Chronogram: an R package for data curation and analysis of infection and vaccination cohort studies

Open Letter: Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium

Airway-resident T cells from unexposed individuals cross-recognize SARS-CoV-2

High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia

Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Lessons from Rwanda: Building systems to protect against infectious diseases and biothreats

Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study

Non-pharmaceutical interventions and the emergence of pathogen variants

Sample size calculations for pathogen variant surveillance in the presence of biological and systematic biases

Emerging pathogen evolution

Strengthening Pathogen and Antimicrobial Resistance Surveillance by Environmental Monitoring in Sub-Saharan Africa: A Stakeholder Survey.

The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle

SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle (RO) to enable RNA replication1. The SARS-CoV-2 RO is composed of double membrane vesicles (DMVs) tethered to the endoplasmic reticulum (ER) by thin membrane connectors2, but the viral proteins and the host factors involved are currently unknown. Here we identify the viral non-structural proteins (NSPs) that generate the SARS-CoV-2 RO. NSP3 and NSP4 generate the DMVs while NSP6, through oligomerization and an amphipathic helix, zippers ER membranes and establishes the connectors. The NSP6ΔSGF mutant, which arose independently in the α, β, γ, η, ι, and λ variants of SARS-CoV-2, behaves as a gain-of-function mutant with a higher ER-zippering activity. We identified three main roles for NSP6: to act as a filter in RO-ER communication allowing lipid flow but restricting access of ER luminal proteins to the DMVs, to position and organize DMV clusters, and to mediate contact with lipid droplets (LDs) via the LD-tethering complex DFCP1-Rab18. NSP6 thus acts as an organizer of DMV clusters and can provide a selective track to refurbish them with LD-derived lipids. Importantly, both properly formed NSP6 connectors and LDs are required for SARS-CoV-2 replication. Our findings, uncovering the biological activity of NSP6 of SARS-CoV-2 and of other coronaviruses, have the potential to fuel the search for broad antiviral agents.

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

SARS-CoV-2 has undergone progressive change with variants conferring advantage rapidly becoming dominant lineages e.g. B.1.617. With apparent increased transmissibility variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the UK. 

Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant

We recently reported vaccine effectiveness (VE) estimates against symptomatic disease with the Delta (B.1.617.2) variant.(1) After a full course, VE reached 88% with the Pfizer/BioNTech BNT162b2 vaccine and 67% with the AstraZeneca ChAdOx1 AZD1222 vaccine. This provided important evidence that despite modest reductions in protection, vaccines remain effective against Delta. However, the very recent emergence of the variant and the relatively low case numbers meant that it was not possible to estimate VE against severe disease.

Immune Evasion of SARS-CoV-2 Variants of Concern is Driven by Low Affinity to Neutralizing Antibodies

Abstract SARS-CoV-2 VOCs immune evasion is mainly due to lower cross-reactivity from previously elicited class I/II neutralizing antibodies, while increased affinity to hACE2 plays a minor role. The affinity between antibodies and VOC is impacted by remodeling of the electrostatic surface potential of the Spike RBDs. P.3 variant is a putative VOC.

Genetic Evidence and Host Immune Response in Persons Reinfected with SARS-CoV-2, Brazil

The dynamics underlying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection remain poorly understood. We identified a small cluster of patients in Brazil who experienced 2 episodes of coronavirus disease (COVID-19) in March and late May 2020. In the first episode, patients manifested an enhanced innate response compared with healthy persons, but neutralizing humoral immunity was not fully achieved. The second episode was associated with different SARS-CoV-2 strains, higher viral loads, and clinical symptoms. Our finding that persons with mild COVID-19 may have controlled SARS-CoV-2 replication without developing detectable humoral immunity suggests that reinfection is more frequent than supposed, but this hypothesis is not well documented.