SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community

Hirotsu, Yosuke; Omata, Masao

doi:10.1016/j.meegid.2021.105088

Cited by 18 publications

(20 citation statements)

References 32 publications

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“…To delineate the possible origin of the five SARS-CoV-2 sequences identified in this study, real-time sequence placement for the SARS-CoV-2 pandemic was performed using an existing phylogenetic tree generated by the sarscov2phylo pipeline, which contains 6,624,590 genomes from GISAID, GenBank, COG-UK, and CNCB. The phylogenetic subtree results suggest that KMUH-3 is closest to ∼200 SARS-CoV-2 sequences collected in Japan during their alpha/B.1.1.7 outbreak ( 59 , 60 ) and that KMUH-4 to KMUH-7 are closest to several SARS-CoV-2 sequences collected in Taiwan during the largest alpha/B.1.1.7 outbreak ( 61 ). Patient number 32 (KMUH-3) had a traveling history to Japan before diagnosed of COVID-19 and patients number 36, 37, 38, and 41 (KMUH-4 to 7) had no traveling history abroad.…”

Section: Discussionmentioning

confidence: 91%

Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

et al. 2022

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have originated in Wuhan City, Hubei Province, China, in December 2019. Infection with this highly dangerous human-infecting coronavirus via inhalation of respiratory droplets from SARS-CoV-2 carriers results in coronavirus disease 2019 (COVID-19), which features clinical symptoms such as fever, dry cough, shortness of breath, and life-threatening pneumonia. Several COVID-19 waves arose in Taiwan from January 2020 to March 2021, with the largest outbreak ever having a high case fatality rate (CFR) (5.95%) between May and June 2021. In this study, we identified five 20I (alpha, V1)/B.1.1.7/GR SARS-CoV-2 (KMUH-3 to 7) lineage viruses from COVID-19 patients in this largest COVID-19 outbreak. Sequence placement analysis using the existing SARS-CoV-2 phylogenetic tree revealed that KMUH-3 originated from Japan and that KMUH-4 to KMUH-7 possibly originated via local transmission. Spike mutations M1237I and D614G were identified in KMUH-4 to KMUH-7 as well as in 43 other alpha/B.1.1.7 sequences of 48 alpha/B.1.1.7 sequences deposited in GISAID derived from clinical samples collected in Taiwan between 20 April and July. However, M1237I mutation was not observed in the other 12 alpha/B.1.1.7 sequences collected between 26 December 2020, and 12 April 2021. We conclude that the largest COVID-19 outbreak in Taiwan between May and June 2021 was initially caused by the alpha/B.1.1.7 variant harboring spike D614G + M1237I mutations, which was introduced to Taiwan by China Airlines cargo crew members. To our knowledge, this is the first documented COVID-19 outbreak caused by alpha/B.1.1.7 variant harboring spike M1237I mutation thus far. The largest COVID-19 outbreak in Taiwan resulted in 13,795 cases and 820 deaths, with a high CFR, at 5.95%, accounting for 80.90% of all cases and 96.47% of all deaths during the first 2 years. The high CFR caused by SARS-CoV-2 alpha variants in Taiwan can be attributable to comorbidities and low herd immunity. We also suggest that timely SARS-CoV-2 isolation and/or sequencing are of importance in real-time epidemiological investigations and in epidemic prevention. The impact of G614G + M1237I mutations in the spike gene on the SARS-CoV-2 virus spreading as well as on high CFR remains to be elucidated.

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Section: Discussionmentioning

confidence: 91%

Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

et al. 2022

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“…Whole genome sequencing analysis was conducted in accordance with a previously described method on 489 nasopharyngeal swabs collected from patients with coronavirus disease 2019 (COVID-19) from September 2021 to March 2022. In brief, SARS-CoV-2 genomic RNA was reverse-transcribed into cDNA and amplified using the Ion AmpliSeq SARS-CoV-2 Research Panel or Ion AmpliSeq SARS-CoV-2 Insight Research Assay (Thermo Fisher Scientific, Waltham, MA, USA) on the Ion Torrent Genexus System in accordance with the manufacturer’s instructions [17-19]. Sequencing reads were processed, and their quality was assessed using Genexus Software with SARS-CoV-2 plugins.…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: genomic surveillance in Japan from September 2021 to March 2022

Hirotsu

Maejima

Shibusawa

et al. 2022

Preprint

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ObjectiveThe new emerging Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently spreading worldwide. We aimed to analyze the genomic evolution of the shifting Omicron virus subtypes.MethodsThe study included 1,297 individuals diagnosed as SARS-CoV-2 positive by PCR test or antigen quantification test from September 2021 to March 2022. Samples were analyzed by whole genome sequencing analysis (n=489) or TaqMan assay (n=808).ResultsAfter the outbreak of the SARS-CoV-2 Delta strain, the Omicron strain spread rapidly in Yamanashi, Japan. BA.1.1 was the predominant sublineage of the Omicron strain from January to mid-February 2022, but the number of cases of sublineage BA.2 began to increase after mid-February, and this sublineage was shown to have replaced BA.1.1 by the end of March 2022. We observed higher viral and antigen levels of sublineage BA.2 than of sublineage BA.1.1 in nasopharyngeal swab samples. However, no difference in viral load by patient age was apparent between sublineages BA.1.1 and BA.2.ConclusionsA transition from sublineage BA.1.1 to sublineage BA.2 was clearly observed over approximately one month. Omicron sublineage BA.2 was found to be more transmissible owing to its higher viral load regardless of patient age.

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“…Although B.1.1.7, P.1, and B.1.351 had already detected in Japan at the end of December 2020, only B.1.1.7 had spread in Japan and it rapidly increased from February 2021 ( 34 , 35 ). A local surveillance in Japan also suggested that the B.1.1.7 became dominant after mid-April ( 36 ). These observations suggested that all participants in this study were likely to be infected with D614G.…”

Section: Discussionmentioning

confidence: 99%

Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections

et al. 2022

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BackgroundSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. The emergence of variants of concern (VOCs) has become one of the most pressing issues in public health. To control VOCs, it is important to know which COVID-19 convalescent sera have cross-neutralizing activity against VOCs and how long the sera maintain this protective activity.MethodsSera of patients infected with SARS-CoV-2 from March 2020 to January 2021 and admitted to Hyogo Prefectural Kakogawa Medical Center were selected. Blood was drawn from patients at 1-3, 3-6, and 6-8 months post onset. Then, a virus neutralization assay against SARS-CoV-2 variants (D614G mutation as conventional strain; B.1.1.7, P.1, and B.1.351 as VOCs) was performed using authentic viruses.ResultsWe assessed 97 sera from 42 patients. Sera from 28 patients showed neutralizing activity that was sustained for 3-8 months post onset. The neutralizing antibody titer against D614G significantly decreased in sera of 6-8 months post onset compared to those of 1-3 months post onset. However, the neutralizing antibody titers against the three VOCs were not significantly different among 1-3, 3-6, and 6-8 months post onset.DiscussionOur results indicate that neutralizing antibodies that recognize the common epitope for several variants may be maintained for a long time, while neutralizing antibodies having specific epitopes for a variant, produced in large quantities immediately after infection, may decrease quite rapidly.

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SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community

Cited by 18 publications

References 32 publications

Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: genomic surveillance in Japan from September 2021 to March 2022

Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections

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