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This study seeks to find the correlation between case fatality rates (CFRs) and third-dose vaccination coverage in 244 counties (si/gun/gu) of South Korea during the omicron variant wave. Multivariate regression analyses report that the higher third-dose vaccination rates were correlated with lower regional CFRs, when controlling for age structure. If the thirddose vaccination rate of a county is higher by 10%, it would have a CFR lower by 0.05% (95% confidence interval, 0.03–0.08%). As the number of cumulative confirmed cases in South Korea was 16,353,495 as of April 20, 2022, a lower CFR by 0.03–0.08% is equivalent to 4,394–12,448 lives (8.6–24.4 per 100,000) spared. County-specific characteristics, such as age structure, intensive care unit availability, and the level of non-pharmaceutical interventions may also affect the extent of this correlation. The conclusion implicates the potential role of coronavirus disease 2019 vaccines in reducing the pressure on the regional healthcare capacity.
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IntroductionMore than 93,000 cases of coronavirus disease (COVID-19) have been reported worldwide. We describe the epidemiology, clinical course, and virologic characteristics of the first 12 U.S. patients with COVID-19. MethodsWe collected demographic, exposure, and clinical information from 12 patients confirmed by CDC during January 20-February 5, 2020 to have COVID-19. Respiratory, stool, serum, and urine specimens were submitted for SARS-CoV-2 rRT-PCR testing, virus culture, and whole genome sequencing. ResultsAmong the 12 patients, median age was 53 years (range: 21-68); 8 were male, 10 had traveled to China, and two were contacts of patients in this series. Commonly reported signs and symptoms at illness onset were fever (n=7) and cough (n=8). Seven patients were hospitalized with radiographic evidence of pneumonia and demonstrated clinical or laboratory signs of worsening during the second week of illness. Three were treated with the investigational antiviral remdesivir. All patients had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset, with lowest rRT-PCR Ct values often detected in the first week. SARS-CoV-2 RNA was detected after reported symptom resolution in seven patients. SARS-CoV-2 was cultured from respiratory specimens, and SARS-CoV-2 RNA was detected in stool from 7/10 patients. ConclusionsIn 12 patients with mild to moderately severe illness, SARS-CoV-2 RNA and viable virus were detected early, and prolonged RNA detection suggests the window for diagnosis is long. Hospitalized patients showed signs of worsening in the second week after illness onset.
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Hantaan virus (HTNV) and Seoul virus (SEOV) have mainly been known as the cause of hemorrhagic fever with renal syndrome (HFRS) in Korea since HTNV has been isolated from Korean field mouse, Apodemus agrarius in 1976 and SEOV has been isolated from Rattus norvegicus in 1980. Soochong virus-1, -2, -3, -4 (SOOVs) were isolated from lung tissues of four Apodemus peninsulae captured on August 1997 at Mt. Gyebang in Hongcheon-gun, Mt. Gachil, Inje-gun, Gangwon Province, and in September 1998 at Mt. Deogyu, Muju-gun, Jeollabuk Province. Apodemus peninsulae is the second-most dominant field rodent species found throughout Korea. To determine phylogenetic analysis of SOOVs, we entirely identified nucleotide sequences of M and L segments. The length of M segment was 3,615 bp and L segment was 6,533 bp. SOOVs were diverged from HTNV by 22.7~23.3% and SEOV by 36.3~37.2%, in M segment. In addition, L segment was diverged from HTNV by 21.8~22.0% and SEOV by 30.3~30.5%. SOOVs sequence compared with Amur virus (AMRV) in M segment showed that SOOVs were different with AMRV about 14.6~16.2% in nucleotide sequences. Neighbor-joining phylogenetic analysis based on entire sequences of the M and L segment indicated that the SOOVs sequences present a separate lineage with HTNV, SEOV and AMRV. SOOVs constituted an individual cluster on the phylogenetic tree and they composed a phylogenic lineage separately. According to these data, SOOVs could be classified as a new hantavirus.
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Animales , Ratones , Ratas , Secuencia de Bases , Virus Hantaan , Orthohantavirus , Fiebre Hemorrágica con Síndrome Renal , Corea (Geográfico) , Pulmón , Murinae , Roedores , Virus SeoulRESUMEN
Apodemus agrarius, which accounts for three-fourths of the wild rodents, mainly inhabits in cultivated fields of Korea. Apodemus peninsulae and Eothenomys regulus are the second and third dominant species, respectively. Soochong virus (SOOV) from A. peninsulae and Puumala-related Muju virus (MUJV) from E. regulus were isolated in 1997 and 1998 in Korea, respectively. But serological characterizations of SOOV and MUJV were not identified clearly. Thus, in order to determine the serotypic classification, simultaneous cross-indirect immunofluorescent antibody (IFA) assay and cross-plaque reduction neutralization (PRN) test against four different hantaviruses were conducted with sera from 17 A. agrarius, 19 A. peninsulae, and 8 E. regulus strains. IFA titers of sera from A. agrarius and A. peninsulae were the highest to Hantaan virus (HTNV) and SOOV, respectively. However, most sera showed similar IFA titers to Seoul virus (SEOV). Therefore it was difficult to do serotyping using the sera from A. agrarius and A. peninsulae by IFA. In case of sera of E. regulus, IFA titers to Puumala virus (PUUV) were higher than HTNV, SOOV and SEOV. Cross-PRN result of A. agrarius to HTNV, SOOV, SEOV and PUUV was 6,890, 5,120, 110 and 30, respectively. In case of A. peninsulae, the mean PRN titer was the highest to SOOV (1:6,820) and those to HTNV, SEOV and PUUV were 1,580, 100 and 30, respectively. The mean PRN titers of E. regulus to HTNV, SOOV, SEOV and PUUV were 70, 10, 80 and 640. SOOV and MUJV could be distinguished from HTNV and SEOV by cross-PRNT. These results demonstrate that SOOV and MUJV could be classified as new serotype of hantavirus.
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Animales , Clasificación , Virus Hantaan , Orthohantavirus , Corea (Geográfico) , Murinae , Virus Puumala , Roedores , Virus Seoul , SerotipificaciónRESUMEN
This study was carried out to determine the seropositivity for Orientia tsutsugamushi infection among wild rodents captured in farms and mountains of Korea. A total 965 wild rodents of 7 species and 48 Crocidura laciura were captured in farms and mountains of 6 province during 1997~2000 in Korea. Serological evidence for O. tsutsugamushi infection was obtained using O. tsutsugamushi antigens by indirect immunofluorescent antibody technique (IFA). Four hundred eighty four Apodemus agrariusus, 246 Apodemus peninsulae, 179 Eothenomys regulus, 44 Microtus fortis, 6 Micromys minutus, 5 Mus musculus, and 1 Cricetula triton were captured in Gyeonggi, Gangwon, Chungnam, Gyeongbuk, Gyeongnam, and Jeonbuk province. Among them, 59 (12.2%) A. agrariusus, 22 (8.9%) A. peninsulae, 12 (6.7%) E. regulus, 5 (11.4%) M. fortis and 1 (16.7%) M. minutus were IF antibody positive against O. tsutsugamushi Gilliam or Karp strain.
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Animales , Ratones , Arvicolinae , Corea (Geográfico) , Murinae , Neptuno , Orientia tsutsugamushi , RoedoresRESUMEN
To investigate the seroprevalence of the Orientia tsutsugamushi infection of Apodemus peninsulae and genomic variations in O. tsutsugamushi isolates, 246 A. peninsulae were trapped in 14 mountainous areas approximately 500 meter above sea level in Korea during the period of 1997 and 2000. Seropositive rate of O. tsutsugamushi among A. peninsulae was 31.8% in Kyunggi, 8.2% in Chunbuk and 7.1% in Kangwon provinces by microimmunofluorescent test. The 56 kDa protein gene was amplified by PCR in the spleens of seropositive A. peninsulae. Two amplicons from seropositive A. peninsulae were sequenced and their phylogeny was analysed on the basis of sequence homology. The 56 kDa genes of A. peninsulae 98-12 strain and A. peninsulae 98-16 strain showed 98.7% nucleotide homology and 96.6% amino acid similarity. A. peninsulae 98-12 and A. peninsulae 98-16 strain were related to Kuroki, Boryong and Karp strains showing 93.3~92.2%, and 87.1~84.6% homologies in nucleotide and amino acids levels, respectively. In the phylogenetic analysis, A. peninsulae 98-12 and A. peninsulae 98-16 strain formed a distinct group with Boryong, Kuroki and Nishino strains and were clearly distinguished from other genetic groups. The results suggest that A. peninsulae might be an important reservoir of O. tsutsugamushi in Korea.