confidence: 99%

“…We previously reported that the R.1 variant (the sublineage of B.1.1.316) spread rapidly in Tokyo in March 2021 3 and that the copy numbers of SARS-CoV-2 in patients infected with the Delta variant were no higher than those of the R.1 and Alpha variants. 4 As a possible cause of the stronger transmissibility of the Omicron variant, higher viral loads in the droplets from patients can be considered.…”

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confidence: 99%

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Viral load of SARS‐CoV‐2 Omicron is not high despite its high infectivity

Yuasa

Nakajima

Takatsuki

et al. 2022

Journal of Medical Virology

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Patients infected with the Omicron variant of severe acute respiratory syndrome coronavirus 2 has increased worldwide since the beginning of 2022 and the variant has spread more rapidly than the Delta variant, which spread in the summer of 2021. It is important to clarify the cause of the strong transmissibility of the Omicron variant to control its spread. In 694 patients with coronavirus disease 2019, the copy numbers of virus in nasopharyngeal swab‐soaked samples and the viral genotypes were examined using quantitative polymerase chain reaction (PCR) and PCR‐based melting curve analysis, respectively. Whole‐genome sequencing was also performed to verify the viral genotyping data. There was no significant difference ( p = 0.052) in the copy numbers between the Delta variant cases (median 1.5 × 10 5 copies/μl, n = 174) and Omicron variant cases (median 1.2 × 10 5 copies/μl, n = 328). During this study, Omicron BA.1 cases (median 1.1 ×10 5 copies/μl, n = 275) began to be replaced by BA.2 cases (median 2.3 × 10 5 copies/μl, n = 53), and there was no significant difference between the two groups ( p = 0.33). Our results suggest that increased infectivity of the Omicron variant and its derivative BA.2 is not caused by higher viral loads but by other factors, such as increased affinity to cell receptors or immune escape.

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Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

Viral load of SARS‐CoV‐2 Omicron is not high despite its high infectivity

Yuasa

Nakajima

Takatsuki

et al. 2022

Journal of Medical Virology

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“…Coronavirus disease 2019 (COVID- 19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly spread worldwide and has yet to be brought under control. Although the major cause of death is respiratory failure, a wide range of unique complications has been observed in COVID-19 patients, including macrophage activating syndrome, multisystem inflammatory syndrome in children (MIS-C), and thrombosis (1,2).…”

Section: Introductionmentioning

confidence: 99%

Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan

Oba

Hosoya

Amamiya

et al. 2021

Front. Cardiovasc. Med.

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Background: Thrombosis is a characteristic complication in coronavirus disease 2019 (COVID-19). Since coagulopathy has been observed over the entire clinical course, thrombosis might be a clue to understanding the specific pathology in COVID-19. Currently, there is limited epidemiological data of COVID-19-associated thrombosis in the Japanese population and none regarding variant strains of SARS-CoV-2. Here, we elucidate the risk factors and the pattern of thrombosis in COVID-19 patients.Methods: The patients consecutively admitted to Tokyo Medical and Dental University Hospital with COVID-19 were retrospectively analyzed. SARS-CoV-2 variants of concern/interest (VOC/VOI) carrying the spike protein mutants E484K, N501Y, or L452R were identified by PCR-based analysis. All thrombotic events were diagnosed by clinical symptoms, ultrasonography, and/or radiological tests.Results: Among the 516 patients, 32 patients experienced 42 thromboembolic events. Advanced age, severe respiratory conditions, and several abnormal laboratory markers were associated with the development of thrombosis. While thrombotic events occurred in 13% of the patients with a severe respiratory condition, those events still occurred in 2.5% of the patients who did not require oxygen therapy. Elevated D-dimer and ferritin levels on admission were independent risk factors of thrombosis (adjusted odds ratio 9.39 and 3.11, 95% confidence interval 2.08–42.3, and 1.06–9.17, respectively). Of the thrombotic events, 22 were venous, whereas 20 were arterial. While patients with thrombosis received anticoagulation and antiinflammatory therapies with a higher proportion, the mortality rate, organ dysfunctions, and bleeding complications in these patients were higher than those without thrombosis. The incidence of thrombosis in COVID-19 became less frequent over time, such as during the replacement of the earlier strains of SARS-CoV-2 by VOC/VOI and during increased use of anticoagulatory therapeutics.Conclusion: This study elucidated that elevated D-dimer and ferritin levels are useful biomarkers of thrombosis in COVID-19 patients. The comparable incidence of arterial thrombosis with venous thrombosis and the development of thrombosis in less severe patients required further considerations for the management of Japanese patients with COVID-19. Further studies would be required to identify high-risk populations and establish appropriate interventions for thrombotic complications in COVID-19.

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Classifying COVID-19 Variants Based on Genetic Sequences Using Deep Learning Models

Basu

Campbell²

2022

Springer Series in Reliability Engineering

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SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021

Cited by 9 publications

References 6 publications

Viral load of SARS‐CoV‐2 Omicron is not high despite its high infectivity

Viral load of SARS‐CoV‐2 Omicron is not high despite its high infectivity

Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan

Classifying COVID-19 Variants Based on Genetic Sequences Using Deep Learning Models

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