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

No-reference stereo image quality assessment based on joint wavelet decomposition and statistical models

The widespread use of 3D acquisition and display technologies has increased the interest of stereo image dataset in various application fields. As a result, it becomes necessary to have an efficient 3D quality assessment method to measure the human perception of stereoscopic images. While most of the state-of-the-art methods belong to the class of full-reference methods which require the original stereo images to be able to assess the quality, we propose in this paper a no-reference quality metric which does not require any information of the original stereo images. The proposed method operates in the wavelet transform domain and adopts a statistical framework to predict the quality of stereo images. More precisely, a joint wavelet decomposition is first performed on the stereo images to exploit simultaneously the intra and inter-views redundancies. A wavelet transform is also applied to their associated estimated disparity maps. Then, relevant features are extracted from the resulting wavelet subbands by resorting to appropriate statistical models. Simulations, carried out on the standard Live 3D image quality database, show that our proposed design model achieves significant improvement compared to the state-of-the-art 3D quality assessment methods

Audio-based queries for video retrieval over Java enabled mobile devices

In this paper we propose a generic framework for efficient retrieval of audiovisual media based on its audio content. This framework is implemented in a client-server architecture where the client application is developed in Java to be platform independent whereas the server application is implemented for the PC platform. The client application adapts to the characteristics of the mobile device where it runs such as screen size and commands. The entire framework is designed to take advantage of the high-level segmentation and classification of audio content to improve speed and accuracy of audio-based media retrieval. Therefore, the primary objective of this framework is to provide an adaptive basis for performing efficient video retrieval operations based on the audio content and types (i.e. speech, music, fuzzy and silence). Experimental results approve that such an audio based video retrieval scheme can be used from mobile devices to search and retrieve video clips efficiently over wireless networks. © 2006SPIE-IS&T

Video Quality Assessment Dataset for Smart Public Security Systems

Security and monitoring systems are more and more demanding in terms of quality, reliability and flexibility especially those dedicated to video surveillance. The quality of the acquired video signal strongly affects the performance of the high level tasks such as visual tracking, face detection and recognition. The design of a video quality assessment metric dedicated to this particular application requires a preliminary study on the common distortions encountered in video surveillance. To this end, we present in this paper a dataset dedicated to video quality assessment in the context of video surveillance. This database consists of a set of common distortions at different levels of annoyance. The subjective tests are performed using a classical pair comparison protocol with some new configurations. The subjective results obtained through the psycho-visual tests are analyzed and compared to some objective video quality assessment metrics. The preliminary results are encouraging and open a new framework for building smart video surveillance based security systems. Database link: https://data.mendeley.com/datasets/prf8p9rwhd/draft?a=d9646d2f-5154-4d49-8eb3-e7989187a24cVII. ACKNOWLEDGMENTS This work was made possible by NPRP grant number NPRP8-140-2-065 from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors.Scopu