Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia

Abstract

Background: Recently, we described the discovery of a novel group 2 coronavirus, coronavirus HKU1 (CoV-HKU1), from a patient with pneumonia. However, the clinical and molecular epidemiological features of CoV-HKU1-associated pneumonia are unknown.

Methods: Prospectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. The epidemiological, clinical, and laboratory characteristics of patients with CoV-HKU1-associated pneumonia were analyzed. The pol, spike (S), and nucleocapsid (N) genes were also sequenced.

Results: NPAs from 10 (2.4%) of 418 patients with community-acquired pneumonia were found to be positive for CoV-HKU1. All 10 cases occurred in spring and winter. Nine of these patients were adults, and 4 had underlying diseases of the respiratory tract. In the 6 patients from whom serum samples were available, all had a 4-fold change in immunoglobulin (Ig) G titer and/or presence of IgM against CoV-HKU1. The 2 patients who died had significantly lower hemoglobin levels, monocyte counts, albumin levels, and oxygen saturation levels on admission and had more-extensive involvement visible on chest radiographs. Sequence analysis of the pol, S, and N genes revealed 2 genotypes of CoV-HKU1.

Conclusions: CoV-HKU1 accounts for 2.4% of community-acquired pneumonia, with 2 genotypes in the study population. Without performance of diagnostic tests, the illness was clinically indistinguishable from other community-acquired pneumonia illnesses.

Table 1

Primers used for amplification and sequencing of the pol, spike (S), and nucleocapsid (N) genes

Figure 1

Phylogenetic tree of pol gene sequences of the 10 coronavirus HKU1 (CoV-HKU1) specimens from patients with community-acquired pneumonia. The tree was inferred from pol gene data by the neighbor-joining method, and bootstrap values were calculated from 1000 trees. The tree was rooted using the pol gene sequence of human coronavirus 229E (HCoV-229E), and 393 nt positions (primer sequences excluded) in each pol gene were included in the analysis. The scale bar indicates the estimated no. of substitutions per 50 bases using the Jukes-Cantor correction. BCoV, bovine coronavirus; HCoV-OC43, human coronavirus OC43; MHV, murine hepatitis virus; PHEV, porcine hemagglutinating encephalomyelitis virus

Table 2

Epidemiological, clinical, and radiological characteristics of patients with community-acquired pneumonia associated with coronavirus HKU1

Table 3

Comparison of clinical, laboratory, and radiological characteristics of patients with coronavirus HKU1 (CoV-HKU1)–associated pneumonia and those of age- and sex-matched controls with non–CoV-HKU1–associated pneumonia

Figure 2

Chest radiographs of the 2 patients who died of coronavirus HKU1–associated community-acquired pneumonia. The chest radiograph of the first patient (A) (patient 2 in table 2) showed patchy airspace shadows in both lungs, with predominant involvement of the lower zones. The chest radiograph of the second patient (B) (patient 10 in table 2), with Luque instrumentation in situ, showed extensive airspace shadows in both lungs, with the middle zones more severely involved

Table 4

Comparison of clinical, laboratory, and radiological characteristics of patients who survived and those who died of coronavirus HKU1–associated pneumonia

Figure 3

Phylogenetic trees and nonsynonymous mutations and corresponding amino acid changes of complete pol spike (S), and nucleocapsid (N) gene sequences of coronavirus HKU1 (CoV-HKU1) specimens from 9 patients with community-acquired pneumonia. The trees were inferred from pol (3A), S (3B), and N (3C) gene data by the neighbor-joining method, and bootstrap values were calculated from 1000 trees. The trees were rooted using pol S, and N gene sequences of human coronavirus OC43 (HCoV-OC43). A total of 2784 nt positions in each pol gene, 4071 nt positions in each S gene, and 1326 nt positions in each N gene were included in the analysis. The scale bar indicates the estimated no. of substitutions per 100 (A) and 50 (B and C) bases, using the Jukes-Cantor correction. The shaded nucleotides are those that differ from the majority at the corresponding location. Because of the large no. of nonsynonymous mutations in the S gene, only the NH₂ terminal 45, of a total of 306 nonsynonymous mutations, is shown

Figure 4

Distribution of nonsynonymous mutations in the spike (S) gene of coronavirus HKU1 (CoV-HKU1). The S protein (1356 aa) of CoV-HKU1 is depicted by the horizontal bar, and the positions of the nonsynonymous mutations are depicted by vertical lines in the bar. HR1, heptad repeat 1 (aa 982–1083); HR2, heptad repeat 2 (aa 1250–1297); SS, N terminal signal sequence (aa 1–13); TM, transmembrane domain (aa 1301–1323)