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

Power Backoff Reduction Techniques for Generalized Multicarrier Waveforms

Amplification of generalized multicarrier (GMC) signals by high-power amplifiers (HPAs) before transmission can result in undesirable out-of-band spectral components, necessitating power backoff, and low HPA efficiency. We evaluate variations of several peak-to-average power ratio (PAPR) reduction and HPA linearization techniques which were previously proposed for OFDM signals. Our main emphasis is on their applicability to the more general class of GMC signals, including serial modulation and DFT-precoded OFDM. Required power backoff is shown to depend on the type of signal transmitted, the specific HPA nonlinearity characteristic, and the spectrum mask which is imposed to limit adjacent channel interference. PAPR reduction and HPA linearization techniques are shown to be very effective when combined

Suppression of intermittent interference using smart antenna with distributed training scheme

In this paper, an adaptive antenna arrays processing based on Sample Matrix Inversion (SMI) algorithm with a novel training scheme is presented. The training scheme used is known as distributed training scheme [1]. The scheme uses distributed placement of the training symbols throughout the packet. The channel estimation, along with this particular training scheme, is designed to track intermittent interference. This type of interference arises due to an uncontrolled and unpredictable environment such as that of a license-exempted case. In this work, we show the comparison between the performance of distributed scheme with pre-amble training method and also with some iterative based adaptation algorithms like LMS and CMA. A lower bound theoretical analysis is made to compare its result to the simulation results. Moreover, analytical expression for the excess MSE are derived for both distributed and preamble training schemes. Short blocks scenario for the creation of intermittent interference is created by using a batch Poisson traffic model

Iterative frequency domain channel estimation for DFT-precoded OFDM systems using in-band pilots

We consider two techniques of in-band frequency domain multiplexed (FDM) pilots using interleaved frequency domain multiple access (IFDMA) signal with a Chu sequence for DFT-precoded OFDM (or single-carrier (SC)) systems. One, called frequency domain superimposed pilot technique (FDSPT), superimposes pilot tones onto scaled or deleted data tones, which preserves spectral efficiency at the expense of a slight performance loss. The other, called frequency expanding technique (FET), multiplexes pilot tones by displacing data tones, which slightly reduces spectral efficiency. Using FDM pilots in SC systems facilitates flexible and efficient assignment of signals to available spectrum. We propose an iterative frequency domain decision-directed interference cancellation technique to reduce the intersymbol interference level of SC signals with FDSPT pilots (resulting from the suppression of data tones). Moreover, we propose a low complexity frequency domain iterative decisiondirected channel estimation (IDDCE) technique for SC systems using FDM pilots. Using IDDCE, the frame error rate (FER) performance for coded SC systems using FET and FDSPT pilots with interference cancellation is found to be about 0.2 dB and about 0.5 dB, respectively, away from the FER performance with known channel frequency response at FER=10-2. FDSPT pilots can also be used for OFDM systems with channel coding. It is found that an extra 1 dB of SNR is required at FER=10-2, compared with that using the conventional FET pilots for OFDM systems