Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020

Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARSCoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARSCoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22 nd , 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25 th , 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.

Development of Coronary Vasospasm during Adenosine-Stress Myocardial Perfusion CT Imaging

Adenosine is a short-acting coronary vasodilator, and it is widely used during pharmacological stress myocardial perfusion imaging. It has a well-established safety profile, and most of its side effects are known to be mild and transient. Until now, coronary vasospasm has been rarely reported as a side effect of adenosine during or after adenosine stress test. This study reports a case of coronary vasospasm which was documented on stress myocardial perfusion CT imaging during adenosine stress test.

Analysis on Quasispecies of HIV-1 env Gene by Single Clone per PCR

The human immunodeficiency viruses (HIV) exhibit tremendous genetic variability in their hosts. It is mainly due to two factors: the error-prone nature of the viral reverse transcriptase enzyme and the effects of environmental constraints such as antiviral therapy, cellular tropism, or HIV-specific immune responses. These quasispecies show fluctuation both in the overall divergence and diversity between individual sequences with different duration after primary infection. For better understand the viral quasispecies, we have performed the longitudinal genetic analysis of HIV-1 env gene V1-C5 region (1.2 kb) by two molecular cloning methods. Diversity indicated that 'single clone per PCR' value was higher than that of 'multiple clones per PCR' in subjects: 0.58-3.15 in subject 1 (P<0.05) and 0.28-2.25 in subject 2 (P<0.05). But divergence was similar in both molecular cloning methods. Phylogenetic analysis of longitudinal sequences at different sampling stages revealed the existence of different topologies individually. These data suggested that 'single clone per PCR' is more efficient than 'multiple clones per PCR' in genetic diversity analysis.

Immunodeficiency Virus Type 1 Infection of H9 Cells

Human immunodeficiency virus type 1 (HIV-1) virus causes severe defect in the immune system and affects the host cell gene expression profoundly. The gene expression pattern will be characterized by changes in cellular mRNA levels that are dependent on both the stage of infection and the biological state of the infected cells. The expression levels of 7,404 cellular RNA transcripts were assessed in H9 cells at different time points after HIV-1 IIIB infection. In total 7 time-points, 959/7,404 (13%) genes were a 2-fold or greater expressed. 387 of 959 genes (40.4%) were up-regulated, and other 572 genes (59.6%) were down-regulated. Three hundred seventeen genes were up-regulated a 2-fold or greater at 72 hr postinfection and 2 to 139 genes were up-regulated at the other time-points. In contrast, 126 to 349 genes were down-regulated a 2-fold or greater in all time-points, excepting 6 hr postinfection. Twenty-three genes were up-regulated a 2-fold or greater over at least four of seven time-points, which were mostly ribosomal proteins and MHCs. Especially, MHCs including HLA-DRA were steadily up-regulated from 24 hr postinfection. Thirty genes were down-regulated a 2-fold or greater in all the time-points, which were mainly related with synthesis and metabolism. These results show that host cell gene expression was altered by HIV-1 infection according to time-points and will provide a framework for studies on interactions between host and HIV-1 infection.

Distribution of HIV-1 Subtypes by Transmission Routes in Korea / 감염

BACKGROUND: Previous data have been reported that subtype B is prevalent in South Korea, but neither the extent nor the proportion of subtypes could be evaluated. This study was designed to analyze the distribution of HIV-1 subtypes, temporal instructions and transmission dynamics between epidemiological groups. METHODS: 1,280 Koreans had been diagnosed as HIV seropositive during the period 1985 to 2000. Among them, 134 individuals were selected for this molecular epidemiological study. 134 DNAs were isolated from uncultured or cultured peripheral blood mononuclear cells. V3-V5 (0.7 kb) fragment of HIV-1 env gene was amplified by nested polymerase chain reaction and was sequenced. RESULTS: HIV-1 isolates from thirty-seven homosexuals were all subtype B (100%). On the other hand, 66 isolates from 94 heterosexuals were subtype B (70%) and 28 were non B subtypes (30%:13 A, 4 C, 2 D, 8 E, 1 G). Only subtype B strains were isolated from 73 males who were infected with HIV inside Korea while 16 B and 20 non B subtype strains were isolated from 36 males who were HIV infected outside of Korea. However, B and non B strains were isolated half and half from females who were infected inside Korea except one. CONCLUSION: The HIV-1 subtype B strains are prevalent in Korea from the early HIV infection until present in both homo and heterosexuals. Non B strains have been transmitted from men who were infected outside Korea to their spouses and casual partners. So, we need further study to monitor subtype B and non B HIV transmission in epidemiological groups of Korea.

Analysis of Viral Phenotype (SI / NSI) and V3 Domain Amino Acid Sequence in the Various HIV - 1 Subtype Isolates

No abstract available.

Phylogenetic Analysis of env Gene V3-V5 Region of HIV-1 Subtype A Isolates from Korean

Phylogenetic analysis was conducted to monitor transmission of HIV and to investigate the genetic structure of primary isolates from 12 HIV-1 subtype A infected Koreans. The individuals infected with subtype A viruses had been diagnosed as HIV-1 seropositives during the period 1987 to 1995 and blood samples have been collected from 1991 to 1997. DNA of each individual was isolated from uncultured or cultured peripheral blood mononuclear cells. V3-V5 (0.7 kb) fragment of HIV-1 rev gene was amplified by nested polymerase chain reaction and the PCR products were sequenced. The mean value of the divergence of nucleotide of HIV-1 euv V3-V5 fragment was 17.0+/-4.06% (8.6~25.8%) within HIV-1 subtype A isolates from Koreans. This diversity was higher than those of African isolates (13.7+/-2.66%). In the phylogenetic tree, Korean subtype A isolates were not grouped together, but intermingled into African isolates. The results of this study suggested that HIV-1 subtype A variants be introduced from multiple sites of Africa into Korea and the big genetic diversity of Korea HIV-1 subtype A isolates may be further influenced by the range of geographic locations in which the infection occurred rather than the elapsed time between infection and collection of samples and the disease progression.

Phylogenetic Analysis of env Gene V3-V5 Region of HIV-1 Subtype A Isolates from Korean

Phylogenetic analysis was conducted to monitor transmission of HIV and to investigate the genetic structure of primary isolates from 12 HIV-1 subtype A infected Koreans. The individuals infected with subtype A viruses had been diagnosed as HIV-1 seropositives during the period 1987 to 1995 and blood samples have been collected from 1991 to 1997. DNA of each individual was isolated from uncultured or cultured peripheral blood mononuclear cells. V3-V5 (0.7 kb) fragment of HIV-1 rev gene was amplified by nested polymerase chain reaction and the PCR products were sequenced. The mean value of the divergence of nucleotide of HIV-1 euv V3-V5 fragment was 17.0+/-4.06% (8.6~25.8%) within HIV-1 subtype A isolates from Koreans. This diversity was higher than those of African isolates (13.7+/-2.66%). In the phylogenetic tree, Korean subtype A isolates were not grouped together, but intermingled into African isolates. The results of this study suggested that HIV-1 subtype A variants be introduced from multiple sites of Africa into Korea and the big genetic diversity of Korea HIV-1 subtype A isolates may be further influenced by the range of geographic locations in which the infection occurred rather than the elapsed time between infection and collection of samples and the disease progression.

Biological Characterization of HIV-1 Isolates from Long-term non-progressors (LTNP) and Rapid Progressors (RP) in Korea

To analyze the correlation between biological phenotypes of HIV-1 isolates and disease progression, we selected 9 long-term non-progressors (LTNP) and 12 rapid progressors (RP) from HIV-1 infected Korean. We isolated HIV-1 isolates by culture of PBMC of LTNP and RP with normal PBMC and measured HIV-1 p24 antigen production. The HIV-1 isolation rate from LTNP was 55.6% (5/9). And 4 HIV-1 LTNP isolates were non-syncytium inducing (NSI) phenotype and showed slow/low replication. The HIV-1 isolation rate from RP was 91.7% (l1/12) which was higher than that from LTNP. Besides 3 RP HIV-1 isolates which showed syncytium inducing (SI) phenotype, 8 RP HIV-1 isolates showed NSI phenotype in normal PBMC and MT-2 cell line. All RP HIV-1 isolates replicated more rapidly than LTNP HIV-1 isolates. Comparing the replication kinetics and syncytium forming capacity of HIV-1 isolates from LTNP and RP, we suggest that the difference of biological phenotype of HIV-1 isolates could be related with disease progression of HIV-1 infected persons.

HIV-1 p24 Antigen Detection by Immune Complex Dissociation and Neutralization in HIV-1 Infected Persons in Korea / 감염

BACKGROUND: HIV-1 p24 antigen assay is useful for the detection of circulating viruses, and infection prior to seroconversion. However, circulating HIV-1 p24 antigen may be complexed with HIV antibody and prevent it from being detected by antigen capture assay. To detect HIV-1 p24 antigen in the specimen, it is necessary to dissociate immune complexes and confirm the presence of HIV-1 p24 antigen after the neutralization with the specific antibody. METHODS: We tested 32 sera from HIV-1 infected persons who were diagnosed from 1987 tO1996 in Korea for HIV-1 p24 antigen by enzyme linked immunosorbent assay (ELISA.) with or without the dissociation of immune complexes. And we confirmed the antigen assay results by the neutralization with HIV-1 specific antibody as a confirmatory test. We also calculated the concentration of HIV-1 p24 antigen in each specimen. RESULTS: Eleven of 32 sera tested were initially positive for HIV-1 p24 antigen. After the dissociation of immune complexes for 29 sera except two of which signal/cutoff ratios were higher than 7.0 and except one which was not enough for the assay,13 were shown to be positive for HIV-1 p24 antigen and their signal/cutoff ratios were increased by 10 times. Five of antigen negative cases were turned to be positive after the immune complex dissociation. After neutralization with HIV-1specific p24 antibody for sera of 13 which were positive for HIV-1 p24 antigen with or without the immune complex dissociation, all were shown to be neutralized. We have observed more than 90% neutralization reduction for 12 sera and more than 50% less than 90% for one. The average concentration of HIV-1 p24 antigen was8.76pg/ml by antigen assay and was increased to 76.81~g/m~ after immune complex dissociation. CONCLUSION: We concluded that the sensitivity and the specificity of HIV-1 p24 antigen assay could be increased by dissociation of the immune complexes and neutralization with the specific antibody.

Study on the Zidovudine Resistance of HIV-1 Isolated Strains in Korea

To examine AZT resistance of HIV-1 isolates from AZT treated or untreated Korean, several biological characteristics such as syncytium formation, HIV-1 reverse transcriptase activity and the p24 antigen production in MT-2 cells infected with 4 HRT_1 isolates were determined. As controls, we tested HIV-1 HTLV-IIIB and pre-drug isolate as AZT susceptible strains, in addition to HIV-1 RTMC/MT-2 and post-drug isolate as AZT resistant strains. When the inoculum size of HIV-1 was 300 TCID50well and 100 TCID50/well, the AZT susceptibility of AZT untreated HIV-1 isolates 8806 and 9571 were similar to that of HIV-1 HTLV-IIIB and AZT-susceptible HIV-1 strains. When we evaluated AZT resistance of isolates HRs-1 8812 and 9113 treated with AZT for 36 months by observation of syncytium formation, HIV-1 8812 showed resistance simillar to that of HIV-1 RTMC/MT-2 strain forming syncytium up to AZT 1microgram/ml, and HIV-1 9113 showed resistance identical with that of AZT-resistant HIV-1 strain which formed syncytium up to AZT 10 microgram/ml. Especially, when we evaluated AZT resistance by HIV-1 reverse transcriptase activty and the p24 antigen production, HIV-1 isolates 8812 and 9113 showed much higher resistance (>10 - 200 fold) compared with HN-1 RTMC/MT-2 and AZT-resistant HIV-1 strain.

Screening of Anti-HIV-1 Activity of Natural Product by MTT Assay

Methanol and/or boiling water extraction of 201 natural products and subsequent MTT assay using MT-4 cell line was carried out to screen the anti-HIV-1 activity. Among 97 methanol extracts, 7 extracts from Chrysanthemi Indicium Flos, Magnoliae Cortex Machili Cortex, Reynoutriae Rhizoma, Lithospermi Radix Agastachis Herba, and Chaenomelis Fructus showed anti-HIV-1 activity and their SI value were 2.25 to 5.77. In addition, among 119 boiling water extracts, 10 extracts from Lonicerae Caulis et Foloium, Elsholtziae Herba, Leonuri Herba, Portulacae Herba, Schizonepetae Herba, Curcumae Rhizoma, Amomi Cardamomi Fructus, Cirsii Radix et Herba, Carpesii Herba, and Siegesbeckiae Herba showed anti-HIV-1 activity and their SI value were 1.30 to 7.64. Methanol extracts of above seven natural products were fractionated and the anti-HRs_1 activity of each fraction was examined. Extraction was carried out with hexane, chloroform, butanol, and water to trace active anti-HIV-1 componets. As a result, the water fraction of Magnoliae Cortex, Machili Cortex, Reynoutriae Rhizoma, Agastachis Herba, Chaenomelis Fructus and the butanol fraction of Chrysanthemi Indicium Flos, Reynoutriae Rhizoma showed anti-HIV-1 activity and their SI value were 1.40 to 8.02. We could reach a conclusion that studies to trace the anti-HIV-1 active component of each natural products in further Sractionation and to identify its structure by Infrared spectroscopy, NMR spectroscopy and gel permeation chromatography were needed.

Characterization of human immunodeficiency virus strains isolated in Korean

No abstract available.

Evaluation of anti-human immunodeficiency virus compounds by MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay

No abstract available.