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1.
Jpn J Infect Dis ; 2022 Apr 28.
Article in English | MEDLINE | ID: covidwho-1818688

ABSTRACT

Respiratory infections are common diseases, the most common causative agent is a virus. In case of novel viral diseases pandemic like the COVID-19, routinely surveillance of respiratory viruses is useful. In this study, to clarify what kind of virus is involved in suspected cases of COVID-19 in the early stages of the pandemic, we attempted to detect various respiratory viruses from 613 specimens that tested negative for SARS-CoV-2 using RT- PCR method. Viruses were detected from 59 (9.6%) patients. Human rhinovirus (HRV), human metapneumovirus (HMPV), human respiratory syncytial virus, and human parechovirus were detected in 29 cases, 25 cases, 3 cases, and 2 cases, respectively. Although this study was conducted in a short period of time and not all specimens were tested, these results indicate that various respiratory viruses, especially HRV and HMPV can be detected even in the early stages of a pandemic, such as COVID-19. Because various respiratory viruses maintain a constant effect during the outbreak of the newly emerged pandemic respiratory virus, to make good use for clinical and public health, from normal period systematic surveillance about respiratory viruses is needed.

2.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-295960

ABSTRACT

Three COVID-19 waves in Japan have been characterized by the presence of distinct PANGO lineages (B.1.1. 162, B.1.1.284, and B.1.1.214). Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance.

3.
Infect Genet Evol ; 94: 105013, 2021 10.
Article in English | MEDLINE | ID: covidwho-1336736

ABSTRACT

Three COVID-19 waves in Japan have been characterized by the presence of distinct PANGO lineages (B.1.1. 162, B.1.1.284, and B.1.1.214). Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance. E484K could be a pivotal amino acid substitution with the potential to mediate immune escape; thus, more attention should be paid to such potential variants of concern to avoid the emergence of mutants of concern. Such comprehensive real-time genome surveillance has become essential for the containment of COVID-19 clusters.


Subject(s)
COVID-19/virology , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics , COVID-19/epidemiology , Humans , Japan/epidemiology , SARS-CoV-2/genetics , Whole Genome Sequencing
4.
J Dermatol ; 48(10): 1588-1592, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1319212

ABSTRACT

In the worldwide coronavirus disease 2019 (COVID-19) outbreak, skin manifestations were seen in COVID-19 patients. We report a case in which a COVID-19 patient developed cutaneous lesions that were diagnosed as erythema nodosum-like lesions, which were associated with COVID-19. Nasopharyngeal swab polymerase chain reaction (PCR) confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Histopathologically, extensive inflammation was seen from the epidermis to the fat tissue. An organized thrombus and disrupted inner elastic lamina were seen in an intradermal vessel. These findings suggest septal panniculitis with cutaneous polyarteritis nodosa. The results of PCR using the specimen of skin lesion was negative. The patient took non-steroidal anti-inflammatory drugs and the skin lesion improved in 3 weeks. To characterize the skin eruption, we reviewed previous reports on COVID-19 (confirmed by the detection of SARS-CoV-2 infection) from Asian countries. The type of eruption and timing of its appearance in this case seemed rare. Differences in skin manifestations between Western and Asian countries were noted.


Subject(s)
COVID-19 , Erythema Nodosum , Exanthema , Asia , Erythema Nodosum/diagnosis , Erythema Nodosum/drug therapy , Humans , SARS-CoV-2
5.
Viruses ; 13(2)2021 02 15.
Article in English | MEDLINE | ID: covidwho-1085038

ABSTRACT

To predict the clinical outcome of coronavirus disease-2019 (COVID-19), we examined relationships among epidemiological data, viral load, and disease severity. We examined viral loads of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) in fatal (15 cases), symptomatic/survived (133 cases), and asymptomatic cases (138 cases) using reverse transcription quantitative real-time PCR (RT-qPCR). We examined 5768 nasopharyngeal swabs (NPS) and attempted to detect the SARS-CoV-2 genome using RT-qPCR. Among them, the viral genome was detected using the method for the 370 NPS samples with a positive rate of 6.4%. A comparison of each age showed that the fatal case was higher than the survived case and asymptomatic patients. Survived cases were older than asymptomatic patients. Notably, the viral load in the fatal cases was significantly higher than in symptomatic or asymptomatic cases (p < 0.05). These results suggested that a high viral load of the SARS-CoV-2 in elderly patients at an early stage of the disease results in a poor outcome. We should, therefore, intervene early to prevent a severe stage of the disease in such cases.


Subject(s)
COVID-19/diagnosis , Nasal Mucosa/virology , SARS-CoV-2/isolation & purification , Viral Load , Adult , Aged , COVID-19/virology , Female , Humans , Japan , Male , Middle Aged , RNA, Viral/analysis , Severity of Illness Index
6.
mSphere ; 5(6)2020 11 11.
Article in English | MEDLINE | ID: covidwho-920897

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.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , Whole Genome Sequencing , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/transmission , Coronavirus Infections/virology , Emigration and Immigration , Haplotypes , Health Policy , Humans , Japan/epidemiology , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , SARS-CoV-2
7.
Case Rep Infect Dis ; 2020: 8814249, 2020.
Article in English | MEDLINE | ID: covidwho-751446

ABSTRACT

Although a variety of existing drugs are being tested for patients with coronavirus disease 2019 (COVID-19), no efficacious treatment has been found so far, particularly for severe cases. We report successful recovery in an elderly patient with severe pneumonia requiring mechanical ventilation and extracorporeal membrane oxygenation (ECMO). Despite administration of multiple antiviral drugs, including lopinavir/ritonavir, chloroquine, and favipiravir, the patient's condition did not improve. However, after administration of another antiviral drug, remdesivir, we were able to terminate invasive interventions, including ECMO, and subsequently obtained negative polymerase chain reaction results. Although further validation is needed, remdesivir might be effective in treating COVID-19.

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