| Literature DB >> 28709419 |
Ji Yeon Lee1, You-Jin Kim2, Eun Hee Chung3, Dae-Won Kim2, Ina Jeong1, Yeonjae Kim4, Mi-Ran Yun2, Sung Soon Kim2, Gayeon Kim5, Joon-Sung Joh6.
Abstract
BACKGROUND: In 2015, the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside the Middle East occurred in South Korea. We summarized the epidemiological, clinical, and laboratory findings of the first Korean case of MERS-CoV and analyzed whole-genome sequences of MERS-CoV derived from the patient. CASEEntities:
Keywords: Complete genome; Genetic analysis; Index case; Korea; Middle East respiratory syndrome Coronavirus
Mesh:
Substances:
Year: 2017 PMID: 28709419 PMCID: PMC5512736 DOI: 10.1186/s12879-017-2576-5
Source DB: PubMed Journal: BMC Infect Dis ISSN: 1471-2334 Impact factor: 3.090
Laboratory data for the first case of Korean Middle East Respiratory Syndrome coronavirus outbreak
| Normal range | D3 | D4 | D5 | D7 | D8 | D9 | D11 | D12 | D13 | D14 | D15 | D17 | D19 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Hemoglobin (g/dL) | 13.0 ~ 17.0 | 13.9 | 13.5 | 12.6 | 14.5 | 13.3 | 13.7 | 12.1 | 10.9 | 10.7 | 12.1 | 11.9 | 10.5 | 9.9 |
| WBC (cells /uL) | 4000 ~ 10,000 | 3900 | 2710 | 2500 | 3330 | 3220 | 3400 | 3100 | 4000 | 7500 | 8300 | 9100 | 6500 | 8100 |
| Neutrophils (%) | 50 ~ 75 | 69 | 68.4 | 56.4 | 73.3 | 75.5 | 80.4 | 77.8 | 79.5 | 89 | 87 | 88.6 | 77.2 | 77.8 |
| Lymphocytes (%) | 20 ~ 44 | 24 | 23.5 | 36.8 | 21.3 | 18.6 | 14.5 | 15.1 | 11.6 | 5 | 6 | 5.6 | 12.3 | 11.9 |
| Platelet count (103 cells /uL) | 130 ~ 400 | 111 | 98 | 139 | 140 | 160 | 168 | 142 | 114 | 56 | 81 | 122 | 162 | |
| BUN (mg/dL) | 5 ~ 20 | 11.1 | 10.5 | 8.3 | 11.1 | 9 | 9 | 8 | 8 | 12 | 14 | 19 | 31 | |
| Creatinine (mg/dL) | 0.5 ~ 1.2 | 1.1 | 0.94 | 0.98 | 0.94 | 1 | 0.8 | 0.7 | 0.9 | 0.7 | 0.7 | 0.7 | 0.8 | |
| AST (U/L) | 0 ~ 40 | 41 | 44 | 56 | 164 | 141 | 176 | 146 | 87 | 54 | 34 | 31 | 56 | 93 |
| ALT (U/L) | 0 ~ 45 | 28 | 30 | 35 | 90 | 82 | 97 | 102 | 75 | 57 | 39 | 33 | 34 | 60 |
| Albumin (g/dL) | 3.3 ~ 5.2 | 3.4 | 2.5 | 2 | 1.7 | 1.7 | 1.5 | 1.4 | 1.9 | 2.1 | ||||
| Total bilirubin (mg/dL) | 0.2 ~ 1.2 | 0.37 | 1.1 | 0.7 | 1.1 | 1.2 | 1.4 | 1.8 | 4.2 | 3.4 | 3.2 | 2.2 | ||
| C-reactive protein (mg/dL) | 0 ~ 3.0 | 7.26 | 7.26 | 7.92 | 9.1 | 8.23 | 13.9 | 9.54 |
Abbreviations: D day, WBC White blood cell count, BUN blood urea nitrogen, AST aspartate aminotransferase, ALT alanine aminotransferase
Fig. 1Imaging changes in the first case of Korean MERS-CoV infection outbreak. Panel a and b (May 15, 2015) shows diffuse ground-glass opacity infiltration and consolidation in central portion of right upper lung lobe. Panel c-g (May 16–20, 2015) shows aggravation of the multiple patchy pulmonary infiltration in right lung and left middle lung field. Panel h and i (July 3, 2015) show peribronchial infiltration and collapse consolidation of the right upper lobe and pleural effusion in right. Panel j and k (June 15, 2016) show that infiltrations in both lungs are generally improved compared to previous findings but fibrosis and distorted bronchial thickening remain in right upper lobe
Fig. 2Transmission of MERS-CoV associated with the first case of the Korean MERS-CoV infection outbreak [4, 8, 32]
Fig. 3Hospital course and treatment of the first case of the Korean MERS-CoV outbreak
Percentage identity between ORFs of the Korean strain and human MERS-CoV representative strains at the amino acid level
| Lineage | Strain | ORF1ab | S | ORF3 | ORF4a | ORF4b | ORF5 | E | M | N | ORF8b |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Outgroup | EMC/2012 | 99.6 | 99.9 | 96.1 | 99.1 | 99.6 | 100.0 | 100.0 | 99.1 | 99.8 | 99.1 |
| Lineage 1 | England-Qatar/2012 | 99.8 | 99.8 | 98.1 | 100.0 | 100.0 | 100.0 | 100.0 | 99.1 | 99.3 | 100.0 |
| MERS − CoV − Jeddah − human − 1 | 99.7 | 99.9 | 95.2 | 99.1 | 99.6 | 100.0 | 100.0 | 99.5 | 100.0 | 99.1 | |
| Lineage 2 | Al-Hasa_1_2013 | 99.8 | 99.9 | 97.1 | 99.1 | 100.0 | 100.0 | 100.0 | 99.1 | 100.0 | 100.0 |
| Abu-Dhabi_UAE_8_2014 | 99.7 | 99.8 | 98.1 | 99.1 | 100.0 | 98.7 | 100.0 | 99.1 | 99.8 | - | |
| Lineage 3 | Riyadh_2014KSA_683/KSA/2014 | 99.6 | 99.9 | 98.1 | 100.0 | 99.2 | 100.0 | 100.0 | 99.5 | 99.5 | 100.0 |
| Lineage 4 | Jeddah_C7770/KSA/2014–04-07 | 99.8 | 99.9 | 98.1 | 100.0 | 100.0 | 100.0 | 100.0 | 99.1 | 99.5 | 97.3 |
| Lineage 5 | Riyadh_KKUH_0780_20150225 | 99.9 | 99.9 | 100.0 | 99.1 | 99.2 | 99.6 | 100.0 | 100.0 | 100.0 | 100.0 |
Fig. 4The maximum likelihood tree was estimated in RAxML from the 94 MERS-CoV genome dataset. Values on branches are bootstrap values from the nucleotide. Only bootstrap values ≥70% are shown as percentages on the basis of 1000 replicates. The black dot indicates the index case. The star spot indicates the closest strain among complete genome sequences. Branch lengths are proportional to the number of substitutions per site (see scale bar). The highlighted red squares indicate the representative sequence used in the further sequence analysis. The camel MERS-CoV sequences are labeled with a camel icon
Fig. 5Phylogenetic tree and sequence alterations. The left panel shows the phylogenetic relation of eight sequences selected from each lineage which were constructed using the maximum likelihood method in MEGA6 with the following settings: GTR + I. The branches with different colors show their lineages depicted in Fig. 4. Each strain name is linked to the branch with a dotted line. The number in parentheses is the alteration count in each strain compared to the Korea index strain. The right panel shows non-synonymous (NS) single-nucleotide differences (vertical colored bars) between the Korean index genome and the representative genomes available. Mutation information is displayed as follows: change in ORF1ab (red), change in S protein (orange), change in ORF3 (yellow), change in ORF4a (green), change in ORF4b (blue), change in ORF5 (navy), change in M (purple), change in N (dark green) and change in ORF8b (sky). The asterisk indicates unique alterations in the Korean index strain
Fig. 6Root-to-tip genetic divergence plotted against the sampling date. The genetic distances from the root were calculated on the maximum likelihood phylogeny. Each y-axis value represents the genetic distance from the tip to the root, and the x-axis value represents the corresponding sampling date of the tip. The points and regression dotted line shown were obtained from the ML tree presented in Fig. 4. The R2 value is indicated above the regression line