Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020

Abstract

In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.

Keywords: HCoV-229E; HCoV-HKU1; HCoV-NL63; HCoV-OC43; ILI; SARI; coronavirus characterization; epidemiology; human coronaviruses; respiratory infections.

Figure 1

Annual trends in HcoV positivity rates (positives/samples tested), 2012–2020.

Figure 2

Temporal distribution of the HCoV detections among patients with an influenza-like illness, by month and year.

Figure 3

Phylogenetic analyses of HCoV-OC43 (A) and HCoV-229E (B) strains detected in patients with ILI/SARI, between 2012 to 2020, in Senegal. The phylogenetic trees are based on nucleotide sequences of the spike protein gene generated using the maximum likelihood tree with the Tamura–Nei evolutionary model, as implemented in MEGA 7 software. One thousand bootstrap replicates were performed to determine the consensus tree presented in this figure, and support for the nodes present in greater than 70% of the trees are annotated. Senegalese strains are represented in black dots.

Figure 4

Phylogenetic analyses of HCoV-HKU1 (A) and HCoV-NL63 (B) strains detected in patients with ILI/SARI, between 2012 to 2020, in Senegal. The phylogenetic trees are based on the nucleotide sequences of the spike protein gene generated using the maximum likelihood tree with the Tamura–Nei evolutionary model, as implemented in MEGA 7 software. One thousand bootstrap replicates were performed to determine the consensus tree presented in this figure, and support for nodes present in greater than 70% of the trees are annotated. Senegalese strains are represented in black dots.