Co-infection with SARS-CoV-2 omicron BA.1 and BA.2 subvariants in a non-vaccinated woman

Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples

Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.

SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing

Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.

A spike-trimer protein-based tetravalent COVID-19 vaccine elicits enhanced breadth of neutralization against SARS-CoV-2 Omicron subvariants and other variants

Multivalent vaccines combining crucial mutations from phylogenetically divergent variants could be an effective approach to defend against existing and future SARS-CoV-2 variants. In this study, we developed a tetravalent COVID-19 vaccine SCTV01E, based on the trimeric Spike protein of SARS-CoV-2 variants Alpha, Beta, Delta, and Omicron BA.1, with a squalene-based oil-in-water adjuvant SCT-VA02B. In the immunogenicity studies in naïve BALB/c and C57BL/6J mice, SCTV01E exhibited the most favorable immunogenic characteristics to induce balanced and broad-spectrum neutralizing potencies against pre-Omicron variants (D614G, Alpha, Beta, and Delta) and newly emerging Omicron subvariants (BA.1, BA.1.1, BA.2, BA.3, and BA.4/5). Booster studies in C57BL/6J mice previously immunized with D614G monovalent vaccine demonstrated superior neutralizing capacities of SCTV01E against Omicron subvariants, compared with the D614G booster regimen. Furthermore, SCTV01E vaccination elicited naïve and central memory T cell responses to SARS-CoV-2 ancestral strain and Omicron spike peptides. Together, our comprehensive immunogenicity evaluation results indicate that SCTV01E could become an important COVID-19 vaccine platform to combat surging infections caused by the highly immune evasive BA.4/5 variants. SCTV01E is currently being studied in a head-to-head immunogenicity comparison phase 3 clinical study with inactivated and mRNA vaccines (NCT05323461).

Dynamics of parasite growth in genetically diverse Plasmodium falciparum isolates

Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal isolates, we measured growth rates (GRs) of three Plasmodium falciparum Cambodian isolates, including IPC_3445 (MRA-1236), IPC_5202 (MRA-1240), IPC_6403 (MRA-1285), and parasite lineages previously cloned from each of these isolates by limiting dilution. Following synchronization, in vitro cultures of each parasite line were maintained over four consecutive asexual cycles (192 h), with thin smears prepared at each 48-h cycle to estimate GR and fold change in parasitemia (FCP). Cell cycle time (CCT), the duration it takes for ring-stage parasites to develop into mature schizonts, was measured by monitoring the development of 0-3-h post-invasion rings for up to 52 h post-incubation. Laboratory lines 3D7 (MRA-102) and Dd2 (MRA-150) were used as controls. Significant differences in GR, FCP, and CCT were observed between parasite isolates and clonal lineages from each isolate. The parasite lines studied here have well-defined growth phenotypes and will facilitate basic malaria research and development of novel malaria interventions. These lines are available to malaria researchers through the MR4 collection of NIAID's BEI Resources Program.

A vigorous study of fractional order mathematical model for SARS-CoV-2 epidemic with Mittag-Leffler kernel

SARS-CoV-2 and its variants have been investigated using a variety of mathematical models. In contrast to multi-strain models, SARS-CoV-2 models exhibit a memory effect that is often overlooked and more realistic. Atangana-Baleanu’s fractional-order operator is discussed in this manuscript for the analysis of the transmission dynamics of SARS-CoV-2. We investigated the transmission mechanism of the SARS-CoV-2 virus using the non-local Atangana-Baleanu fractional-order approach taking into account the different phases of infection and transmission routes. Using conventional ordinary derivative operators, our first step will be to develop a model for the proposed study. As part of the extension, we will incorporate fractional order derivatives into the model where the used operator is the fractional order operator of order Ψ1. Additionally, some basic aspects of the proposed model are examined in addition to calculating the reproduction number and determining the possible equilibrium. Stability analysis of the model is conducted to determine the necessary equilibrium conditions as they are also required in developing a numerical setup. Utilizing the theory of nonlinear functional analysis, for the model, Ulam-Hyers’ stability is established. We present a numerical scheme based on Newton’s polynomial in order to set up an iterative algorithm for the proposed ABC system. The application of this scheme to a variety of values of Φ1 indicates that there is a relationship between infection dynamics and the derivative’s order. We present further simulations which demonstrate the importance and cruciality of different parameters, as well as their effect on the dynamics and administer the disease. Furthermore, this study will provide a better understanding of the mechanisms underlying contagious diseases, thus supporting the development of policies to control them.

Leading Pathogens Involved in Co-Infection and Super-Infection with COVID-19: Forensic Medicine Considerations after a Systematic Review and Meta-Analysis

The COVID-19 pandemic raised concerns about the potential for co-infection or over-infection with other respiratory infections, as they can complicate the diagnosis, treatment and prognosis of the disease. This is also a challenge for forensic pathologists, who may come across cases where the presence of co-infection or over-infection is suspected or confirmed, and it is important that they take this into account when determining the cause of death. The aim of this systematic review is to analyse the prevalence of each specific pathogen co-infecting or over-infecting patients with SARS-CoV-2 infection. In total, 575 studies were selected from the Scopus and Pub-Med online databases and 8 studies were included in a meta-analysis. Male gender, advanced age and nursing home care are risk factors associated with the development of co-infection, whereas age, tachypnoea, hypoxaemia and bacterial infection are predictors of mortality. Overall, however, having a SARS-CoV-2 infection does not represent a real risk for the development of co-infections/super-infections.

Modeling and numerical analysis of a fractional order model for dual variants of SARS-CoV-2☆

This paper considers the novel fractional-order operator developed by Atangana-Baleanu for transmission dynamics of the SARS-CoV-2 epidemic. Assuming the importance of the non-local Atangana-Baleanu fractional-order approach, the transmission mechanism of SARS-CoV-2 has been investigated while taking into account different phases of infection and various transmission routes of the disease. To conduct the proposed study, first of all, we shall formulate the model by using the classical operator of ordinary derivatives. We utilize the fractional order derivative and the model will be extended to a model containing fractional order derivatives. The operator being used is the fractional differential operator and has fractional order Φ1. The model is analyzed further and some basic aspects of the model are investigated besides calculating the basic reproduction number and the possible equilibria of the proposed model. The equilibria of the model are examined for stability purposes and necessary conditions for stability are obtained. Stability is also necessary in terms of numerical setup. The theory of non-linear functional analysis is employed and Ulam-Hyers’s stability of the model is presented. The approach of newton’s polynomial is considered and a new numerical scheme is developed which helped in presenting an iterative process for the proposed ABC system. Based on this scheme, sample curves are obtained for various values of Φ1 and a pattern is derived between the dynamics of the infection and the order of the derivative. Further simulations are presented which show the cruciality and importance of various parameters and the impact of such parameters on the dynamics and control of the disease is presented. The findings of this study will also provide strong conceptual insights into the mechanisms of contagious diseases, assisting global professionals in developing control policies.

Global asymptotic stability, extinction and ergodic stationary distribution in a stochastic model for dual variants of SARS-CoV-2

Several mathematical models have been developed to investigate the dynamics SARS-CoV-2 and its different variants. Most of the multi-strain SARS-CoV-2 models do not capture an important and more realistic feature of such models known as randomness. As the dynamical behavior of most epidemics, especially SARS-CoV-2, is unarguably influenced by several random factors, it is appropriate to consider a stochastic vaccination co-infection model for two strains of SARS-CoV-2. In this work, a new stochastic model for two variants of SARS-CoV-2 is presented. The conditions of existence and the uniqueness of a unique global solution of the stochastic model are derived. Constructing an appropriate Lyapunov function, the conditions for the stochastic system to fluctuate around endemic equilibrium of the deterministic system are derived. Stationary distribution and ergodicity for the new co-infection model are also studied. Numerical simulations are carried out to validate theoretical results. It is observed that when the white noise intensities are larger than certain thresholds and the associated stochastic reproduction numbers are less than unity, both strains die out and go into extinction with unit probability. More-over, it is observed that, for weak white noise intensities, the solution of the stochastic system fluctuates around the endemic equilibrium (EE) of the deterministic model. Frequency distributions are also studied to show random fluctuations due to stochastic white noise intensities. The results presented herein also reveal the impact of vaccination in reducing the co-circulation of SARS-CoV-2 variants within a given population.

The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies

WHO-defined SARS-CoV-2 variants of concern (VOC) drive therapeutics and vaccine development. The Omicron VOC is dominating the arena since November 2021, but the number of its sublineages is growing in complexity. Omicron represent a galaxy with a myriad of stars that suddenly rise and expand before collapsing into apparent extinction when a more fit sublineage appears. This has already happened with BA.1, BA.2, and BA.4/5 and is happening with BA.2.75. We review here the current PANGO phylogeny, focusing on sublineages with Spike mutations, and show how frequently xxxxxxxx convergent evolution has occurred in these sublineages. We finally summarize how Omicron evolution has progressively defeated the anti-Spike monoclonal antibodies authorized so far, leaving clinicians to again fall back on COVID19 convalescent plasma from vaccinated donors as the only antibody-based therapy available.

Mathematical modeling of the dynamics of COVID-19 variants of concern: Asymptotic and finite-time perspectives

The COVID-19 pandemic has seen multiple waves, in part due to the implementation and relaxation of social distancing measures by the public health authorities around the world, and also caused by the emergence of new variants of concern (VOCs) of the SARS-Cov-2 virus. As the COVID-19 pandemic is expected to transition into an endemic state, how to manage outbreaks caused by newly emerging VOCs has become one of the primary public health issues. Using mathematical modeling tools, we investigated the dynamics of VOCs, both in a general theoretical framework and based on observations from public health data of past COVID-19 waves, with the objective of understanding key factors that determine the dominance and coexistence of VOCs. Our results show that the transmissibility advantage of a new VOC is a main factor for it to become dominant. Additionally, our modeling study indicates that the initial number of people infected with the new VOC plays an important role in determining the size of the epidemic. Our results also support the evidence that public health measures targeting the newly emerging VOC taken in the early phase of its spread can limit the size of the epidemic caused by the new VOC (Wu et al., 2139Wu, Scarabel, Majeed, Bragazzi, & Orbinski, ; Wu et al., 2021).

Omicron BA.2 Lineage, the "Stealth" Variant: Is It Truly a Silent Epidemic? A Literature Review

The epidemic curve of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is silently rising again. Worldwide, the dominant SARS-CoV-2 variant of concern (VOC) is Omicron, and its virological characteristics, such as transmissibility, pathogenicity, and resistance to both vaccine- and infection-induced immunity as well as antiviral drugs, are an urgent public health concern. The Omicron variant has five major sub-lineages; as of February 2022, the BA.2 lineage has been detected in several European and Asian countries, becoming the predominant variant and the real antagonist of the ongoing surge. Hence, although global attention is currently focused on dramatic, historically significant events and the multi-country monkeypox outbreak, this new epidemic is unlikely to fade away in silence. Many aspects of this lineage are still unclear and controversial, but its apparent replication advantage and higher transmissibility, as well as its ability to escape neutralizing antibodies induced by vaccination and previous infection, are rising global concerns. Herein, we review the latest publications and the most recent available literature on the BA.2 lineage of the Omicron variant.