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The SARS-CoV-2 PANGO lineage C.1.2 has been under monitoring by global health authorities as it has spread worldwide. Here, Bhiman and colleagues characterise the emergence of the lineage, and its neutralisation sensitivity using data from vaccinees and previously infected individuals.

SARS-CoV-2 variant-specific neutralizing antibodies (nAbs) mediate protection against infection by the cognate variant to distinct extents, while the majority of protection elicited by natural infection is not mediated by nAbs.

The 501Y.V2 variant of SARS-CoV-2 in South Africa became dominant over other variants within weeks of its emergence, suggesting that this variant is linked to increased transmissibility or immune escape.

Substitutions in SARS-CoV-2 spike protein present in the B.1.351 variant first detected in South Africa, when expressed in pseudoviruses, mediate escape from neutralization by monoclonal antibodies under clinical development and by plasma from individuals previously infected with SARS-CoV-2, but do not prevent binding of convalescent plasma to recombinant spike protein containing B.1.351 lineage substitutions.

Genomic epidemiology studies have indicated southern Africa as likely sources of emergence of six Omicron lineages since November 2021. Here, the authors trace the geographic origins and dispersion patterns of these six lineages and highlight Gauteng province in South Africa as likely to have played a key role.

A minority of HIV-1–infected individuals develop broadly neutralizing antibodies, which are considered an important goal of many HIV vaccine strategies. Moore et al. now report their study of the evolution of a broadly neutralizing antibody response targeting a glycan on the viral envelope in two HIV-1–infected individuals. Their findings show that the targeted glycan is absent early in acute infection but develops over time as the virus escapes initial antibody-mediated pressure.

South Africa experienced a resurgence in COVID-19 in 2022 driven by Omicron subvariants BA.4 and BA.5. Here, the authors investigate the severity of infections caused by these subvariants, and find no difference in the risk of severe outcomes when compared to Omicron BA.1, whilst all Omicron subvariants were less severe than Delta.

High-throughput, single-copy sequencing of SARS-CoV-2 spike in a longitudinal cohort of people with and without HIV infection demonstrates striking intra-host diversity and adaptive evolution of SARS-CoV-2 in people with advanced HIV infection.

SARS-CoV-2 wastewater surveillance could provide an important means of monitoring population trends as clinical testing decreases. Here, the authors demonstrate the use of wastewater to track variants of concern through a sentinel wastewater surveillance system in South Africa.

Emergence of the Omicron BA.1/2 SARS-CoV-2 subvariants led to a wave of infection South Africa. Here, the authors use serological data from a prospective household study to characterise infection rates in the context of diverse immune histories following vaccination and exposure to different variants.

A study quantifying the neutralization of severe acute respiratory syndrome coronavirus 2 variants in individuals infected with Omicron/BA.1 shows that vaccinated individuals previously infected with Omicron have enhanced protection against reinfection with current variants, \including Omicron/BA.2, while Omicron/BA.1 infected unvaccinated individuals have limited protection.

T cell responses to spike protein from the SARS-CoV-2 Omicron variant (B.1.1.529) are broadly similar to the responses to ancestral, Beta (B.1.351) and Delta (B.1.617.2) spike protein in vaccinated, infected and unvaccinated individuals.

The genomic profile and early transmission dynamics of the Omicron strain of SARS-CoV-2.

Plasma from individuals vaccinated with BNT162b2 exhibits 22-fold less neutralization capacity against Omicron (B.1.1.529) than against an ancestral SARS-CoV-2 strain but residual neutralization is maintained in those with high levels of neutralization of ancestral virus.

The World Health Organization framework for tracking SARS-CoV-2 variants has been updated to reflect the continued evolution of the virus; this framework could be adapted for other emerging respiratory diseases with epidemic and pandemic potential.

Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic.

Alum coupled to protein immunogens via site-specific phosphoserine-containing linkers enhances long-lived B cell responses and can selectively direct antibodies toward protective neutralizing epitopes.

Here, the authors present cryoEMPEM, a method for high-resolution structural analysis of vaccine-elicited polyclonal antibody responses. They apply cryoEMPEM in combination with standard serology experiments to characterize the polyclonal antibody (pAb) responses elicited in rhesus macaques by HIV Env trimer immunogens and were able to determine up to 8 different polyclonal antibody structures in complex with their respective antigen from a single cryoEM dataset.

Knowledge on how antibody responses have evolved is critical for the induction of protective immunity. Here the authors analyse, using high-throughput sequencing of both exon and intron regions, the mutation and lineage development of an HIV-neutralizing antibody to find an unexpected early emergence of broadly neutralizing species.

A group convened and led by the Virus Evolution Working Group of the World Health Organization reports on its deliberations and announces a naming scheme that will enable clear communication about SARS-CoV-2 variants of interest and concern.

Genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth COVID-19 pandemic wave in South Africa, shows continued viral diversification and provides insights into the potential mechanisms underlying the ability of the new lineages to outcompete their predecessors.

A longitudinal study of an individual patient developing neutralizing antibodies against HIV-1 (targeting the V1V2 region of gp120) reveals how such neutralizing antibodies develop and evolve over time, providing important insights relevant to vaccine development.

Interrogation of 1,365 near whole-genome sequences of SARS-CoV-2 variants isolated in South Africa during the first 6 months of the global pandemic reveals three major monophyletic lineages responsible for more than half of the infections in the country and underscores the value of integrating genomic surveillance methods to inform the national pandemic response.

In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.

Cross-neutralization assays of early variants and the 501Y.V2 variant of SARS-CoV-2 show that plasma from individuals infected with 501Y.V2 effectively neutralizes all variants, indicating that a vaccine that targets 501Y.V2 may also be effective against other SARS-CoV-2 variants.

Penny Moore and colleagues identify viral variants from an HIV-1 infected individual that drove maturation of the antibody response from an unmutated common ancestor, ultimately resulting in both broadly neutralizing and strain-specific antibody sublineages.