The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Supplementary Material for: Glycolytic and Mitochondrial Metabolism in Pancreatic Islets from MSG-Treated Obese Rats Subjected to Swimming Training

<b><i>Backgrounds/Aims: </i></b>Obese rats obtained by neonatal monosodium glutamate (MSG) administration present insulin hypersecretion. The metabolic mechanism by which glucose catabolism is coupled to insulin secretion in the pancreatic β-cells from MSG-treated rats is understood. The purpose of this study was to evaluate glucose metabolism in pancreatic islets from MSG-treated rats subjected to swimming training. <b><i>Methods: </i></b>MSG-treated and control (CON) rats swam for 30 minutes (3 times/week) over a period of 10 weeks. Pancreatic islets were isolated and incubated with glucose in the presence of glycolytic or mitochondrial inhibitors. <b><i>Results: </i></b>Swimming training attenuated fat pad accumulation, avoiding changes in the plasma levels of lipids, glucose and insulin in MSG-treated rats. Adipocyte and islet hypertrophy observed in MSG-treated rats were attenuated by exercise. Pancreatic islets from MSG-treated obese rats also showed insulin hypersecretion, greater glucose transporter 2 (GLUT2) expression, increased glycolytic flux and reduced mitochondrial complex III activity. <b><i>Conclusion: </i></b>Swimming training attenuated islet hypertrophy and normalised GLUT2 expression, contributing to a reduction in the glucose responsiveness of pancreatic islets from MSG-treated rats without altering glycolytic flux. However, physical training increased the activity of mitochondrial complex III in pancreatic islets from MSG-treated rats without a subsequent increase in glucose-induced insulin secretion

Impaired Muscarinic Type 3 (m3) Receptor/pkc And Pka Pathways In Islets From Msg-obese Rats

Monosodium glutamate-obese rats are glucose intolerant and insulin resistant. Their pancreatic islets secrete more insulin at increasing glucose concentrations, despite the possible imbalance in the autonomic nervous system of these rats. Here, we investigate the involvement of the cholinergic/protein kinase (PK)-C and PKA pathways in MSG β-cell function. Male newborn Wistar rats received a subcutaneous injection of MSG (4 g/kg body weight (BW)) or hyperosmotic saline solution during the first 5 days of life. At 90 days of life, plasma parameters, islet static insulin secretion and protein expression were analyzed. Monosodium glutamate rats presented lower body weight and decreased nasoanal length, but had higher body fat depots, glucose intolerance, hyperinsulinemia and hypertrigliceridemia. Their pancreatic islets secreted more insulin in the presence of increasing glucose concentrations with no modifications in the islet-protein content of the glucose-sensing proteins: the glucose transporter (GLUT)-2 and glycokinase. However, MSG islets presented a lower secretory capacity at 40 mM K+ (P &lt; 0.05). The MSG group also released less insulin in response to 100 μM carbachol, 10 μM forskolin and 1 mM 3-isobutyl-1-methyl-xantine (P &lt; 0.05, P &lt; 0.0001 and P &lt; 0.01). These effects may be associated with a the decrease of 46 % in the acetylcholine muscarinic type 3 (M3) receptor, and a reduction of 64 % in PKCα and 36 % in PKAα protein expressions in MSG islets. Our data suggest that MSG islets, whilst showing a compensatory increase in glucose-induced insulin release, demonstrate decreased islet M3/PKC and adenylate cyclase/PKA activation, possibly predisposing these prediabetic rodents to the early development of β-cell dysfunction. © 2013 Springer Science+Business Media Dordrecht.40745214528Tengholm, A., Gylfe, E., Oscillatory control of insulin secretion (2009) Mol Cell Endocrinol, 297 (1-2), pp. 58-72. , 18706473 10.1016/j.mce.2008.07.009 1:CAS:528:DC%2BD1cXhsFajt7rNCnop, M., Welsh, N., Jonas, J.C., Jorns, A., Lenzen, S., Eizirik, D.L., Mechanisms of pancreatic beta-cell death in type 1 and type 2 diabetes: Many differences, few similarities (2005) Diabetes, 54 (SUPPL. 2), pp. 97-S107. , 16306347 10.2337/diabetes.54.suppl-2.S97 1:CAS:528:DC%2BD2MXht12gs7nFRibeiro, R.A., Santos-Silva, J.C., Vettorazzi, J.F., Cotrim, B.B., Mobiolli, D.D., Boschero, A.C., Carneiro, E.M., Taurine supplementation prevents morpho-physiological alterations in high-fat diet mice pancreatic beta-cells (2012) Amino Acids, 43 (4), pp. 1791-1801. , 22418865 10.1007/s00726-012-1263-5 1:CAS:528:DC%2BC38XhtlOls77NAhren, B., Autonomic regulation of islet hormone secretion-implications for health and disease (2000) Diabetologia, 43 (4), pp. 393-410. , 10819232 10.1007/s001250051322 1:CAS:528:DC%2BD3cXit12hsLk%3DOlney, J.W., Sharpe, L.G., Brain lesions in an infant rhesus monkey treated with monsodium glutamate (1969) Science, 166 (3903), pp. 386-388. , 5812037 10.1126/science.166.3903.386 1:CAS:528:DyaE3cXhtFSrtw%3D%3DMaiter, D., Underwood, L.E., Martin, J.B., Koenig, J.I., Neonatal treatment with monosodium glutamate: Effects of prolonged growth hormone (GH)-releasing hormone deficiency on pulsatile GH secretion and growth in female rats (1991) Endocrinology, 128 (2), pp. 1100-1106. , 1989848 10.1210/endo-128-2-1100 1:CAS:528:DyaK3MXpvFentg%3D%3DMartins, A.C., Souza, K.L., Shio, M.T., Mathias, P.C., Lelkes, P.I., Garcia, R.M., Adrenal medullary function and expression of catecholamine-synthesizing enzymes in mice with hypothalamic obesity (2004) Life Sci, 74 (26), pp. 3211-3222. , 15094322 10.1016/j.lfs.2003.10.034 1:CAS:528:DC%2BD2cXjt1Sitr0%3DBalbo, S.L., Grassiolli, S., Ribeiro, R.A., Bonfleur, M.L., Gravena, C., Brito Mdo, N., Andreazzi, A.E., Torrezan, R., Fat storage is partially dependent on vagal activity and insulin secretion of hypothalamic obese rat (2007) Endocrine, 31 (2), pp. 142-148. , 17873325 10.1007/s12020-007-0021-z 1:CAS:528:DC%2BD2sXhtVSgtb%2FOLucinei Balbo, S., Gravena, C., Bonfleur, M.L., De Freitas Mathias, P.C., Insulin secretion and acetylcholinesterase activity in monosodium l-glutamate-induced obese mice (2000) Horm Res, 54 (4), pp. 186-191. , 11416236 10.1159/000053257 1:STN:280:DC%2BD3Mzlt1SjtQ%3D%3DBalbo, S.L., Bonfleur, M.L., Carneiro, E.M., Amaral, M.E., Filiputti, E., Mathias, P.C., Parasympathetic activity changes insulin response to glucose and neurotransmitters (2002) Diabetes Metab, 28 (6 PART 2), pp. 13-17. , discussion 13S108-112Nardelli, T.R., Ribeiro, R.A., Balbo, S.L., Vanzela, E.C., Carneiro, E.M., Boschero, A.C., Bonfleur, M.L., Taurine prevents fat deposition and ameliorates plasma lipid profile in monosodium glutamate-obese rats (2011) Amino Acids, 41 (4), pp. 901-908. , 21042817 10.1007/s00726-010-0789-7 1:CAS:528:DC%2BC3MXhtFKitLbKPaes, A.M., Carniatto, S.R., Francisco, F.A., Brito, N.A., Mathias, P.C., Acetylcholinesterase activity changes on visceral organs of VMH lesion-induced obese rats (2006) Int J Neurosci, 116 (11), pp. 1295-1302. , 17000530 10.1080/00207450600920910 1:CAS:528:DC%2BD28XhtFOrsLbIMitrani, P., Srinivasan, M., Dodds, C., Patel, M.S., Autonomic involvement in the permanent metabolic programming of hyperinsulinemia in the high-carbohydrate rat model (2007) Am J Physiol Endocrinol Metab, 292 (5), pp. 1364-E1377. , 17227957 10.1152/ajpendo.00672.2006 1:CAS:528:DC%2BD2sXls1yisL8%3DScomparin, D.X., Gomes, R.M., Grassiolli, S., Rinaldi, W., Martins, A.G., De Oliveira, J.C., Gravena, C., De Freitas Mathias, P.C., Autonomic activity and glycemic homeostasis are maintained by precocious and low intensity training exercises in MSG-programmed obese mice (2009) Endocrine, 36 (3), pp. 510-517. , 19856134 10.1007/s12020-009-9263-2 1:CAS:528:DC%2BD1MXhsVaksrbEAndreazzi, A.E., Scomparin, D.X., Mesquita, F.P., Balbo, S.L., Gravena, C., De Oliveira, J.C., Rinaldi, W., Mathias, P.C., Swimming exercise at weaning improves glycemic control and inhibits the onset of monosodium l-glutamate-obesity in mice (2009) J Endocrinol, 201 (3), pp. 351-359. , 19297408 10.1677/JOE-08-0312 1:CAS:528:DC%2BD1MXntFGnsb0%3DBernardis, L.L., Patterson, B.D., Correlation between 'Lee index' and carcass fat content in weanling and adult female rats with hypothalamic lesions (1968) J Endocrinol, 40 (4), pp. 527-528. , 4868415 10.1677/joe.0.0400527 1:STN:280:DyaF1c7ptFWgsg%3D%3DRibeiro, R.A., Vanzela, E.C., Oliveira, C.A., Bonfleur, M.L., Boschero, A.C., Carneiro, E.M., Taurine supplementation: Involvement of cholinergic/phospholipase C and protein kinase A pathways in potentiation of insulin secretion and Ca 2+ handling in mouse pancreatic islets (2010) Br J Nutr, 104 (8), pp. 1148-1155. , 20591207 10.1017/S0007114510001820 1:CAS:528:DC%2BC3cXht1Oms7fPHarms, P.G., Ojeda, S.R., A rapid and simple procedure for chronic cannulation of the rat jugular vein (1974) J Appl Physiol, 36 (3), pp. 391-392. , 4814312 1:STN:280:DyaE2c7gsleltg%3D%3DBergmeyer, H.U., Bernt, E., Determination of glucose with glucose oxidase and peroxidase (1974) Methods of Enzymatic Analysis, pp. 1105-1212. , H.U. Bergeyer (eds) Verlag Chemie WeinheinBonora, E., Targher, G., Alberiche, M., Bonadonna, R.C., Saggiani, F., Zenere, M.B., Monauni, T., Muggeo, M., Homeostasis model assessment closely mirrors the glucose clamp technique in the assessment of insulin sensitivity: Studies in subjects with various degrees of glucose tolerance and insulin sensitivity (2000) Diabetes Care, 23 (1), pp. 57-63. , 10857969 10.2337/diacare.23.1.57 1:STN:280:DC%2BD3czpsVyisA%3D%3DMatthews, D.R., Hosker, J.P., Rudenski, A.S., Naylor, B.A., Treacher, D.F., Turner, R.C., Homeostasis model assessment: Insulin resistance and beta-cell function from fasting plasma glucose and insulin concentrations in man (1985) Diabetologia, 28 (7), pp. 412-419. , 3899825 10.1007/BF00280883 1:CAS:528:DyaL2MXlslKnu7k%3DStraub, S.G., Sharp, G.W., Glucose-stimulated signaling pathways in biphasic insulin secretion (2002) Diabetes Metab Res Rev, 18 (6), pp. 451-463. , 12469359 10.1002/dmrr.329 1:CAS:528:DC%2BD3sXotFensw%3D%3DGrassiolli, S., Bonfleur, M.L., Scomparin, D.X., De Freitas Mathias, P.C., Pancreatic islets from hypothalamic obese rats maintain K+ ATP channel-dependent but not-independent pathways on glucose-induced insulin release process (2006) Endocrine, 30 (2), pp. 191-196. , 17322578 10.1385/ENDO:30:2:191 1:CAS:528:DC%2BD2sXhslKjtL4%3DWu, G., Morris, Jr.S.M., Arginine metabolism: Nitric oxide and beyond (1998) Biochem J, 336 (PART 1), pp. 1-17. , 9806879 1:CAS:528:DyaK1cXotVGltrs%3DGilon, P., Henquin, J.C., Mechanisms and physiological significance of the cholinergic control of pancreatic beta-cell function (2001) Endocr Rev, 22 (5), pp. 565-604. , 11588141 10.1210/er.22.5.565 1:CAS:528:DC%2BD3MXotVWmu7o%3DGrassiolli, S., Gravena, C., De Freitas Mathias, P.C., Muscarinic M2 receptor is active on pancreatic islets from hypothalamic obese rat (2007) Eur J Pharmacol, 556 (1-3), pp. 223-228. , 17174301 10.1016/j.ejphar.2006.11.022 1:CAS:528:DC%2BD2sXls1GisA%3D%3DGautam, D., Han, S.J., Hamdan, F.F., Jeon, J., Li, B., Li, J.H., Cui, Y., Wess, J., A critical role for beta cell M3 muscarinic acetylcholine receptors in regulating insulin release and blood glucose homeostasis in vivo (2006) Cell Metab, 3 (6), pp. 449-461. , 16753580 10.1016/j.cmet.2006.04.009 1:CAS:528:DC%2BD28Xmt1eku7k%3DLeech, C.A., Castonguay, M.A., Habener, J.F., Expression of adenylyl cyclase subtypes in pancreatic beta-cells (1999) Biochem Biophys Res Commun, 254 (3), pp. 703-706. , 9920805 10.1006/bbrc.1998.9906 1:CAS:528:DyaK1MXhtVegtL4%3DDelmeire, D., Flamez, D., Hinke, S.A., Cali, J.J., Pipeleers, D., Schuit, F., Type VIII adenylyl cyclase in rat beta cells: Coincidence signal detector/generator for glucose and GLP-1 (2003) Diabetologia, 46 (10), pp. 1383-1393. , 13680124 10.1007/s00125-003-1203-8 1:CAS:528:DC%2BD3sXnvVCgurY%3DLeiser, M., Fleischer, N., CAMP-dependent phosphorylation of the cardiac-type alpha 1 subunit of the voltage-dependent Ca2+ channel in a murine pancreatic beta-cell line (1996) Diabetes, 45 (10), pp. 1412-1418. , 8826979 10.2337/diabetes.45.10.1412 1:CAS:528:DyaK28XmtFCnt74%3DSeino, S., Shibasaki, T., PKA-dependent and PKA-independent pathways for cAMP-regulated exocytosis (2005) Physiol Rev, 85 (4), pp. 1303-1342. , 16183914 10.1152/physrev.00001.2005 1:CAS:528:DC%2BD2MXhtFeqsr3LDolz, M., Bailbe, D., Giroix, M.H., Calderari, S., Gangnerau, M.N., Serradas, P., Rickenbach, K., Portha, B., Restitution of defective glucose-stimulated insulin secretion in diabetic GK rat by acetylcholine uncovers paradoxical stimulatory effect of beta-cell muscarinic receptor activation on cAMP production (2005) Diabetes, 54 (11), pp. 3229-3237. , 16249449 10.2337/diabetes.54.11.3229 1:CAS:528:DC%2BD2MXht1Shsr7OToft-Nielsen, M.B., Damholt, M.B., Madsbad, S., Hilsted, L.M., Hughes, T.E., Michelsen, B.K., Holst, J.J., Determinants of the impaired secretion of glucagon-like peptide-1 in type 2 diabetic patients (2001) J Clin Endocrinol Metab, 86 (8), pp. 3717-3723. , 11502801 10.1210/jc.86.8.3717 1:CAS:528:DC%2BD3MXlvFektLc%3DFerreira, F., Barbosa, H.C., Stoppiglia, L.F., Delghingaro-Augusto, V., Pereira, E.A., Boschero, A.C., Carneiro, E.M., Decreased insulin secretion in islets from rats fed a low protein diet is associated with a reduced PKAalpha expression (2004) J Nutr, 134 (1), pp. 63-67. , 14704294 1:CAS:528:DC%2BD2cXitlCmtA%3D%3DBonfleur, M.L., Ribeiro, R.A., Balbo, S.L., Vanzela, E.C., Carneiro, E.M., De Oliveira, H.C., Boschero, A.C., Lower expression of PKAalpha impairs insulin secretion in islets isolated from low-density lipoprotein receptor (LDLR(-/-)) knockout mice (2011) Metabolism, 60 (8), pp. 1158-1164. , 21306750 10.1016/j.metabol.2010.12.010 1:CAS:528:DC%2BC3MXptlCntb0%3DWajchenberg, B.L., Beta-cell failure in diabetes and preservation by clinical treatment (2007) Endocr Rev, 28 (2), pp. 187-218. , 17353295 10.1210/10.1210/er.2006-0038 1:CAS:528:DC%2BD2sXkvFentr0%3