CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants

SARS-CoV-2 epidemiology, kinetics, and evolution: A narrative review

Since winter 2019, SARS-CoV-2 has emerged, spread, and evolved all around the globe. We explore 4 y of evolutionary epidemiology of this virus, ranging from the applied public health challenges to the more conceptual evolutionary biology perspectives. Through this review, we first present the spread and lethality of the infections it causes, starting from its emergence in Wuhan (China) from the initial epidemics all around the world, compare the virus to other betacoronaviruses, focus on its airborne transmission, compare containment strategies ("zero-COVID" vs. "herd immunity"), explain its phylogeographical tracking, underline the importance of natural selection on the epidemics, mention its within-host population dynamics. Finally, we discuss how the pandemic has transformed (or should transform) the surveillance and prevention of viral respiratory infections and identify perspectives for the research on epidemiology of COVID-19.

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike-antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Insights into respiratory illness at the population level through parallel analysis of pharmaceutical and viral markers in wastewater

Wastewater as a medium contains information on both circulating pathogens and drug consumption at the population level. This study combines tracking of respiratory viruses and quantification of pharmaceuticals as untargeted indicators of symptoms related to acute respiratory infections and influenza-like illnesses such as coughing, fever and pain. From January 2021 to June 2024, raw wastewater samples from ten locations covering 23% of the Swiss population were analysed. This encompassed 15 pharmaceuticals and four priority respiratory viruses including severe acute respiratory syndrome coronavirus virus-2 (SARS-CoV-2), respiratory syncytial virus (RSV), influenza A and influenza B viruses. The pharmaceutical compounds dextromethorphan, pheniramine, clarithromycin, acetaminophen and codeine showed a strong correlation with respiratory virus loads in wastewater. This enabled the estimation of pathogen-specific and cumulative symptom treatment in the population. In 2021 and 2024, notable increases in pharmaceutical loads without corresponding increases in viral loads signalled high community symptoms linked to unsurveilled pathogens. This study demonstrates that pharmaceutical surveillance can inform respiratory disease burden and highlights the value of integrated surveillance for assessing emerging public health threats beyond those routinely monitored.

Longitudinal Assessment of Solid Organ Transplant Recipients With SARS-CoV-2 Infection

BACKGROUND

Compared with immunocompetent individuals, those who are immunocompromised, including solid organ transplant (SOT) recipients, have higher SARS-CoV-2-related morbidity and mortality. We determined the duration of SARS-CoV-2 RNA positivity to evaluate viral persistence in SOT recipients.

METHODS

This study prospectively followed SOT recipients who recently tested positive for SARS-CoV-2. The duration of viral RNA shedding in nasal swabs and stool samples was tracked, and viral genome sequencing was performed where possible. Persistent infection was defined as a positive nucleic acid amplification test (NAAT) for SARS-CoV-2 at 28 days or later after initial infection. This duration was chosen based on the U.S. Centers for Disease Control and Prevention (CDC) recommendation that immunocompromised individuals isolate for at least 20 days [1], compared with 10 days for non-immunocompromised individuals.

RESULTS

Of 30 SOT recipients, 12 (40%) had positive SARS-CoV-2 RNA in nasal swabs or stool (cycle threshold [Ct] < 40) at 28 or more days after the first positive SARS-CoV-2 test. Immunocompromised (IC) subject 015 had high viral loads (Ct < 30) at 28 days, with continued detection for 54 days.

CONCLUSIONS

In 12 of 30 SOT subjects, SARS-CoV-2 RNA was detected at or beyond 28 days post-detection (dpd), despite vaccination and antibody and/or antiviral treatment in most participants. Three subjects tested positive for SARS-CoV-2 RNA past 50 dpd. Viral persistence in the setting of host immune suppression, coupled with exposure to antiviral treatments, raises concern about the selection of unusual viral variants.

Use of allele-specific qPCR and PCR-RFLP analysis for rapid detection of the SARS-CoV-2 variants in Tunisia: A cheap flexible approach adapted for developing countries

Monitoring the emergence and propagation of SARS-COV2 variants, especially Omicron variants, remains a major concern in developing countries, including Tunisia. We here report lessons of simple approaches used to track prevalent Omicron variants in the city and district of Sfax, Tunisia, between June 2022 and April 2023. Initially, the screening approach was designed by selecting and verifying key SARS-CoV-2 mutations using publicly available sequencing data. Then, the analytical performance of the screening tests was rigorously assessed before being implemented on 227 confirmed COVID-19 cases. In a first stage, from June to September 2022, allele-specific (AS)-qPCR detection of deletions ΔHV69-70 (S gene) and ΔKSF141-143 (ORF1a gene) allowed identification of BA.5 as the predominant variant (128 out of 165 cases; 77.5%) which quickly replaced the pre-existing lineages BA.4 (15.7%) and BA.2 (6.7%). In a second stage, from October 2022 to April 2023, circulation of additional variants was demonstrated using concomitant detection of new relevant mutations by PCR-RFLP (n=62). Detection of mutations Y264H (ORF1b) and V445P/G446S (S gene) resulted in the identification of 38 cases of the BQ.1 variant and 14 cases of the XBB variant, respectively. Further restriction analysis of the S gene was conducted to screen more recent sublineages, including CH.1.1. For all sequenced cases (n=115), our rapid detection assays showed perfect concordance with sequencing results in identifying SARS-CoV-2 variants. These findings highlight the potential of simple, cheap and proven methods for rapid genotyping and monitoring of SARS-COV2 variants. Therefore, these methods appear as valuable tools for effective infection control and prevention in developing countries.

SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA

In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests. However, use of those tests waned after the end of the COVID-19 Public Health Emergency on May 11, 2023. In Dane County, Wisconsin, we partnered with local- and state-level public health agencies and the South Central Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). During August 15, 2023-February 29, 2024, we received 227 RAT samples, from which we generated 127 sequences with >10× depth of coverage for >90% of the SARS-CoV-2 genome. In a subset of tests, lower cycle threshold values correlated with sequence success. Our results demonstrated that collecting and sequencing results from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.

The impact of pre-existing immunity on the emergence of within-host immune-escape mutations in Omicron lineages

The Omicron variant of SARS-CoV-2 circulating amongst highly immunized populations is anticipated to induce immunological pressures, potentially compromising existing immunity. This study investigates vaccine-induced immunity's impact on within-host diversity of Omicron variants and evaluates sub-consensus mutations at spike protein antigenic sites. Next-generation sequencing assessed the within-host diversity of 728 Omicron-positive samples (421 vaccinated; 307 unvaccinated). Quantitative analysis revealed limited vaccine impact, regardless of lineage, vaccine type or doses. Non-lineage mutations (39, 33 and 25 in BA.2*, BA.4* and BA.5* lineages, respectively) were detected, some showing higher incidence in vaccinated individuals. Six mutations detected at sub-consensus levels at antigenic sites suggest increased immune pressure on the spike protein in vaccinated individuals. Four high-prevalence antigenic mutations, absent from global GISAID sequences, were identified. Although within-host diversity did not significantly differ between vaccination statuses, detected mutations suggest that vaccine-induced immunity may influence within-host mutation patterns.

Hypericin Suppresses SARS-CoV-2 Replication and Synergizes with Antivirals via Dual Targeting of RdRp and 3CLpro

The continuous emergence of SARS-CoV-2 variants underscores the need for novel antiviral candidates. Hypericin (HY), a compound derived from Hypericum perforatum, exhibited potent in vitro activity against SARS-CoV-2 in Vero E6 cells, with low cytotoxicity (CC50 > 200 nM). HY showed no significant activity against Influenza A (H1N1) or dengue virus serotype 2, supporting its selective action. Antiviral effects were most evident when HY was administered post-infection, in a concentration-dependent manner, while cellular pretreatment or viral pre-incubation produced limited effects. Notably, HY also displayed virucidal activity, significantly reducing viral titers at 4 °C, 22 °C, and 37 °C. Combination treatments with remdesivir or nirmatrelvir enhanced antiviral efficacy by 50-70% relative to monotherapy, depending on compound concentration. Molecular simulations revealed stable interactions with conserved residues in RdRp and 3CLpro, suggesting a low risk of resistance. Together, these findings highlight the potential of HY as a selective antiviral and virucidal agent against SARS-CoV-2, particularly in combination regimens.

Long-term neuropsychiatric and neuropsychological impact of the pandemic in Italian COVID-19 family clusters, including children and parents

AIM

This study investigated the long-term neuropsychiatric and neuropsychological impact of COVID-19 on children and their parents in households with COVID-19 exposure.

METHODS

A prospective cohort study was conducted on 46 families attending the COVID-19 Follow-up Clinic at the Department for Women's and Children's Health, Padua (Italy) from December 2021 to November 2022. Self-perceived stress-related, emotional-behavioral, and post-traumatic stress (PTSD-related) symptoms were assessed in both children and parents. Children with underlying neuropsychiatric conditions were excluded from the study.

RESULTS

A total of 81 parents (median age = 38 years [IQR: 43-48], females = 44 [54.3%]), and 77 children (median age = 8 years [IQR: 5-11], females = 33 [42.9%]) participated in the study. Overall,125 (79%) and 33 (21%) participants were classified as COVID-19 cases and non-COVID-19 cases, respectively. The time interval between the COVID-19 family outbreak and the neuropsychiatric and psychological assessment was ≤4 months (median=3 months [IQR=0]) for 89 (56.3%) participants and >4 months for 69 (43.8%) (median=11.5 months [IQR=5-12]) participants. A total of 136 (86.1%) participants reported stress-related symptoms, with emotional stress being the most common. A positive correlation was observed between self-perceived stress-related symptoms in children and their parents within the same family (r=0.53, p=0.0005). Among children aged 6-18 years, 16 (37.2%) had clinical scores for internalizing symptoms at the Child Behavior Checklist (CBCL), while none children aged 1.5-5 years showed clinical score for internalizing symptoms. Similarly, total difficulty scores at the Strengths and Difficulties Questionnaire (SDQ 4-17) and assessment of PTSD-related symptoms through the Trauma Symptom Checklist for Young Children (TSCYC) questionnaire were within non-clinical cut-offs in 45 (84.9%) and 43 (75.4%) children aged 3-12 years, respectively. The Trauma Symptom Checklist for Children (TSCC) resulted in the non-clinical cut-off for 36 (92.3%) children aged 8-18 years. While a higher prevalence of self-perceived stress-related symptoms was found in COVID-19 cases compared to non-COVID-19 cases (p=.01), no differences were observed for emotional-behavioral and PTSD-related symptoms between the two groups.

CONCLUSIONS

This study documented the impact of the COVID-19 pandemic on Italian children and their family's stress levels. Further research is needed to confirm our findings and explore the long-term effects of the pandemic on families.

Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study

Wastewater-based surveillance (WBS) allows the analysis of pathogens, chemicals or other biomarkers in wastewater to derive unbiased epidemiological information at population scale. After re-gaining attention during the SARS-CoV-2 pandemic, the field holds promise as a surveillance and early warning system by tracking emerging pathogens with pandemic potential. Expanding the current toolbox of analytical techniques for wastewater analysis, we explored the use of Hyperplex PCR (hpPCR) to analyse SARS-CoV-2 mutations in wastewater samples collected weekly in up to 22 sites across Sweden between October 2022 and December 2023. The samples were tested using a probe panel ranging from 10- to 18-plex, continuously adapted within 1-2 weeks to quantify relevant mutations of concern over time. For cross-validation, the samples were simultaneously analysed with commonly used methods including quantitative PCR (qPCR) and next-generation sequencing (NGS). hpPCR is demonstrated herein to provide (1) systematic single nucleotide specificity with a straightforward probe design, (2) high multiplexity with minimal panel re-optimization requirements and (3) 4-5-week earlier mutation detection relative to NGS with comparable performance of mutation frequency quantification (Pearson r = 0.88, n = 50). Hence, hpPCR is shown to be a powerful complementary tool to the current workflow involving NGS and qPCR by facilitating the assembly of dynamic high-plex panels compatible with high-frequency monitoring of multiple key pathogens and/or variants in WBS.

Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its daughter lineages

The COVID-19 pandemic offered an unprecedented glimpse into the evolution of its causative virus, SARS-CoV-2. It has been estimated that since its outbreak in late 2019, the virus has explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain. Spike protein of the virus exhibits the largest sequence variation in particular, with many individual mutations impacting target recognition, cellular entry, and endosomal escape of the virus. Moreover, recent studies unveiled a significant increase in the total charge on the spike protein during the evolution of the virus in the initial period of the pandemic. While this trend has recently come to a halt, we perform a sequence-based analysis of the spike protein of 2665 SARS-CoV-2 variants which shows that mutations in ionizable amino acids continue to occur with the newly emerging variants, with notable differences between lineages from different clades. What is more, we show that within mutations of amino acids which can acquire positive charge, the spike protein of SARS-CoV-2 exhibits a prominent preference for lysine residues over arginine residues. This lysine-to-arginine ratio increased at several points during spike protein evolution, most recently with BA.2.86 and its sublineages, including the recently dominant JN.1, KP.3, and XEC variants. The increased ratio is a consequence of mutations in different structural regions of the spike protein and is now among the highest among viral species in the Coronaviridae family. The impact of high lysine-to-arginine ratio in the spike proteins of BA.2.86 and its daughter lineages on viral fitness remains unclear; we discuss several potential mechanisms that could play a role and that can serve as a starting point for further studies.

Entry Efficiency, Protease Dependence, and Antibody-Mediated Neutralization of SARS-CoV-2 Sublineages KP.3.1.1 and XEC

BACKGROUND

The SARS-CoV-2 variants KP.3.1.1 and XEC currently dominate the COVID-19 epidemic. However, their cell tropism, proteolytic processing, and susceptibility to neutralization by monoclonal antibodies remain incompletely characterized.

METHODS

We employed pseudotyped viruses to assess the entry efficiency of KP.3.1.1 and XEC in various cell lines, their dependence on TMPRSS2 for lung cell entry, and their ability to use ACE2 for infection. Additionally, we evaluated their susceptibility to neutralization by monoclonal antibodies BD55-4637 and BD55-5514.

RESULTS

KP.3.1.1 and XEC entered cell lines with similar efficiency as the parental JN.1 lineage and utilized TMPRSS2 for Calu-3 lung cell entry. Unlike JN.1, KP.3.1.1 and XEC failed to efficiently use murine ACE2 for cell entry. Both variants were effectively neutralized by the monoclonal antibodies BD55-4637 and BD55-5514, suggesting therapeutic potential.

CONCLUSIONS

Our findings demonstrate that JN.1, KP.3.1.1, and XEC, like their predecessor BA.2.86, rely on TMPRSS2 for lung cell entry and remain sensitive to certain neutralizing monoclonal antibodies. However, these variants differ in their ability to utilize ACE2 species orthologs for cell entry.

VirusWarn: A mutation-based early warning system to prioritize concerning SARS-CoV-2 and influenza virus variants from sequencing data

The rapid evolution of respiratory viruses is characterized by the emergence of variants with concerning phenotypes that are efficient in antibody escape or show high transmissibility. This necessitates timely identification of such variants by surveillance networks to assist public health interventions. Here, we introduce VirusWarn, a comprehensive system designed for detecting, prioritizing, and warning of emerging virus variants from large genomic datasets. VirusWarn uses both manually-curated rules and machine-learning (ML) classifiers to generate and rank pathogen sequences based on mutations of concern and regions of interest. Validation results for SARS-CoV-2 showed that VirusWarn successfully identifies variants of concern in both assessments, with manual- and ML-derived criteria from positive selection analyses. Although initially developed for SARS-CoV-2, VirusWarn was adapted to Influenza viruses and their dynamics, and provides a robust performance, integrating a scheme that accounts for fixed mutations from past seasons. HTML reports provide detailed results with searchable tables and visualizations, including mutation plots and heatmaps. Because VirusWarn is written in Nextflow, it can be easily adapted to other pathogens, demonstrating its flexibility and scalability for genomic surveillance efforts.

A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves

The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.

Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency

Accurate estimation of the effects of mutations on SARS-CoV-2 viral fitness can inform public-health responses such as vaccine development and predicting the impact of a new variant; it can also illuminate biological mechanisms including those underlying the emergence of variants of concern. Recently, Lan et al. reported a model of SARS-CoV-2 secondary structure and its underlying dimethyl sulfate reactivity data (Lan et al., 2022). I investigated whether base reactivities and secondary structure models derived from them can explain some variability in the frequency of observing different nucleotide substitutions across millions of patient sequences in the SARS-CoV-2 phylogenetic tree. Nucleotide basepairing was compared to the estimated 'mutational fitness' of substitutions, a measurement of the difference between a substitution's observed and expected frequency that is correlated with other estimates of viral fitness (Bloom and Neher, 2023). This comparison revealed that secondary structure is often predictive of substitution frequency, with significant decreases in substitution frequencies at basepaired positions. Focusing on the mutational fitness of C→U, the most common type of substitution, I describe C→U substitutions at basepaired positions that characterize major SARS-CoV-2 variants; such mutations may have a greater impact on fitness than appreciated when considering substitution frequency alone.

Efficacy and safety of sipavibart for prevention of COVID-19 in individuals who are immunocompromised (SUPERNOVA): a randomised, controlled, double-blind, phase 3 trial

BACKGROUND

Sipavibart is an anti-spike monoclonal antibody that neutralises SARS-CoV-2 with exceptions, including Phe456Leu-containing variants (eg, KP.2* and KP.3*). This trial assessed sipavibart efficacy and safety for prevention of symptomatic COVID-19 in participants who are immunocompromised.

METHODS

In this ongoing, double-blind, international, phase 3 trial, we enrolled participants who were immunocompromised and aged 12 years or older at 197 hospitals, university health centres, and clinical trial units in 18 countries. Participants were randomly allocated 1:1 to a sipavibart group (intramuscular sipavibart 300 mg on days 1 and 181) or a comparator group (tixagevimab 300 mg-cilgavimab 300 mg on day 1 and placebo on day 181 or placebo on days 1 and 181), stratified by previous COVID-19 vaccination and infection status and use of tixagevimab-cilgavimab. The primary efficacy outcomes were symptomatic COVID-19 caused by any variant or symptomatic COVID-19 caused by non-Phe456Leu-containing variants within 181 days of dosing, assessed in the SARS-CoV-2-negative set, comprising all participants without a positive RT-PCR test for SARS-CoV-2 at baseline and who received at least one trial intervention dose. Safety outcomes for adverse events were assessed 90 days following the first dose and for serious adverse events throughout the study in the safety analysis set (ie, all participants who received at least one injection of sipavibart or comparator). This study is registered with ClinicalTrials.gov, NCT05648110.

FINDINGS

Participants were screened from March 31 to Oct 27, 2023; 3349 participants (56·8% female) were randomly assigned: 1674 to the sipavibart group (five no first dose; 1669 sipavibart) and 1675 to the comparator group (nine no first dose; 1105 tixagevimab-cilgavimab and 561 placebo). Within 181 days of dosing, 122 (7·4%) of 1649 participants in the sipavibart group and 178 (10·9%) of 1631 participants in the comparator group had symptomatic COVID-19 due to any variant (relative risk reduction [RRR] 34·9% [97·5% CI 15·0 to 50·1]; p=0·0006), 54 (3·3%) participants in the sipavibart group and 90 (5·5%) participants in the comparator group had symptomatic COVID-19 due to non-Phe456Leu-containing variants (RRR 42·9% [95% CI 19·9 to 59·3]; p=0·0012), and 47 (2·9%) participants in the sipavibart group and 64 (3·9%) participants in the comparator group had symptomatic COVID-19 due to Phe456Leu-containing variants (30·4% [-1·8 to 52·5]). Adverse events occurred in 833 (49·9%) of 1671 participants in the sipavibart group and 857 (51·5%) of 1663 participants in the comparator group within 3 months of the first dose. One COVID-19-related death occurred in the comparator group. Serious adverse events considered related to trial intervention occurred in two (0·1%) of 1671 participants in the sipavibart group and seven (0·4%) of 1663 participants in the comparator group (none fatal). No serious cardiovascular or thrombotic events were considered to be related to sipavibart.

INTERPRETATION

The primary analysis showed efficacy and safety of sipavibart in preventing symptomatic COVID-19 in participants who are immunocompromised when susceptible (ie, non-Phe456Leu-containing) variants dominated, although no efficacy was shown against resistant (ie, Phe456Leu-containing) variants that dominate as of November, 2024.

FUNDING

AstraZeneca.

Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived

Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the outset of the coronavirus disease 2019 pandemic can provide insight into the circumstances leading to its emergence. Early SARS-CoV-2 genomic diversity has been classified into two distinct viral lineages, denoted "A" and "B," which we hypothesized were separately introduced into humans. Recently published data contain two genomes with a haplotype suggested to be an evolutionary intermediate to these two lineages, known as "T/T." We used a phylodynamic approach to analyze SARS-CoV-2 genomes from early 2020 to determine whether these two T/T genomes represent an evolutionarily intermediate haplotype between lineages A and B, or if they are a later descendent of either of these two lineages. We find that these two recently published T/T genomes do not represent an evolutionarily intermediate haplotype and were, instead, derived from either lineage A or lineage B. However, we cannot conclusively determine from which lineage they were derived. After including additional data from the start of the pandemic, including these two T/T genomes, we again find a discrepancy in the molecular clock when inferring the ancestral haplotype of SARS-CoV-2, corroborating existing evidence for the separate introductions of SARS-CoV-2 lineages A and B into the human population in late 2019.

mapPat: tracking pathogens evolution in space and time

Motivation

The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, computational methods are critical for the implementation of effective genomic surveillance strategies.

Results

Here, we introduce mapPat, an R Shiny application for the interactive visualization of pathogens genomic data in space and time. mapPat is designed as a user-friendly dashboard and allows the dynamic monitoring of the evolution of variants, lineages, and mutations in the genome of a pathogen at glance through informative geographic maps and elegant data visuals. mapPat provides a fine-grained map of pathogens evolution and circulation and represents a useful addition to the catalogue of bioinformatics methods for the genomic surveillance of pathogens.

Availability and implementation

mapPat is available at GitHub (https://github.com/F3rika/mapPat.git).

A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2. (SARS-CoV-2) and its variant strains, including Alpha, Beta, Gamma, Delta, and now Omicron, pose a significant challenge. With the constant evolution of the virus, Omicron and its subtypes BA.1, BA.2, BA.3, BA.4, and BA.5 have developed the capacity to evade neutralization induced by previous vaccination or infection. This evasion highlights the urgency in discovering new monoclonal antibodies (mAbs) with neutralizing activity, especially broadly neutralizing antibodies (bnAbs), to combat the virus.In the current study, we introduced a fully human neutralizing mAb, CR9, that targets Omicron variants. We demonstrated the mAb's effectiveness in inhibiting Omicron replication both in vitro and in vivo. Structural analysis using cryo-electron microscopy (cryo-EM) revealed that CR9 binds to an epitope formed by RBD residues, providing a molecular understanding of its neutralization mechanism. Given its potency and specificity, CR9 holds promise as a potential adjunct therapy for treating Omicron infections. Our findings highlight the importance of continuous mAb discovery and characterization in addressing the evolving threat of COVID-19.

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023

Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and BA.2.86, designated XDR, has been detected mainly in Brazil. In this study, we reconstructed the spatiotemporal dynamics and estimated the absolute and relative transmissibility of the XDR lineage. The XDR lineage displayed a recombination breakpoint in the ORF1a-coding region, and the most closely related sequences to the 5' and 3' ends of the recombinant correspond to JD.1.1 and JN.1.1 lineages, respectively. The first XDR sequences were detected in November 2023 in the Northeastern Brazilian region, and their prevalence rapidly surged from <1% to 25% by February 2024. The Bayesian phylogeographic analysis supports that the XDR lineage likely emerged in the Northeastern Brazilian region around late October 2023 and rapidly disseminated within and outside Brazilian borders from mid-November onward. The median effective reproductive number of the XDR lineage in Brazil during the initial expansion phase was estimated to be around 1.5, and the average relative instantaneous reproduction numbers of XDR and JN* lineages were estimated to be 1.37 and 1.29 higher than that of co-circulating XBB* lineages. In summary, these findings support that the recombinant lineage XDR arose in the Northeastern Brazilian region in October 2023, shortly after the first detection of JN.1 sequences in the country. In Brazil, the XDR lineage exhibited a higher transmissibility level than its parental XBB.* lineages and is spreading at a rate similar to or slightly faster than the JN.1* lineages.IMPORTANCEThis study highlights the emergence and rapid dissemination of the recombinant SARS-CoV-2 XDR lineage, derived from the Omicron lineages JD.1.1 and JN.1.1. The XDR lineage exhibited equivalent transmissibility to its JN.1* parental lineages and quickly spread across Brazil in late 2023. The findings underscore the critical role of real-time genomic surveillance in detecting novel variants with higher transmission potential. By utilizing phylogenetic and epidemiological methods, this research provides important insights into the molecular dynamics of XDR, which could inform public health responses and vaccine composition updates. The study's significance lies in its ability to document the impact of recombination on viral evolution, offering valuable information to the field of virology and pandemic preparedness.

Cross-reactive sarbecovirus antibodies induced by mosaic RBD-nanoparticles

Therapeutic monoclonal antibodies (mAbs) against SARS-CoV-2 become obsolete as spike substitutions reduce antibody binding. To induce antibodies against conserved receptor-binding domain (RBD) regions for protection against SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD-nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs from mosaic-8b-immunized rabbits, some on par with Pemgarda (the only currently FDA-approved therapeutic mAb). Deep mutational scanning, in vitro selection of spike resistance mutations, and cryo-EM structures of spike-antibody complexes demonstrated targeting of conserved epitopes. Rabbit mAbs included critical D-gene segment features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment. Thus, mosaic RBD-nanoparticle immunization coupled with multiplexed screening represent an efficient way to generate and select therapeutic pan-sarbecovirus and pan-SARS-2 variant mAbs.

Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion

Coronaviruses express their structural and accessory genes via a set of subgenomic RNAs, whose synthesis is directed by transcription regulatory sequences (TRSs) in the 5' genomic leader and upstream of each body open reading frame. In SARS-CoV-2, the TRS has the consensus AAACGAAC; upon searching for emergence of this motif in the global SARS-CoV-2 sequences, we find that it evolves frequently, especially in the 3' end of the genome. We show well-supported examples upstream of the Spike gene-within the nsp16 coding region of ORF1b-which is expressed during human infection, and upstream of the canonical Envelope gene TRS, both of which have evolved convergently in multiple lineages. The most frequent neo-TRS is within the coding region of the Nucleocapsid gene, and is present in virtually all viruses from the B.1.1 lineage, including the variants of concern Alpha, Gamma, Omicron and descendants thereof. Here, we demonstrate that this TRS leads to the expression of a novel subgenomic mRNA encoding a truncated C-terminal portion of Nucleocapsid, which is an antagonist of type I interferon production and contributes to viral fitness during infection. We observe distinct phenotypes when the Nucleocapsid coding sequence is mutated compared to when the TRS alone is ablated. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level.

Safety and Intranasal Retention of a Broad-Spectrum Anti-SARS-CoV-2 Monoclonal Antibody SA55 Nasal Spray in Healthy Volunteers: A Phase I Clinical Trial

BACKGROUND

A broad-spectrum anti-SARS-CoV-2 monoclonal antibody (mAb), SA55, is highly effective against SARS-CoV-2 variants. This trial aimed at demonstrating the safety, tolerability, local drug retention and neutralizing activity, systemic exposure level, and immunogenicity of the SA55 nasal spray in healthy individuals.

METHODS

This phase I, dose-escalation clinical trial combined an open-label design with a randomized, controlled, double-blind design. Healthy participants aged 18-65 years were enrolled and received a single dose of the SA55 nasal spray (1 mg or 2 mg) or multiple doses of SA55 nasal spray/placebo for 7 days (1 or 2 mg/dose, 3 or 6 doses/day). Safety monitoring was conducted throughout the study. Nasal swabs and venous blood samples were collected to analyze local drug concentration/neutralization, systemic exposure, and immunogenicity.

RESULTS

From 2 June to 11 August 2023, 80 participants were enrolled and received study intervention. The severity of adverse reactions (ADRs) reported during the study was mild in all cases, and all ADRs were laboratory test abnormalities without corresponding symptoms or vital signs. A total of 9 ADRs were reported, of which all were mild in severity. Overall ADR incidence rate was 16.67% (8/48) in single-dose groups and 4.17% (1/24) in multiple-dose groups. The nasal local drug concentration and neutralizing activity were generally stable within 4-8 h, with favorable neutralization activity against Omicron BF.7 and XBB strains.

CONCLUSIONS

This study demonstrated favorable safety and tolerability of the SA55 nasal spray in healthy volunteers, exhibited satisfactory neutralizing activity against Omicron variants intranasally, and indicated low systemic toxicity risk.

Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein

The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations and a deletion in the KP.3.1.1 spike protein (S) affect ACE2 binding and antibody escape. Mass spectrometry revealed a new glycan site at residue N30 and altered glycoforms at neighboring N61. Cryo-EM structures showed that the N30 glycan and rearrangement of adjacent residues did not significantly change the overall spike structure, up-down ratio of the receptor-binding domains (RBDs), or ACE2 binding. Furthermore, a KP.3.1.1 S structure with hACE2 further confirmed an epistatic effect between F456L and Q493E on ACE2 binding. Our analysis shows SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.

VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data

RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring diversity from error-prone reads is challenging. Here, we present VILOCA (VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data), a method for mutation calling and reconstruction of local haplotypes from short- and long-read viral sequencing data. Local haplotypes refer to genomic regions that have approximately the length of the input reads. VILOCA recovers local haplotypes by using a Dirichlet process mixture model to cluster reads around their unobserved haplotypes and leveraging quality scores of the sequencing reads. We assessed the performance of VILOCA in terms of mutation calling and haplotype reconstruction accuracy on simulated and experimental Illumina, PacBio and Oxford Nanopore data. On simulated and experimental Illumina data, VILOCA performed better or similar to existing methods. On the simulated long-read data, VILOCA is able to recover on average [Formula: see text] of the ground truth mutations with perfect precision compared to only [Formula: see text] recall and [Formula: see text] precision of the second-best method. In summary, VILOCA provides significantly improved accuracy in mutation and haplotype calling, especially for long-read sequencing data, and therefore facilitates the comprehensive characterization of heterogeneous within-host viral populations.

Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages

The SARS-CoV-2 BA.2.86 variant, also known as Pirola, has acquired over 30 amino acid changes in the Spike protein, evolving into >150 sublineages within ten months of its emergence. Among these, the JN.1, has been rapidly increasing globally becoming the most prevalent variant. To facilitate the identification of BA.2.86 sublineages, we designed the PiroMet-1 and PiroMet-2 assays in silico and validated them using BA.2.86 viral RNA and clinical samples to ascertain analytical specificity and sensitivity. Both assays resulted very specific with limit of detection of about 1-2 RNA copies/μL. The assays were then applied in a digital RT-PCR format to wastewater samples, combined with the OmMet assay (which identifies Omicron sublineages except BA.2.86 and its descendants) and the JRC-UCE.2 assay (which can universally recognize all SARS-CoV-2 variants). When used together with the OmMet and JRC-CoV-UCE.2 assays, the PiroMet assays accurately quantified BA.2.86 sublineages in wastewater samples. Our findings support the integration of these assays into routine SARS-CoV-2 wastewater surveillance as a timely and cost-effective complement to sequencing for monitoring the prevalence and spread of BA.2.86 sublineages within communities.

"Outlaw" mutations in quasispecies of SARS-CoV-2 inhibit replication

The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or bona fide genomes. Here we tested the hypothesis that mutations that did not appear in consensus genomes were, in fact, as frequent as the mutations that appeared during the various epidemic episodes, but were not expressed because lethal. To identify these mutations, we analysed the genomes of 90 nasopharyngeal samples and the quasispecies determined by next-generation sequencing. Mutations observed in the quasispecies and not in the consensus genomes were considered to be lethal, what we called "outlaw" mutations. Among these mutations, we analysed the 21 most frequent. Eight of these "outlaws" were in the RNA polymerase and we were able to use a structural biology model and molecular dynamics simulations to demonstrate the functional incapacity of these mutated RNA polymerases. Three other mutations affected the spike, a major protein involved in the pathogenesis of COVID-19. Overall, by analysing the SARS-CoV-2 quasispecies obtained during sequencing, this method made it possible to identify "outlaws," showing areas that could potentially become the target of treatments.

TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication

SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. Here we show that the host E3-ubiquitin ligase TRIM7 acts as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7-/- mice exhibit increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients reveal that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M-K14/K15R virus shows reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology.

Single spike mutation differentiating XBB.1 and XBB.1.5 enhances SARS-CoV-2 cell-to-cell transmission and facilitates serum-mediated enhancement

Introduction

The ongoing emergence of SARS-CoV-2 variants poses significant challenges to existing therapeutics. The spike (S) glycoprotein is central to both viral entry and cell-to-cell transmission via syncytia formation, a process that confers resistance to neutralizing antibodies. The mechanisms underlying this resistance, particularly in relation to spike-mediated fusion, remain poorly understood.

Methods

We analyzed two clinical SARS-CoV-2 isolates differing by a single amino acid substitution in the S protein. Using biochemical and cell-based assays, we evaluated entry kinetics, syncytia formation, and the neutralizing efficacy of convalescent sera. These parameters were further correlated with S-mediated cell-cell fusion activity.

Results

The single amino acid substitution significantly altered entry kinetics and enhanced syncytia formation. This modification did not diminished the neutralizing capacity of convalescent sera, but it increased the efficiency of S-induced cell-cell fusion. These findings highlight the mutation's impact on viral transmissibility and immune evasion.

Discussion

Our study demonstrates that even minor changes in the S protein can profoundly influence SARS-CoV-2 transmissibility and resistance to antibody-mediated neutralization. Understanding the molecular basis of S-mediated cell-cell fusion is crucial for anticipating the impact of emerging variants and developing next-generation therapeutic strategies. These insights provide a framework for predicting variant fitness and optimizing treatment approaches against future SARS-CoV-2 variants.

Genomic Surveillance of SARS-CoV-2 in Taiwan: A Perspective on Evolutionary Data Interpretation and Sequencing Issues

This review presents a comprehensive perspective on the genomic surveillance of SARS-CoV-2 in Taiwan, with a focus on next-generation sequencing and phylogenetic interpretation. This article aimed to explore how Taiwan has utilized genomic sequencing technologies and surveillance to monitor and mitigate the spread of COVID-19. We examined databases and sources of genomic sequences and highlighted the role of data science methodologies in the explanation and analyses of evolutionary data. This review addressed the challenges and limitations inherent in genomic surveillance, such as concerns regarding data quality and the necessity for interdisciplinary expertise for accurate data interpretation. Special attention was given to the unique challenges faced by Taiwan, including its high population density and major transit destination for international travelers. We underscored the far-reaching implications of genomic surveillance data for public health policy, particularly in influencing decisions regarding travel restrictions, vaccine administration, and public health decision-making. Studies were examined to demonstrate the effectiveness of using genomic data to implement public health measures. Future research should prioritize the integration of methodologies and technologies in evolutionary data science, particularly focusing on phylodynamic analytics. This integration is crucial to enhance the precision and applicability of genomic data. Overall, we have provided an overview of the significance of genomic surveillance in tracking SARS-CoV-2 variants globally and the pivotal role of data science methodologies in interpreting these data for effective public health interventions.

Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana

Botswana, like the rest of the world, has been significantly impacted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1, clade 22E). These genomes were sourced from both epidemiologically linked and unlinked samples collected in three close locations within the district of Greater Gaborone. In this study, we assessed the worldwide prevalence of the FN.1 lineage, evaluated its mutational profile, and conducted a phylogeographic analysis to reveal its global dispersal dynamics. Among approximately 16 million publicly available SARS-CoV-2 sequences generated by 30 September 2023, only 87 were of the FN.1 lineage, including 22 from Botswana, 6 from South Africa, and 59 from the UK. The estimated time to the most recent common ancestor of the 87 FN.1 sequences was 22 October 2022 [95% highest posterior density: 2 September 2022-24 November 2022], with the earliest of the 22 Botswana sequences having been sampled on 7 December 2022. Discrete trait reconstruction of FN.1 identified Botswana as the most probable place of origin. The FN.1 lineage is derived from the BQ.1.1 lineage and carries two missense variants in the spike protein, S:K182E in NTD and S:T478R in RDB. Among the over 90 SARS-CoV-2 lineages circulating in Botswana between September 2020 and July 2023, FN.1 was most closely related to BQ.1.1.74 based on maximum likelihood phylogenetic inference, differing only by the S:K182E mutation found in FN.1. Given the early detection of numerous novel variants from Botswana and its neighbouring countries, our study underscores the necessity of continuous surveillance to monitor the emergence of potential VOCs, integrating molecular and spatial data to identify dissemination patterns enhancing preparedness efforts.

Genomic analysis of the early COVID-19 pandemic in Haiti reveals Caribbean-specific variant dynamics

Pathogen sequencing during the COVID-19 pandemic has generated more whole genome sequencing data than for any other epidemic, allowing epidemiologists to monitor the transmission and evolution of SARS-CoV-2. However, large parts of the world are heavily underrepresented in sequencing efforts, including the Caribbean islands. We performed genome sequencing of SARS-CoV-2 from upper respiratory tract samples collected in Haiti during the spring of 2020. We used phylogenetic analysis to assess the pandemic dynamics in the Caribbean region and observed that the epidemic in Haiti was seeded by multiple introductions, primarily from the United States. We identified the emergence of a SARS-CoV-2 lineage (B.1.478) from Haiti that spread into North America, as well as evidence of the undocumented spread of SARS-CoV-2 within the Caribbean. We demonstrate that the genomic analysis of a relatively modest number of samples from a severely under-sampled region can provide new insight on a previously unobserved spread of a specific lineage, demonstrating the importance of geographically widespread genomic epidemiology.

Trends and impacts of SARS-CoV-2 genome sharing: a comparative analysis of China and the global community, 2020-2023

Objective

The global sharing of pathogen genome sequences has been significantly expedited by the COVID-19 pandemic. This study aims to elucidate the global landscape of SARS-CoV-2 genome sharing between 2020 and 2023 with a focus on quantity, timeliness, and quality. Specifically, the characteristics of China are examined.

Methods

SARS-CoV-2 genomes along with associated metadata were sourced from GISAID database. The genomes were analyzed to evaluate the quantity, timeliness, and quality across different countries/regions. The metadata characteristics of shared genomes in China in 2023 were examined and compared with the actual demographic data of China in 2023.

Results

From 2020 to 2023, European countries consistently maintained high levels of genomic data sharing in terms of quantity, timeliness, and quality. In 2023, China made remarkable improvements in sequence sharing, ranking among the top 3.89% globally for quantity, 22.78% for timeliness, and 17.78% for quality. The genome sharing in China in 2023 covered all provinces with Shanghai Municipality contributing the most genomes. Human samples accounted for 99.73% of the shared genomes and exhibited three distinct peaks in collection dates. Males constituted 52.06%, while females constituted 47.94%. Notably, there was an increase in individuals aged 65 and above within the GISAID database compared to China's overall population in 2023.

Conclusion

The global sharing of SARS-CoV-2 genomes in 2020-2023 exhibited disparities in terms of quantity, timeliness, and quality. However, China has made significant advancements since 2023 by achieving comprehensive coverage across provinces, timely dissemination of data, and widespread population monitoring. Strengthening data sharing capabilities in countries like China during the SARS-CoV-2 pandemic will play a crucial role in containing and responding to future pandemics caused by emerging pathogens.

Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye

SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of Türkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.

Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTPs) participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome sequencing (WGS). The Greater Toronto Airports Authority (GTAA), operator of Toronto Pearson International Airport (Toronto Pearson), has been participating in WW surveillance since January 2022. As a major international airport in Canada and the largest national hub, this airport is an ideal location for tracking globally emerging SARS-CoV-2 variants of concern (VOCs). In this study, WW collected from Toronto Pearson's two terminals and pooled aircraft sewage was processed for WGS using a tiled-amplicon approach targeting the SARS-CoV-2 virus genome. Data generated was analyzed to monitor trends of SARS-CoV-2 lineage frequencies. Initial detections of emerging lineages were compared between Toronto Pearson WW samples, municipal WW samples collected from the surrounding regions, and Ontario clinical data as published by Public Health Ontario. Results enabled the early detection of VOCs and individual mutations emerging in Ontario. On average, the emergence of novel lineages at the airport preceded clinical detections by 1-4 weeks, and up to 16 weeks in one case. This project illustrates the efficacy of WW surveillance at transitory transportation hubs and sets an example that could be applied to other viruses as part of a pandemic preparedness strategy and to provide monitoring on a mass scale.

Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022-February 2024)

The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been characterized by the virus's ongoing evolution, leading to the appearance of more transmissible variants that have often triggered infection surges. In this study, we analyzed the SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over this period, 251 distinct lineages and sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, and JN.1 (parental lineage BA.2.86), all of which harbor S protein mutations linked to enhanced transmissibility and immune escape. Despite the relatively low numbers of new infections during this period, and the lack of any major waves, unlike earlier phases of the pandemic, these lineages demonstrated varying periods of dominance, with Omicron 5 prevailing from November 2022 to February 2023, XBB variants leading from March to November 2023, and JN.1 generating a wavelet from December 2023 to February 2024. These findings suggest that the SARS-CoV-2 epidemic in Cyprus has reached endemicity, with new variants gradually replacing previously circulating variants irrespective of seasonal patterns. This study highlights the critical importance of ongoing surveillance of SARS-CoV-2 evolution in Cyprus and emphasizes the role of preventive measures in limiting virus transmission, providing valuable insights for safeguarding public health.

The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID-MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

The spatiotemporal analysis of SARS-CoV-2 transmission in China since the termination of the dynamic zero-COVID policy

China's dynamic zero-COVID policy has effectively curbed the spread of SARS-CoV-2, while inadvertently creating immunity gaps within its population. Subsequent surges in COVID-19 cases linked to various SARS-CoV-2 lineages post-policy termination necessitate a thorough investigation into the epidemiological landscape. This study addresses this issue by analyzing a comprehensive dataset of 39,456 high-quality genomes collected nationwide over an 11-month period since policy termination. Through lineage assignment, phylogenetic analysis, pandemic pattern comparison, phylodynamic reconstruction, and recombination detection, we found that China's post-epidemic period could be divided into three stages, along with dynamic changes in dominant lineages. Geographical clustering of similar lineages implies the importance of cross-border cooperation among neighboring regions. Compared to the USA, UK, and Japan, China exhibits unique trajectories of lineage epidemics, characterized by initial lagging followed by subsequent advancement, indicating the potential influence of diverse prevention and control policies on lineage epidemic patterns. Hong Kong, Shanghai, and Hubei emerge as pivotal nodes in the nationwide spread, marking a shift in the transmission center from east to central regions of China. Although China hasn't experienced significant variant emergence, the detection and validation of the novel recombination event, XCN lineage, underscore the ongoing virus evolution. Overall, this study systematically analyzes the spatiotemporal transmission of SARS-CoV-2 virus in China since the termination of the dynamic zero-COVID policy, offering valuable insights for regional surveillance and evidence-based public health policymaking.

Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater

During the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without relying solely on clinical testing. As more sublineages were discovered, it increased the difficulty in identifying distinct variants in a mixed population sample, particularly those without a known lineage. Here, we compare the sequencing technology from Illumina and from Oxford Nanopore Technologies, in order to determine their efficacy at detecting variants of differing abundance, using 248 wastewater samples from various Quebec and Ontario cities. Our study used two analytical approaches to identify the main variants in the samples: the presence of signature and marker mutations and the co-occurrence of signature mutations within the same amplicon. We observed that each sequencing method detected certain variants at different frequencies as each method preferentially detects mutations of distinct variants. Illumina sequencing detected more mutations with a predominant lineage that is in low abundance across the population or unknown for that time period, while Nanopore sequencing had a higher detection rate of mutations that are predominantly found in the high abundance B.1.1.7 (Alpha) lineage as well as a higher sequencing rate of co-occurring mutations in the same amplicon. We present a workflow that integrates short-read and long-read sequencing to improve the detection of SARS-CoV-2 variant lineages in mixed population samples, such as wastewater.

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections

We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n = 15). All patients received remdesivir and some also received nirmatrelvir-ritonavir (n = 3) or therapeutic monoclonal antibodies (n = 4). Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient sequentially treated with nirmatrelvir-ritonavir and remdesivir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.

SARS-CoV-2 Variants from Long-Term, Persistently Infected Immunocompromised Patients Have Altered Syncytia Formation, Temperature-Dependent Replication, and Serum Neutralizing Antibody Escape

SARS-CoV-2 infection of immunocompromised individuals often leads to prolonged detection of viral RNA and infectious virus in nasal specimens, presumably due to the lack of induction of an appropriate adaptive immune response. Mutations identified in virus sequences obtained from persistently infected patients bear signatures of immune evasion and have some overlap with sequences present in variants of concern. We characterized virus isolates obtained greater than 100 days after the initial COVID-19 diagnosis from two COVID-19 patients undergoing immunosuppressive cancer therapy, wand compared them to an isolate from the start of the infection. Isolates from an individual who never mounted an antibody response specific to SARS-CoV-2 despite the administration of convalescent plasma showed slight reductions in plaque size and some showed temperature-dependent replication attenuation on human nasal epithelial cell culture compared to the virus that initiated infection. An isolate from another patient-who did mount a SARS-CoV-2 IgM response-showed temperature-dependent changes in plaque size as well as increased syncytia formation and escape from serum-neutralizing antibodies. Our results indicate that not all virus isolates from immunocompromised COVID-19 patients display clear signs of phenotypic change, but increased attention should be paid to monitoring virus evolution in this patient population.

Influenza A, influenza B, and SARS-COV-2 circulation patterns in midwest Brazil during the 2022-2023 period

Until 2022, the COVID-19 pandemic caused by the SARS-CoV-2, had profoundly impacted the world. Consequently, Brazil, including the state of Goiás, was also significantly affected. Furthermore, in the second half of 2022, the state of Goiás experienced an unusual rise in influenza cases, despite it being an off-season period for influenza viruses in this region. As SARS-CoV-2 and Influenza infection have similar clinical manifestations, surveillance strategies are crucial for public health. Understanding how SARS-CoV-2 and Influenza viruses co-circulate is important for surveillance and monitoring of these patterns of respiratory infections. In this context, this investigation monitored Influenza A and B cases from symptomatic individuals diagnosed as negative for COVID-19. Between September 2022 and May 2023, among the 779 samples tested, 126 (16.2%) were positive for Influenza A, whereas 93 samples (11.9%) were positive for Influenza B. In this period, the peak Influenza infection cases did not coincide with the peak of SARS-CoV-2 infections, suggesting a seasonal shift in viral circulation patterns.

Reconstructing SARS-CoV-2 lineages from mixed wastewater sequencing data

Wastewater surveillance of SARS-CoV-2 has emerged as a critical tool for tracking the spread of COVID-19. In addition to estimating the relative case numbers using quantitative PCR, SARS-CoV-2 genomic RNA can be extracted from wastewater and sequenced. There are many existing techniques for using the sequenced RNA to determine the relative abundance of known lineages in a sample. However, it is very challenging to predict novel lineages from wastewater data due to its mixed composition and unreliable genomic coverage. In this work, we present a novel technique based on non-negative matrix factorization which is able to reconstruct lineage definitions by analyzing data from across different samples. We test the method both on synthetic and real wastewater sequencing data. We show that the technique is able to determine major lineages such as Omicron and Delta as well as sub-lineages such as BA.5.2.1. We provide a method for determining emerging lineages in wastewater without the need for genomic data from clinical samples. This could be used for routine monitoring of SARS-CoV-2 as well as other emerging viral pathogens in wastewater. Additionally, it may be used to determine more full-genome sequences for viruses with fewer available genomes.

CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment

SARS-CoV-2 infection induces the generation of virus-specific CD4+ and CD8+ effector and memory T cells. However, the contribution of T cells in controlling SARS-CoV-2 during infection is not well understood. Following infection of C57BL/6 mice, SARS-CoV-2-specific CD4+ and CD8+ T cells are recruited to the respiratory tract, and a vast proportion secrete the cytotoxic molecule granzyme B. Using depleting antibodies, we found that T cells within the lungs play a minimal role in viral control, and viral clearance occurs in the absence of both CD4+ and CD8+ T cells through 28 days postinfection. In the nasal compartment, depletion of both CD4+ and CD8+ T cells, but not individually, results in persistent, culturable virus replicating in the nasal epithelial layer through 28 days postinfection. Viral sequencing analysis revealed adapted mutations across the SARS-CoV-2 genome, including a large deletion in ORF6. Overall, our findings highlight the importance of T cells in controlling virus replication within the respiratory tract during SARS-CoV-2 infection.

SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response

During the coronavirus disease 2019 (COVID-19) pandemic, the number and types of dashboards produced increased to convey complex information using digestible visualizations. The pandemic saw a notable increase in genomic surveillance data, which genomic epidemiology dashboards presented in an easily interpretable manner. These dashboards have the potential to increase the transparency between the scientists producing pathogen genomic data and policymakers, public health stakeholders, and the public. This scoping review discusses the data presented, functional and visual features, and the computational architecture of six publicly available SARS-CoV-2 genomic epidemiology dashboards. We found three main types of genomic epidemiology dashboards: phylogenetic, genomic surveillance, and mutational. We found that data were sourced from different databases, such as GISAID, GenBank, and specific country databases, and these dashboards were produced for specific geographic locations. The key performance indicators and visualization used were specific to the type of genomic epidemiology dashboard. The computational architecture of the dashboards was created according to the needs of the end user. The genomic surveillance of pathogens is set to become a more common tool used to track ongoing and future outbreaks, and genomic epidemiology dashboards are powerful and adaptable resources that can be used in the public health response.

Anti-SARS-CoV-2 total immunoglobulin and neutralising antibody responses in healthy blood donors throughout the COVID-19 pandemic: a longitudinal observational study

INTRODUCTION

Quantifying antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and neutralising antibodies may help to understand protection at the individual and population levels. Determination of neutralising antibodies using classical virus neutralisation tests (VNT) is considered the gold standard, but they are costly and time-intensive. Enzyme-linked immunosorbent assay (ELISA)-based surrogate VNTs (sVNT) or anti-SARS-CoV-2 spike protein receptor binding domain immunoglobulins (anti-S-RBD Ig) may be suitable alternatives to VNTs. We aimed to (a) explore the correlations between anti-S-RBD Ig, VNT, and sVNT measurements and (b) describe humoral immunity against SARS-CoV-2 after vaccination, natural infection, and vaccine breakthrough infection in healthy blood donors.

METHODS

We measured total anti-SARS-CoV-2 Ig in 5714 serum samples from 2748 healthy individuals visiting the Swiss Red Cross Blood Donation Centre in Basel from 03/2020 to 04/2022. We used the Elecsys® Anti-SARS-CoV-2 immunoassay (Roche) against the N- and S-receptor binding domain (RBD) proteins. In a subset of 548 samples from 123 donors, we conducted sVNTs against the Wuhan wild-type SARS-CoV-2 (SARS-CoV-2 Neutralizing Antibodies Detection Kit; Adipogen™). In 100 samples from 40 donors, we correlated sVNT and VNTs against the wild-type (D614G WU1) virus. Surveys were sent to the blood donors to collect data on their SARS-CoV-2 infection and vaccination status. Using this data, donors were categorised as "vaccination only", "infection before vaccination", "post-vaccine breakthrough infection", and "natural infection only".

RESULTS

Our longitudinal observation study cohort consisted of 50.7% males with a median age of 31 years (range 18-75 y). Anti-SARS-CoV-2 N protein positivity rates per month indicate 57.1% (88/154) of the cohort was infected up to 04/2022. No differences in seropositivity were found between sexes, age groups, blood types (AB0 or RhD), and cytomegalovirus serostatus. We observed a high correlation between anti-S-RBD Ig and inhibition percentage (Spearman's ρ = 0.92, Kendall's τ = 0.77, p <0.0001). We determined the sensitivity and specificity for the manufacturers' thresholds for detecting virus-neutralising effects and computed the "best" cut-off based on our real-world data. We categorised 722/1138 (63.5%) donors as vaccination only (82.3%), post-vaccine breakthrough infection (7.8%), infection before vaccination (5.8%), and natural infection only (4.2%). We observed a lower inhibition percentage in the natural infection-only group than in all other vaccinated groups. The infection before vaccination group had higher anti-S-RBD Ig titres after the first vaccine dose than the other vaccinated groups.

CONCLUSION

In total, 57.1% of healthy blood donors were infected with SARS-CoV-2, but natural infection without evidence of vaccination seems to result in substantially lower neutralising antibody levels. An estimate of antibody neutralisation may be helpful to assess reinfection risk. Total anti-S-RBD Ig correlates with surrogate virus neutralisation test results, a surrogate for neutralisation; therefore, we suggest that total anti-S-RBD Ig may estimate the level of neutralising antibodies. The threshold for protection from an unfavourable clinical outcome must be evaluated in prospective clinical cohorts.

Epid data explorer: A visualization tool for exploring and comparing spatio-temporal epidemiological data

The analysis of large sets of spatio-temporal data is a fundamental challenge in epidemiological research. As the quantity and the complexity of such kind of data increases, automatic analysis approaches, such as statistics, data mining, machine learning, etc., can be used to extract useful information. While these approaches have proven effective, they require a priori knowledge of the information being sought, and some interesting insights into the data may be missed. To bridge this gap, information visualization offers a set of techniques for not only presenting known information, but also exploring data without having a hypothesis formulated beforehand. In this paper, we introduce Epid Data Explorer (EDE), a visualization tool that enables exploration of spatio-temporal epidemiological data. EDE allows easy comparisons of indicators and trends across different geographical areas and times. It facilitates this exploration through ready-to-use pre-loaded datasets as well as user-chosen datasets. The tool also provides a secure architecture for easily importing new datasets while ensuring confidentiality. In two use cases using data associated with the COVID-19 epidemic, we demonstrate the substantial impact of implemented lockdown measures on mobility and how EDE allows assessing correlations between the spread of COVID-19 and weather conditions.

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections

We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n=15). All patients received remdesivir and some also received nirmatrelvir-ritonavir or monoclonal antibodies. Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient treated with remdesivir and nirmatrelvir-ritonavir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.