Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Sekizuka T

PROVIDER: S-EPMC7657588 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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

Sekizuka Tsuyoshi T Itokawa Kentaro K Hashino Masanori M Kawano-Sugaya Tetsuro T Tanaka Rina R Yatsu Koji K Ohnishi Asami A Goto Keiko K Tsukagoshi Hiroyuki H Ehara Hayato H Sadamasu Kenji K Taira Masakatsu M Shibata Shinichiro S Nomoto Ryohei R Hiroi Satoshi S Toho Miho M Shimada Tomoe T Matsui Tamano T Sunagawa Tomimasa T Kamiya Hajime H Yahata Yuichiro Y Yamagishi Takuya T Suzuki Motoi M Wakita Takaji T Kuroda Makoto M

mSphere 20201111 6

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 seve ...[more]

PMID: 33177213

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Project description:BackgroundSince the first recognition of the pandemic characteristics of SARS-CoV-2 infection, and before substantial case fatality data were available worldwide, public health agencies warned the public about the increased dangers of SARS-CoV-2 to persons with a variety of underlying physical conditions, many of which are more commonly found in persons over 50 years of age or in certain ethnic groups.ObjectiveTo investigate the statistical rather than the physiological basis in support of the abovementioned warnings, this study examines correlations globally on a nation-by-nation basis between the statistical data concerning COVID-19 fatalities and the statistics of potential comorbidities that may influence the severity of infection.MethodsThis study considers the statistics describing the populations of the 99 countries with the greatest numbers of SARS-CoV-2 infections at the time of the data cutoff. As national compilations of direct measures of immune system strength are not publicly available, the frequency of fatalities in those countries due to a variety of serious diseases is used as a proxy for the susceptibility of those populations to those same diseases.ResultsThe analysis produces plots and calculations of correlations and cross-correlations of COVID-19 case fatality rates and the risks of other potential cofactors. It exposes some reasons that may underlie the degree to which advanced age increases the risk of mortality of infection with SARS-CoV-2. In contrast with the strong influences of comorbidities on the seriousness of consequences of influenzas and their associated pneumonias, the correlations of the same set of risk factors with SARS-CoV-2 infection are considerably weaker. The general characteristics of the observed correlations strengthened through 3 cycles of analysis, starting in September 2020. The strongest correlations were with chronic kidney disease and coronary disease (approximately 0.28 and 0.20, respectively).ConclusionsThis study confirms early clinical observations that infection with SARS-CoV-2 presents an increased risk to persons over the age of 65 years. It does not support the suggestions presented by government agencies early in the pandemic that the risks are much greater for persons with certain common potential comorbidities.

Project description:Objective: Coronavirus disease 2019 (COVID-19) cases caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to increase worldwide. Although some data from pediatric series are available, more evidence is required, especially in neonates, a group with specific characteristics that deserve special attention. This study aimed to describe general and clinical characteristics, management, and treatment of postnatal-acquired (community and nosocomial/hospital-acquired) COVID-19 neonatal cases in Spain. Methods: This was a national prospective epidemiological study that included cases from a National Registry supported by the Spanish Society of Neonatology. Neonates with postnatal SARS-CoV-2 infection were included in this study. General data and infection-related information (mode and source of transmission, age at diagnosis, clinical manifestations, need for hospitalization, admission unit, treatment administered, and complementary studies performed, hospital stay associated with the infection) were collected. Results: A total of 40 cases, 26 community-acquired and 14 nosocomial were registered. Ten were preterm newborns (2 community-acquired and 8 nosocomial COVID-19 cases). Mothers (in both groups) and healthcare workers (in nosocomial cases) were the main source of infection. Hospital admission was required in 22 community-acquired cases [18 admitted to the neonatal intermediate care unit (NIMCU) and 4 to the neonatal intensive care unit (NICU)]. Among nosocomial COVID-19 cases (n = 14), previously admitted for other reasons, 4 were admitted to the NIMCU and 10 to the NICU. Ten asymptomatic patients were registered (5 in each group). In the remaining cases, clinical manifestations were generally mild in both groups, including upper respiratory airways infection, febrile syndrome or acute gastroenteritis with good overall health. In both groups, most severe cases occurred in preterm neonates or neonates with concomitant pathologies. Most of the cases did not require respiratory support. Hydroxychloroquine was administered to 4 patients in the community-acquired group and to 2 patients in the nosocomial group. Follow-up after hospital discharge was performed in most patients. Conclusions: This is the largest series of COVID-19 neonatal cases in Spain published to date. Although clinical manifestations were generally mild, prevention, treatment, and management in this group are essential.

Dataset Information

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

Publications

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

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