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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Plasmonic nanoantennas on VO₂ films for active switching of near-field intensity and radiation from nanoemitters

In this paper, we propose novel plasmonic switches based on plasmonic nanoantennas lying on top of a thin film of a phase change material such as vanadium dioxide (VO2), such that the near-field properties of these nanoantennas can be actively switched by varying the phase of the VO2 film. We employ finite difference time domain (FDTD) simulations to first demonstrate that the near-field intensity in the vicinity of the plasmonic nanoantennas can be substantially switched by changing the phase of the vanadium dioxide film from the semiconductor state to the metallic state. We demonstrate that a ring-bowtie nanoantenna (RBN) switch can switch the near-field intensity by ∼ 59.5 times and ring-rhombus nanoantenna (RRN) switch can switch the near-field intensity by a factor of ∼ 80.8. These values of the maximum intensity switching ratios are substantially higher than those previously reported in the literature. In addition, we optimize the various geometrical parameters of the plasmonic switches to maximize the intensity switching ratio and to understand how the different parameters affect the performance of the plasmonic switches. In this paper, we also show that the intensity of emission from a nanoemitter placed in the gap between the two arms of a plasmonic nanoantenna can be significantly switched by changing the phase of the VO2 film between its semiconductor state and the metallic state. To quantify the switching of emission from the nanoemitters placed in the near-field of the nanoantennas, we define and calculate a parameter, called FESR, the ratio of fluorescent enhancement factors in the on-state and off-state of the plasmonic switch. The maximum fluorescence enhancement switching ratio (FESR) of ∼ 163 is obtained for the RBN switch and FESR of ∼ 200 is obtained for RRN switch. The plasmonic switches being proposed by us can be easily fabricated by employing the conventional nanofabrication and thin film deposition processes.</jats:p

Dynamics of Vaginal Microbiota During Estrous Cycle in Cows through Metagenomic Approach

Abstract Background: Using 16s rRNA sequencing of the V3-V4 hypervariable region, the present study is aimed to check vaginal microbiota diversity throughout different stages of the estrous cycle, with attention to hormonal changes and microorganism diversity. Metagenomic research was conducted on vaginal swab samples obtained from healthy cows' at different stages of the estrous cycle. Results: Total sixteen cows were synchronized with dobble PG regime. Nine cows demonstrated estrus within 96 hours and were eligible for the experiment. Vaginal samples for metagenomics and blood samples for hormonal analysis were collected during estrus, metestrus, diestrus and proestrus of synchronized Estrous cycle. The study's findings revealed that the diestrus phase has a different diversity than the other three estrous cycle phases, implying that hormones affect bacterial diversity. Proteobacteria and Firmicutes are the most abundant phyla at the phylum level, accounting for 94 % of bacterial diversity. Actinobacteriota, Patescibacteria, Cyanobacteria, Bacteroidota, and others are fewer common phyla. Proteobacteria are most common throughout the estrus, metestrus, and proestrus stages of the estrous cycle at the phylum level, there was no discernible distinction between the follicular and luteal phases. After statistical correction, Bacillaceae, Alcaligenes, and Enterobacteriaceae &amp; Morganellacea families are more significant. At the diestrus stage, the Family Enterobacteriaceae is lower than at other stages; otherwise, all statistically significant genera are high at diestrus stages. The luteal phase had higher levels of Micrococcus, Stenotrophomonas, UGC-010, Massilia, and Methylobacillus than the follicular phase, however, statistical analysis revealed no substantial difference between the two phases. Lactobacillus genus is present on two samples including the estrus stage and diestrus stages. Conclusions: This study represents an important step towards the understanding of microbial diversity within different stages of the estrous cycle of the dairy cow. The study results revealed dynamics of metabiota during estrous cycle.</jats:p

Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology

Humanity has seen numerous pandemics during its course of evolution. The list includes several incidents from the past, such as measles, Ebola, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS), etc. The latest edition to this is coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of August 18, 2020, COVID-19 has affected over 21 million people from 180 + countries with 0.7 million deaths across the globe. Genomic technologies have enabled us to understand the genomic constitution of pathogens, their virulence, evolution, and rate of mutation, etc. To date, more than 83,000 viral genomes have been deposited in public repositories, such as GISAID and NCBI. While we are writing this, India is the third most affected country by COVID-19, with 2.7 million cases and &amp;gt; 53,000 deaths. Gujarat is the 11th highest affected state with a 3.48% death rate compared to the national average of 1.91%. In this study, a total of 502 SARS-CoV-2 genomes from Gujarat were sequenced and analyzed to understand its phylogenetic distribution and variants against global and national sequences. Further variants were analyzed from diseased and recovered patients from Gujarat and the world to understand its role in pathogenesis. Among the missense mutations present in the Gujarat SARS-CoV-2 genomes, C28854T (Ser194Leu) had an allele frequency of 47.62 and 7.25% in deceased patients from the Gujarat and global datasets, respectively. In contrast, the allele frequency of 35.16 and 3.20% was observed in recovered patients from the Gujarat and global datasets, respectively. It is a deleterious mutation present in the nucleocapsid (N) gene and is significantly associated with mortality in Gujarat patients with a p-value of 0.067 and in the global dataset with a p-value of 0.000924. The other deleterious variant identified in deceased patients from Gujarat (p-value of 0.355) and the world (p-value of 2.43E-06) is G25563T, which is located in Orf3a and plays a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct clusters under the GH clade of GISAID. This study will shed light on the viral haplotype in SARS-CoV-2 samples from Gujarat, India.</jats:p

Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology

AbstractHumanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and &gt;18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent.Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID.</jats:p