SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise

Sekizuka, Tsuyoshi; Kuramoto, Shigeru; Nariai, Eri; Taira, Masakatsu; Hachisu, Yushi; Tokaji, Akihiko; Shinohara, Michiyo; Kishimoto, Tsuyoshi; Itokawa, Kentaro; Kobayashi, Yusuke; Kadokura, Keisuke; Kamiya, Hajime; Matsui, Takeshi; Suzuki, Motoi; Kuroda, Makoto

doi:10.3389/fmicb.2020.01316

Cited by 20 publications

(30 citation statements)

References 9 publications

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“…The SARS-CoV-2 haplotype network analysis, however, suggested that the second wave of COVID-19 cases in late March had a distinctly different origin from the lineage of the first wave. The lineage of the second wave could have been imported by returnees or travelers from Europe, North America, or other countries ( 13 ) (see the image in the cyan frame in Fig. 2 ) but not from the remaining Wuhan lineage.…”

Section: Resultsmentioning

confidence: 99%

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Sekizuka

Itokawa

Hashino

et al. 2020

mSphere

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After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries. IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

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Section: Resultsmentioning

confidence: 99%

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Sekizuka

Itokawa

Hashino

et al. 2020

mSphere

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“…Currently, individual case reports, case series, regional analyses, and meta-analyses are conducted under ethical regulations and structured protocols[ 17 ],[ [64] , [65] , [66] ]. These close observations by trained clinical staff characterized the unique symptoms in COVID-19, including olfaction and gustatory impairments[ 67 ].…”

Section: Discussionmentioning

confidence: 99%

“…These close observations by trained clinical staff characterized the unique symptoms in COVID-19, including olfaction and gustatory impairments[ 67 ]. However, the meta-analysis on the symptoms will appear later[ 17 ],[ 64 ]. Moreover, the majority of young patients with COVID-19 are suspected to be asymptomatic[ 68 ].…”

Section: Discussionmentioning

confidence: 99%

Virus database annotations assist in tracing information on patients infected with emerging pathogens

Nakashima

Takeya

Kuba

et al. 2020

Informatics in Medicine Unlocked

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The global pandemic of SARS-CoV-2 has disrupted human social activities. In restarting economic activities, successive outbreaks by new variants are concerning. Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. Among the detectable multiple mutations, we retraced the mutation in the spike protein. With the aid of the protein database, structural modelling yielded a testable scientific hypothesis on viral entry to host cells. Simultaneously, annotations for locations and collection dates suggested that the variant virus emerged somewhere in the world in approximately February 2020, entered the USA and propagated nationwide with periodic sampling fluctuation likely due to an approximately 5-day incubation delay. Thus, public database annotations are useful for automated elucidation of the early spreading patterns in relation to human behaviours, which should provide objective reference for local governments for social decision making to contain emerging substrains. We propose that additional annotations for past paths and symptoms of the patients should further assist in characterizing the exact virulence and origins of emerging pathogens.

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“…The nearness of SARS-CoV-2 genomic information empowers scientists for more investigation and examination on it, for example, the hereditary variation examination and SNP seclusion, nucleotide varieties at the genomic positions have been analyzed between the COVID-19 cases and control samples of Italian and Spanish cohorts 17 ; between the symptomatic and asymptomatic COVID-19 severity patients 18 ; some genomic mutational sites have been also identified in Europe and North America 19 ; also the complete genome sequences of SARS-CoV-2 have been studied to understand the genomic structures and the most common mutations within 20 . Apart from these the haplotype network analysis has also been done on the genomic contents of Japanese people 21…”

Section: Discussionmentioning

confidence: 99%

Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2

Ray

Sarkar

Rath

et al. 2020

Preprint

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The COVID-19 pandemic is having a devastating effect on the healthcare system and the economy of the world. The unavailability of a specific treatment regime and a candidate vaccine yet opens up scope for new approaches and discoveries of drugs for mitigation of the sufferings of humankind due to the disease. The present isolated whole-genome sequences of SARS-CoV-2 from 11 different nations subjected to evolutionary study and genome-wide association study through in silico approaches including multiple sequence alignment, phylogenetic study through MEGA7 and have been analyzed through DNAsp respectively. These investigations recognized the nucleotide varieties and single nucleotide mutations/polymorphisms on the genomic regions as well as protein-coding regions. The resulted mutations have diversified the genomic contents of SARS-CoV-2 according to the altered nucleotides found in 11 genome sequences. India and Nepal have found to have progressively more distinct species of SARS-CoV-2 with variations in Spike protein and Nucleocapsid protein-coding sites. These genomic variations might be the explanation behind the less case fatality rate of India and Nepal dependent on the populaces. The anticipated idea of this investigation upgrades the information about genomic medication and might be useful in the planning of antibodies against SARS-CoV-2.

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SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise

Cited by 20 publications

References 9 publications

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Virus database annotations assist in tracing information on patients infected with emerging pathogens

Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2

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