Identification of B.1.346 Lineage of SARS-CoV-2 in Japan: Genomic Evidence of Re-entry of Clade 20C.

SARS-CoV-2 whole-genome sequencing of samples from COVID-19 patients is useful for informing infection control. Datasets of these genomes assembled from multiple hospitals can give critical clues to regional or national trends in infection. Herein, we report a lineage summary based on data collected from hospitals located in the Tokyo metropolitan area. We performed SARS-CoV-2 whole-genome sequencing of specimens from 198 patients with COVID-19 at 13 collaborating hospitals located in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions were performed to differentiate and classify the viral lineages. More than 90% of the identified strains belonged to Clade 20B, which has been prevalent in European countries since March 2020. Only two lineages (B.1.1.284 and B.1.1.214) were found to be predominant in Japan. However, one sample from a COVID-19 patient admitted to a hospital in the Kanto region in November 2020 belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in the western United States since November 2020. The patient had no history of overseas travel or any known contact with anyone who had travelled abroad. Consequently, the Clade 20C strain belonging to the B.1.346 lineage appeared likely to have been imported from the western United States to Japan across the strict quarantine barrier. B.1.1.284 and B.1.1.214 lineages were found to be predominant in the Kanto region, but a single case of the B.1.346 lineage of clade 20C, probably imported from the western United States, was also identified. These results illustrate that a decentralized network of hospitals offers significant advantages as a highly responsive system for monitoring regional molecular epidemiologic trends.

Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C (preprint)

ObjectivesWhole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan. MethodsWe performed whole genome sequencing in specimens of 198 COVID-19 patients at 13 collaborating hospitals in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions underwent to differentiate and classify the viral lineages. ResultsMore than 90% of the strains belonged to Clade 20B and two lineages (B.1.1.284 and B.1.1.214) have been detected predominantly in the Kanto region. However, one sample from a COVID-19 patient in November 2020, belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in western United States. The patient had no history of overseas travel and no contact with anyone who had travelled abroad, suggesting that this strain appeared likely to have been imported from western United States, across the strict quarantine barrier. ConclusionB.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region and B.1.346 of clade 20C in one patient was probably imported from western United States. These results illustrate that a decentralized network of hospitals can be significantly advantageous for monitoring regional molecular epidemiologic trends. Highlights{middle dot} Whole SARS-CoV-2 genome sequencing is useful for infection control {middle dot} B.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region {middle dot} B.1.346 of Clade 20C was detected in one COVID-19 patient in November {middle dot} Molecular genomic data sharing provides benefits to public health against COVID-19

[Clinical Course of 11 Cases of SARS-CoV-2 Infection Occurred in A Large Cruise Ship�E�Factors Associated with Severity and Prolonged Hospitalization]

The number of the patients with coronavirus disease 2019 (COVID-19) is increasing, and shortage of hospital beds for these patients is a cause for serious concern. Here, we report the clinical course of 11 patients who were admitted to our hospital with COVID-19 that developed during their quarantine period in a large cruise ship, and discuss the factors associated with the disease severity and length of hospitalization. The median age of the 11 patients was 62 years, and 36% were men. The disease severity was mild in 7 patients, moderate in 4 patients, and severe in none of the patients. The median time from symptom onset to disease remission was 13 days for patients with moderately severe disease, and 7 days for patients with mild disease. The median interval from symptom onset to confirmation of the first negative result of PCR was 16 days for patients with moderately severe disease, and 14 days for patients with mild disease. The median time from symptom onset to discharge was 22.5 days for patients with moderately severe disease cases, and 16 days for patients with mild disease. Some patients needed prolonged hospitalization because of persistently positive results of PCR even after remission of symptoms. Comparison between the patient groups with moderately severe disease and mild disease showed that the patients with moderately severe disease were older and had higher serum ferritin and serum amyloid protein (SAA) levels than the patients with mild disease. Even in patients with mild to moderate COVID-19, two to three weeks were required from symptom onset to confirmation of the first negative result of PCR, and this was one of the major factors for prolonged hospitalization. The serum ferritin levels and SAA levels might be predictors of the disease severity.