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

Clinical Decision-Making

Eye removal surgery can be challenging clinically for the surgeon and emotionally for the patient. There are three main techniques of eye removal including evisceration (removal of the intraocular contents and cornea with retention of the patient’s sclera and natural extraocular muscle attachments), enucleation (removal of the entire globe with lysis of the natural attachments of the extraocular muscles and severing of the optic nerve proper), and exenteration (removal of the entire orbital contents, including the globe if present). The choice of technique is dependent upon the disease process being addressed and patient factors such as the condition of the native sclera, medical comorbidities, anticoagulation, and the presence and extent of traumatic damage

Optic nerve sheath fenestration: a revised lateral approach for nerve access

Idiopathic intracranial hypertension (IIH), also known as pseudotumor cerebri, describes a disease of poorly understood pathophysiology with a specific set of signs and symptoms including potentially irreversible and blinding visual loss. Optic nerve sheath fenestration (ONSF) is a well-described surgical treatment for patients with IIH and progressive visual loss despite maximally tolerated medical therapy. A number of optic nerve access procedures have been described including medial transconjunctival, superomedial lid crease, and lateral orbitotomy with and without bone takedown. The purpose of this report is to describe a revised lateral approach for temporal optic nerve access that obviates the need to traverse through the intraconal fat of the central surgical space in the previously described lateral approach techniques

Cicatricial ectropion and madarosis associated with panitumumab treatment of metastatic colorectal cancer

To report a case of cicatricial ectropion and madarosis with the use of anti-epidermal growth factor receptor medication panitumumab. An 82-year-old man with metastatic colorectal cancer presented with cicatricial ectropion and madarosis after starting panitumumab, an anti-epidermal growth factor receptor medication used to treat metastatic colorectal cancer. His findings resolved several weeks after discontinuation of panitumumab and treatment with lubrication and antibiotic/steroid ointment. This case demonstrates the importance to consider potential medication side effects when treating periocular conditions in patients taking anti-epidermal growth factor receptor (anti-EGFR) agents

Probing of the Nasolacrimal Duct

Congenital nasolacrimal duct obstructions may present with mucoid discharge, epiphora, or lacrimal swelling, and is most commonly located at the distal end of the nasolacrimal duct. Nasolacrimal duct probing may be performed to treat an obstruction after conservative measures have failed. Patients should be educated about the risks and benefits of the procedure, including alternatives

Probing of the Nasolacrimal Duct - Chapter 173

Congenital nasolacrimal duct obstructions may present with mucoid discharge, epiphora, or lacrimal swelling and is most commonly located at the distal end of the nasolacrimal duct. Nasolacrimal duct probing may be performed to treat an obstruction after conservative measures have failed. Patients should be educated about the risks and benefits of the procedure, including alternatives

Where the Lung Meets the Eye

"The cavernous sinus is an important neurovascular crossing point. Careful examination of patients presenting with multiple cranial neuropathies may suggest a lesion of this region but the differential is wide and often difficult to confirm.1 Potential infectious and inflammatory etiologies as well as local malignant invasion should be addressed. However, metastases from distant sites are more rarely seen.

Corneal perforation with uveal prolapse: An initial presentation of orbital metastatic breast cancer

Metastasis to the orbit is a rare and typically late manifestation of a systemic malignancy. Breast cancer is the most common orbital metastatic malignancy and as the prevalence of breast cancer rises, the incidence of orbital metastasis is expected to increase concomitantly. The purpose of this report is to illustrate a unique case of orbital metastatic breast cancer with grave ophthalmic sequelae and to review the salient findings and features of orbital metastatic disease. Herein, we describe the case of a 61-year-old woman with no known history of malignancy who presented with a large compressive orbital mass that resulted in corneal perforation with uveal prolapse after initial treatment for orbital cellulitis followed by orbital pseudotumor. Anterior orbitotomy with biopsy of the mass ultimately revealed a diagnosis of metastatic breast carcinoma. As the incidence of breast cancer increases, ophthalmologists will play an increasingly important role in detecting both undiagnosed and recurrent breast cancer