Molecular diagnosis for the novel coronavirus SARS-CoV-2: lessons learnt from the Ghana experience

Background: A novel coronavirus, SARS-CoV-2 is currently causing a worldwide pandemic. The first cases of SARS-CoV-2 infection were recorded in Ghana on March 12, 2020. Since then, the country has been combatting countrywide community spread. This report describes how the Virology Department, Noguchi Memorial Institute for Medical Research (NMIMR) is supporting the Ghana Health Service (GHS) to diagnose infections with this virus in Ghana.Methods: The National Influenza Centre (NIC) in the Virology Department of the NMIMR, adopted real-time Polymerase Chain Reaction (rRT-PCR) assays for the diagnosis of the SARS-CoV-2 in January 2020. Samples from suspected cases and contact tracing across Ghana were received and processed for SARS-CoV-2. Samples were ‘pooled’ to enable simultaneous batch testing of samples without reduced sensitivity.Outcomes: From February 3 to August 21, the NMIMR processed 283 946 (10%) samples. Highest number of cases were reported in June when the GHS embarked on targeted contact tracing which led to an increase in number of samples processed daily, peaking at over 7,000 samples daily. There were several issues to overcome including rapid consumption of reagents and consumables. Testing however continued successfully due to revised procedures, additional equipment and improved pipeline of laboratory supplies. Test results are now provided within 24 to 48 hours of sample submission enabling more effective response and containment.Conclusion: Following the identification of the first cases of SARS-CoV-2infection by the NMIMR, the Institute has trained other centres and supported the ramping up of molecular testing capacity in Ghana. This provides a blueprint to enable Ghana to mitigate further epidemics and pandemics

A: Influenza A subtypes by year, season, and age.

B: Influenza B lineages by year, season, and age. (DOCX)</p

Map of Ghana showing selected influenza sentinel sites located throughout the country.

Also shown are the ecological variations of the country. Southern Ghana is green with semi-arid conditions, while Northern Ghana is dry and hot. Southern Ghana is densely populated (Accra-2,291,352) while population density in Northern Ghana is low (562,919-Tamale, Northern Region). Note: Only 19/31 sentinel sites are identified. Those located on Ghana Armed Forces military sites, with the exception of 37 Military Hospital, are not depicted for security reasons. The map was obtained from Centre for Remote Sensing and Geographical Information Services (CERSGIS). This was created using ESRI ArcMap version 10.8 with the boundaries obtained from Ghana Statistical Service (GSS).</p

Influenza positivity rates among ILI and SARI cases in Ghana by epidemiological weeks from 2011 to 2019.

Intensity thresholds were generated using the MEM web application (R version 4.2.1) and shown with dotted lines.</p

Demographic characteristics of influenza-like illness (ILI) and severe acute respiratory illness (SARI) cases in Ghana from 2011 to 2019.

Demographic characteristics of influenza-like illness (ILI) and severe acute respiratory illness (SARI) cases in Ghana from 2011 to 2019.</p

Symptom distribution of ILI and SARI cases based on influenza sub-types in Ghana.

*Pearson Chi-square test was used to obtain the p-values.</p

Distribution of influenza A subtypes and B lineages by months in Ghana from 2011 to 2019.

Influenza positivity rate and the number of influenza A subtypes and B lineages was plotted against months for SARI.</p

Bonferroni analysis.

(DOCX)</p

Distribution of influenza A subtypes and B lineages by months in Ghana from 2011 to 2019.

Influenza positivity rate and the number of influenza A subtypes and B lineages was plotted against months for ILI.</p

Influenza associated ILI and SARI by symptoms.

(DOCX)</p