Africa’s response to the COVID-19 pandemic : A review of the nature of the virus, impacts and implications for preparedness

Background: COVID-19 continues to wreak havoc in different countries across the world, claiming thousands of lives, increasing morbidity and disrupting lifestyles. The global scientific community is in urgent need of relevant evidence, to understand the challenges and knowledge gaps, as well as the opportunities to contain the spread of the virus. Considering the unique socio-economic, demographic, political, ecological and climatic contexts in Africa, the responses which may prove to be successful in other regions may not be appropriate on the continent. This paper aims to provide insight for scientists, policy makers and international agencies to contain the virus and to mitigate its impact at all levels. Methods: The Affiliates of the African Academy of Sciences (AAS), came together to synthesize the current evidence, identify the challenges and opportunities to enhance the understanding of the disease. We assess the potential impact of this pandemic and the unique challenges of the disease on African nations. We examine the state of Africa’s preparedness and make recommendations for steps needed to win the war against this pandemic and combat potential resurgence. Results: We identified gaps and opportunities among cross-cutting issueswhich must be addressed or harnessed in this pandemic. Factors such as the nature of the virus and the opportunities for drug targeting, point of care diagnostics, health surveillance systems, food security, mental health, xenophobia and gender-based violence, shelter for the homeless, water and sanitation, telecommunications challenges, domestic regional coordination and financing. Conclusion: Based on our synthesis of the current evidence, while there are plans for preparedness in several African countries, there are significant limitations. A multi-sectoral efforts from the science, education, medical, technology, communication, business, and industry sectors, as well as local communities, must work collaboratively to assist countries in order to win this fight

Molecular type distribution and fluconazole susceptibility of clinical Cryptococcus gattii isolates from South African laboratory-based surveillance, 2005–2013

Como es el caso a nivel mundial, Cryptococcus gattii es una causa menos frecuente de criptococosis que Cryptococcus neoformans en Sudáfrica. Realizamos tipificación de secuencias multilocus (MLST) y pruebas de susceptibilidad a fluconazol de 146 aislamientos seleccionados al azar de 750 Pacientes sudafricanos con enfermedad por C. gattii identificados mediante vigilancia de laboratorio mejorada, de 2005 a 2013. El tipo molecular dominante fue VGIV (101/146, 70 %), seguido de VGI (40/146, 27%), VGII (3/146, 2%) y VGIII (2/146, 1%). Entre los 146 aislamientos de C. gattii, se identificaron 99 tipos de secuencia (ST) diferentes, con ST294 (14/146, 10 %) y ST155 (10/146, 7%) siendo el más comúnmente observado. Los valores de CIM50 y CIM90 de fluconazol de 105 (de 146) aislados de C. gattii seleccionados al azar fueron de 4 μg/ml y 16 μg/ml, respectivamente. Los aislamientos VGIV tenían un valor MIC50 más bajo en comparación con los aislamientos no VGIV, pero estos los valores estaban dentro de una dilución doble uno del otro. Los pacientes seropositivos para el VIH tenían una probabilidad ajustada diez veces mayor de una infección por VGIV en comparación con los pacientes seronegativos para el VIH. aunque con números pequeños (99/136; 73% vs. 2/10; 20%), el intervalo de confianza (IC) fue ancho (IC 95%: 1,93-55,31, p = 0,006). La filogenia del genoma completo de 98 aislamientos del tipo molecular más prevalente de Sudáfrica, VGIV, identificó que este tipo molecular es altamente diversos, con dos grupos interesantes de diez y seis aislamientos estrechamente relacionados identificados respectivamente. Uno de estos grupos consistía únicamente en pacientes de la provincia de Mpumalanga en Sudáfrica, lo que sugiere una fuente ambiental similar. Este estudio aportó nuevos conocimientos sobre la estructura de la población mundial de este importante patógeno humano.As is the case globally, Cryptococcus gattii is a less frequent cause of cryptococcosis than Cryptococcus neoformans in South Africa. We performed multilocus sequence typing (MLST) and fluconazole susceptibility testing of 146 isolates randomly selected from 750 South African patients with C. gattii disease identified through enhanced laboratory surveil lance, 2005 to 2013. The dominant molecular type was VGIV (101/146, 70%), followed by VGI (40/146, 27%), VGII (3/146, 2%) and VGIII (2/146, 1%). Among the 146 C. gattii iso lates, 99 different sequence types (STs) were identified, with ST294 (14/146, 10%) and ST155 (10/146, 7%) being most commonly observed. The fluconazole MIC50 and MIC90 val ues of 105 (of 146) randomly selected C. gattii isolates were 4 μg/ml and 16 μg/ml, respec tively. VGIV isolates had a lower MIC50 value compared to non-VGIV isolates, but these values were within one double-dilution of each other. HIV-seropositive patients had a ten fold increased adjusted odds of a VGIV infection compared to HIV-seronegative patients, though with small numbers (99/136; 73% vs. 2/10; 20%), the confidence interval (CI) was wide (95% CI: 1.93–55.31, p = 0.006). Whole genome phylogeny of 98 isolates of South Afri ca’s most prevalent molecular type, VGIV, identified that this molecular type is highly diverse, with two interesting clusters of ten and six closely related isolates being identified respectively. One of these clusters consisted only of patients from the Mpumalanga Prov ince in South Africa, suggesting a similar environmental source. This study contributed new insights into the global population structure of this important human pathogen

Molecular type distribution and fluconazole susceptibility of clinical Cryptococcus gattii isolates from South African laboratory-based surveillance, 2005-2013.

As is the case globally, Cryptococcus gattii is a less frequent cause of cryptococcosis than Cryptococcus neoformans in South Africa. We performed multilocus sequence typing (MLST) and fluconazole susceptibility testing of 146 isolates randomly selected from 750 South African patients with C. gattii disease identified through enhanced laboratory surveillance, 2005 to 2013. The dominant molecular type was VGIV (101/146, 70%), followed by VGI (40/146, 27%), VGII (3/146, 2%) and VGIII (2/146, 1%). Among the 146 C. gattii isolates, 99 different sequence types (STs) were identified, with ST294 (14/146, 10%) and ST155 (10/146, 7%) being most commonly observed. The fluconazole MIC50 and MIC90 values of 105 (of 146) randomly selected C. gattii isolates were 4 μg/ml and 16 μg/ml, respectively. VGIV isolates had a lower MIC50 value compared to non-VGIV isolates, but these values were within one double-dilution of each other. HIV-seropositive patients had a ten-fold increased adjusted odds of a VGIV infection compared to HIV-seronegative patients, though with small numbers (99/136; 73% vs. 2/10; 20%), the confidence interval (CI) was wide (95% CI: 1.93-55.31, p = 0.006). Whole genome phylogeny of 98 isolates of South Africa's most prevalent molecular type, VGIV, identified that this molecular type is highly diverse, with two interesting clusters of ten and six closely related isolates being identified, respectively. One of these clusters consisted only of patients from the Mpumalanga Province in South Africa, suggesting a similar environmental source. This study contributed new insights into the global population structure of this important human pathogen

Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009

In South Africa, Cryptococcus neoformans is the most common cause of adult meningitis. We performed multi locus sequence typing and fluconazole susceptibility testing of clinical C. neoformans isolates collected from 251 South African patients with cryptococcosis through national surveillance from 2005 to 2009. We examined the association between clinical characteristics of patients and genotype, and the effect of genotype on in-hospital mortality. We performed whole genome phylogenetic analysis of fifteen C. neoformans isolates with the molecular type VNB and tested their virulence in a Galleria mellonella model. Most isolates had the molecular type VNI (206/251, 82%), followed by VNII (25/251, 10%), VNB (15/251, 6%), and VNIV (5/251, 2%); 67 sequence types were identified. There were no differences in fluconazole minimum inhibitory concentration (MIC) values among molecular types and the majority of strains had low MIC values (MIC50 of 1 µg/mL and MIC90 of 4 µg/mL). Males were almost twice as likely of being infected with a non-VNI genotype (adjusted odds ratio [OR]: 1.65, 95% confidence interval [CI]: 0.25–10.99; p = 0.61). Compared to patients infected with a VNI genotype, those with a non-VNI genotype had a 50% reduced adjusted odds of dying in hospital (95% CI: 0.03–7.57; p = 0.62). However, for both these analyses, our estimates had wide confidence intervals spanning 1 with large p-values. Fifteen VNB strains were not as virulent in a G. mellonella larval model as the H99 reference strain. A majority of these VNB strains belonged to the VNBII clade and were very closely related by phylogenetic analysis