Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020, in Gabon

Introduction

In December 2019, an atypical pneumonia emerged in China. A total of 44 case-patients were reported from December 31, 2019, to January 4, 2020, with an unknown etiology (https://apps.who.int/iris/handle/10665/330760). In January 2020, a 2019 novel coronavirus was identified, and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 caused an outbreak in China and rapidly spread in the whole world.¹ From January 20, 2020, the first cases were reported in North America.² In Europe on January 24, 2020, the first cases were reported by the World Health Organization (WHO).³ On March 11, the WHO declared COVID-19 a pandemic disease⁴ and reported 118,319 confirmed cases and 4292 deaths (https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf). In Central Africa, Gabon reported its first case of COVID-19 on March 12, 2020. On December 15, 2020, nearly a year after its discovery, this disease continues to rise in the world with 70 million cumulative cases and 1.6 million deaths globally since the beginning of the pandemic (https://www.who.int/publications/m/item/weekly-epidemiological-update---15-december-2020).

The literature reports that COVID-19 has an incubation period of 1–14 days and it affects both children and adults. Symptoms present in children are similar to those found in adults with an incubation period of 1–14 days; however, over 90% of affected children are asymptomatic or have no severe form of the disease.⁴ The SARS-CoV-2 virus is detected in several clinical samples, such as nasopharyngeal samples, oropharyngeal samples, sputum, saliva, serum, urine and stool.^5,6 The viral load can vary between the different clinical samples, throughout the infection after the onset of the first symptoms or could depend on the severity of the disease.^5,6 The study of the infectivity of SARS-CoV-2 includes the analysis of viral loads, the host’s immune response but also the genomic analysis of the strains circulating in order to provide a response to the pandemic and develop a vaccine candidate.^7–9

15 first mutations have been identified in the genome, particularly in the main sequence, in the genes encoding non-structural protein, the polymerase, the spike glycoprotein (S), the membrane glycoprotein, and the nucleocapsid phosphoprotein.¹⁰ The mutation D614G in the gene coding S protein could be associated with a more virulent variant leading to a higher mortality rate (http://dx.doi.org/10.1038/s10038-020-0808-9). More recently, several mutations were identified in the spike region gene in a new variant of SARS-CoV-2 in the United Kingdom and South Africa (https://www.who.int/csr/don/21-december-2020-sars-cov2-variant-united-kingdom/en/).

The first cases of COVID-19 have been widely documented in many countries. However few data are available from sub-Saharan Africa, and more particularly from Central Africa. The aim of this study is to report epidemiological and molecular data on the SARS-CoV-2 virus.

Methods

Results

Recent history of travel and context of COVID-19 screening

The surveillance of COVID-19 in Gabon revealed that more than three-quarters of positive cases (87.9%) had no recent travel history, 67 (80.7%) were in contact with confirmed cases, and 6 (7.2%) persons participated in voluntary screening (Figure 1A). The 10 (12.1%) people who had traveled from affected areas came from France (n=9) and Senegal (n=1) (Figure 1B).

Figure 1. (A-B): Context of COVID-19 screening.

A. Causes of COVID-19 screening. B. Travel history of confirmed cases.

The prevalence was similar in the three categories of confirmed cases, the contact cases (6.7%), the voluntary screening cases (6.3%) and people who reported having traveled recently (13.7%), (X²=5.07, p=0.08). All positive cases who presented themselves for voluntary screening were asymptomatic, whereas all the confirmed cases who had a recent travel history abroad had respiratory symptoms. Among the 67 contacts cases 55 were asymptomatic.

Viral load of SARS-CoV-2 in oropharyngeal and nasopharyngeal clinical samples

The viral loads in oropharyngeal samples ranged from 2.86 log₁₀ copies/mL (7.25×10³ copies/mL) to 7.51 log₁₀ copies/mL (3.21×10⁷ copies/mL) with a median of 3.96 log₁₀ copies/mL (9.13×10³ copies/mL) (Figure 2A). In the nasopharyngeal samples the viral load ranged from 2.50 log₁₀ copies/mL (3.16×10³ copies/mL) to 7.70 log₁₀ copies/mL (4.98×10⁷ copies/mL) with a median of 4.68 log₁₀ copies/mL (47.67×10³ copies/mL). The viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03) (Figure 2A).

Figure 2. (A-C): Viral load of SARS-CoV-2 in clinical samples.

A: Viral load from oropharyngeal and nasopharyngeal samples. B: Comparison of viral loads in two age groups. C: Comparison of viral loads in symptomatic and asymptomatic people.

There was no significant difference in viral loads between children under 15 years old and people over 15 years old (p=0.9895) (Figure 2B). Likewise, there was no correlation between clinical symptoms and viral loads (p=0.06042) (Figure 2C).

Discussion

Between, March 12, 2020, and April 30, 2020, 83 confirmed cases of COVID-19 were detected in Gabon. During the 50-day period, the progression of the disease was slow and comparable to the spread of COVID-19 in Nigeria during the first 45 days. However, in several countries in Africa, such as Cameroon, South Africa, Tunisia, Morocco, the burden of COVID-19 was higher, with more than 500 confirmed cases reported 35 days after the first case.¹² This difference could probably due to the population density which would be higher in these countries. Several studies which described more confirmed cases showed that more than three quarters of patients were found in the [30–79] age group.^13,14 Despite the fact that all ages were susceptible, others studies showed that the majority of cases were over 30 and more specifically between 30 and 60 years old.^14,15 The 30-years-olds in our study were one of the most represented age groups (32.4%).

More than 70% of the cases were asymptomatic in our study. Two studies which reported the first cases of COVID-19 in China and Europe mentioned that 5% of case were asymptomatic.^3,16 The proportion of asymptomatic cases varied according to the studies, values ranged from 1% to 78%^7,17,18 (http://dx.doi.org/doi:10.1136/bmj.m1375). The percentage of asymptomatic cases (73.5%) in Gabon during this period was within the range of the value reported worldwide meaning that asymptomatic carrier transmission was effective in Gabon. Moreover, there may have been presymptomatic transmission in Gabon such as the one described in Gernamy where an asymptomatic businessman from China transmitted the virus to a healthy German businessman. The Chinese visitor reportedly had symptoms of COVID-19 upon his return.¹⁹ Several reports cases have recorded similar facts and shown asymptomatic and presymptomatic transmission.^20,21 Approximately 98% of patients would had an incubation period of 5 days on average ranging from 2 to 14 days, although this period could be up to 24 days.⁴ These data could explain the spread of the virus in Gabon despite the high number of asymptomatic cases (73%).

Review authors described symptoms of COVID-19 as predominantly flu-like symptoms such as fever (80–90%), cough (50%), lethargy (20–40%) and in some cases diarrhea.⁴ In some more vulnerable patients including the elderly and people with chronic diseases, the symptoms progress to pneumonia and respiratory distress, requiring in 20% of cases hospital treatment.⁴ In addition, 80% of COVID-19 infections in China were mild flu-like symptoms.⁴ Our data corroborated those of this study. Indeed, a large number of symptomatic patients developed mild flu-like symptoms (90% of symptomatic patients) (Table 2). Only two patients had respiratory distress and 78 (94%) had no chronic disease (Table 2). However, since our data only considered the first cases in Gabon, the number of cases was low and probably underestimated.

In the 50 days following the report of the first case of COVID-19 on March 12, 2020, 87% of confirmed cases declared that they had not made a recent trip (Figure 1A), which would suggest that the virus was introduced in Gabon before March. The WHO declared the COVID-19 pandemic on March 11, 2020 meaning that a large number of countries across the African continent were affected by this period. The flow of travelers and international trade between Gabon and various affected countries would explain the introduction of the virus in Gabon. The slow spread is said to be linked to the fact that the government acted by closing borders, closing schools, quarantine of all suspected and confirmed cases and restricting movement as early as the end of March.

Some studies report a very high SARS-CoV-2 viral load in nasal swabs and others in throat swabs.⁸ We found that the viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03) (Figure 2A). Our data is similar to a study which compared the viral load in different clinical samples (saliva, spectrum, urine, nasopharyngeal and oropharyngeal samples) and showed that the viral load was the highest in the nasopharynx.⁵ One review based on seven studies measured and compared the viral load in pre-symptomatic, asymptomatic and symptomatic patients. It reported little to no difference between the SARS-CoV-2 viral load in the three categories of patients.⁸ Our results which showed no correlation between the viral load and the clinical symptom of patients are in accordance with these studies. Some studies compared the SARS-CoV-2 viral loads in patients of different age groups in order to establish a possible link between the viral load, the duration of symptoms and the age of the patients. They concluded that there was no significant difference with regard to viral load or the duration of virus detection between adults and children.⁸ The number of patients in each age group and the relationship between viral load and infectivity should be considered. Our study shows that there is no difference between patients under 15 and patients over 15 (Figure 2).

It is important to characterize the virus SAR-CoV-2 by identifying the genotype circulating in Gabon in order to set up an efficient response to this pandemic. The first SARS-CoV-2 genome of the isolate Wuhan-Hu-1 was sequenced in China (accession number NC_045512 or MN908947) in January 2020. The literature reported a frequent mutation in the S gene (position 23403A>G) coding the variant of S protein D614G¹⁰ (http://dx.doi.org/10.1038/s10038-020-0808-9). This mutation emerged in Europe and North America on January 29 and February 28, 2020 respectively.²² Initially, the D614 and G614 variants reached an equal ratio in Europe and North America at the end of February, then in March, the G614 variant started to circulate predominantly in both continents from March.²² We performed the whole genome of three of the samples from the first cases as part of a study on the genotyping of strains of SARS-CoV-2 circulating in Gabon.²³ These samples 34 (Accesion number GenBank MW512911, GISAID EPI_ISL_8886131), 56 (Accesion number GenBank MW512912, GISAID EPI_ISL_8886132) and 62 (Accesion number GenBank MW512913, GISAID EPI_ISL_8886133) belonged to lineage B.1, A, B.1.356 respectively. The introduction of lineage B was characteristic of the D614G mutation. These information corroborated that of a study which reported the emergence of the G614 variant in Africa on March 13, 2020.²² At this time, the circulation of both the D614 and G614 variants in Europe and the world suggested a simultaneous introduction of the two strains in Gabon. A Japanese study showed a significant positive correlation between the S protein 614G variant and fatality rates (http://dx.doi.org/10.1038/s10038-020-0808-9). They analyzed the frequency of mutations in the SARS-CoV-2 genome in 28 countries which they grouped into three clusters in which they show a correlation between the mutations and the fatality rate (http://dx.doi.org/10.1038/s10038-020-0808-9). The whole genome of 64 Gabonese strains of the beginning of the pandemic provided information on the predominant lineage B.1.1 (51/64) of this period.²³

In conclusion, this study reported the first data on the COVID-19 pandemic in Gabon. The data showed that most of the infected people were asymptomatic. The viral load was higher in the nasopharyngeal samples. Biochemical and immunological investigations would provide additional data and increase knowledge about the circulation and the impact of the virus in Gabon and more generally in Africa.

Data availability

BioStudies: “Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020 and molecular characterization of the spike protein, in Gabon”. Accession number S-BSST800: https://identifiers.org/biostudies:S-BSST800.

Consent

Informed consent for publication of the participants/patients’ details was obtained from the participants/patients/parents/guardian/relative of the participant/patient.’

Ethics declaration

This study was approved by the national ethics committee (N°0003/2020/CNER/SG/P) and was performed in accordance with the ethical standards of the Declaration of Helsinki of 1964. Consent was obtained before sampling.