Epidemiology characteristics of human coronaviruses in patients with respiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou

Abstract

Human coronavirus (HCoV) is one of the most common causes of respiratory tract infection throughout the world. To investigate the epidemiological and genetic variation of HCoV in Guangzhou, south China, we collected totally 13048 throat and nasal swab specimens from adults and children with fever and acute upper respiratory infection symptoms in Gunazhou, south China between July 2010 and June 2015, and the epidemiological features of HCoV and its species were studied. Specimens were screened for HCoV by real-time RT-PCR, and 7 other common respiratory viruses were tested simultaneously by PCR or real-time PCR. HCoV was detected in 294 cases (2.25%) of the 13048 samples, with most of them inpatients (251 cases, 85.4% of HCoV positive cases) and young children not in nursery (53.06%, 156 out of 294 HCoV positive cases). Four HCoVs, as OC43, 229E, NL63 and HKU1 were detected prevalent during 2010-2015 in Guangzhou, and among the HCoV positive cases, 60.20% were OC43, 16.67% were 229E, 14.97% were NL63 and 7.82% were HKU1. The month distribution showed that totally HCoV was prevalent in winter, but differences existed in different species. The 5 year distribution of HCoV showed a peak-valley distribution trend, with the detection rate higher in 2011 and 2013 whereas lower in 2010, 2012 and 2014. The age distribution revealed that children (especially those <3 years old) and old people (>50 years) were both high risk groups to be infected by HCoV. Of the 294 HCoV positive patients, 34.69% (101 cases) were co-infected by other common respiratory viruses, and influenza virus was the most common co-infecting virus (30/101, 29.70%). Fifteen HCoV-OC43 positive samples of 2013-2014 were selected for S gene sequencing and phylogenetic analysis, and the results showed that the 15 strains could be divided into 2 clusters in the phylogenetic tree, 12 strains of which formed a separate cluster that was closer to genotype G found in Malaysia. It was revealed for the first time that genotype B and genotype G of HCoV-OC43 co-circulated and the newly defined genotype G was epidemic as a dominant genotype during 2013-2014 in Guanzhou, south China.

Fig 1. Monthly distribution of human coronavirus (HCoV) and other 7 common respiratory viruses from 13048 patients with acute respiratory infection symptoms in Guangzhou from July 2010 to June 2015.

Virus-positive patient number of each month and the monthly detection rate (% of monthly detected cases) were shown. (A) influenza virus (Flu) type A and type B; (B) respiratory syncytial virus (RSV) type A and type B; (C) parainfluenza virus (PIV) type1-3; (D) adenovirus (ADV); (E) human metapneumovirus (HMPV); (F) human rhinovirus (HRV); (G) human bocavirus (HBoV); (H) human coronavirus (HCoV).

Fig 2. Age distribution of human coronavirus (HCoV) and other 7 common respiratory viruses from 13048 patients with acute respiratory infection symptoms in Guangzhou from July 2010 to June 2015.

The number of virus-positive patients in different age groups, and the corresponding detection rate (% of detected cases in corresponding age group) were shown. (A) influenza virus (Flu) type A and type B; (B) respiratory syncytial virus (RSV) type A and type B; (C) parainfluenza virus (PIV) type1- 3; (D) adenovirus (ADV); (E) human metapneumovirus (HMPV); (F) human rhinovirus (HRV); (G) human bocavirus (HBoV); (H) human coronavirus (HCoV).

Fig 3. Monthly distributions of HCoV and its species from 13048 patients with acute respiratory infection symptoms in Guangzhou during 2010–2015.

Four HCoV species (229E, OC43, NL63 and HKU1) were detected in Guangzhou during 2010–2015. The number of positive patients and the monthly detection rate (% of monthly detected cases) of total human coronavirus (HCoV) and the four detected HCoV species were shown. (A) the monthly detection rate (%) of total human coronavirus (HCoV) and the four detected HCoV species; (B)-(E) HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 positive case number of each month and the monthly detection rate.

Fig 4. Year distributions of HCoV and its species from 13048 patients with acute respiratory infection symptoms in Guangzhou from July 2010 to June 2015.

The number of positive patients and the detection rate (% of detected cases in the corresponding year) were shown. The time span of the year on x-axis referred to a 12 months span from July of corresponding year to June of the next year. (A)-(E) total HCoV, HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 positive case number and the detection rate of each year during 2010–2015.

Fig 5. Age distribution of HCoV and its species from 13048 patients with acute respiratory infection symptoms in Guangzhou during 2010–2015.

The number of positive patients in different age groups and the corresponding detection rate (% of detected cases in corresponding age group) were shown. (A) the detection rate (%) of total human coronavirus (HCoV) and the four detected HCoV species in different age groups; (B)-(E) HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 positive case number and detection rate in different age groups.

Fig 6. Phylogenetic analysis of 15 HCoV-OC43 strains detected in Guangzhou from 2013–2014 based on partial S gene sequence.

Phylogenetic tree with 1,000 bootstrap replicates was generated using the neighbor-joining method with Mega 5.0 software. Trees were constructed using the maximum-likelihood method based on sequences of partial S genes of 2524nt. (A) Phylogenetic analysis of 15 HCoV-OC43 strains detected in Guangzhou from 2013–2014. Partial S gene sequences of 15 strains (labeled with red triangle) were comparatively analyzed with reference sequences of 33 representative HCoV-OC43 strains in the GenBank database. The 15 strains could be divided into 2 clusters. (B) Genotype analysis of the 15 strains identified in this study (presented with red circle). A, B, C, D, E, F and G represent known genotypes of OC43. Of the 15 OC43 Guangzhou strains from 2013–2014, 3 strains were closer to genotype B, whereas the other 12 strains were closer to the new genotype G.