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On 8–11 April 2024, a Keystone meeting on human immunodeficiency virus and emerging and re-emerging viruses convened in Hannover, Germany, aiming to unite researchers studying viruses of global concern, and gain a deep understanding of unique and shared viral disease mechanisms to facilitate pandemic preparedness.

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.

A Cenozoic reconstruction of the δ³⁴S of marine sulfate suggests a shift in the locus of pyrite burial from shallow seas to the open ocean during the early Eocene.

Khairallah et al., investigate the host proteins associated with a strong neutralizing antibody response to SARS-CoV-2. High neutralizing antibody responses to SARS-CoV-2 are associated with specific protein expression patterns, especially HSPA8 and pathways like fatty acid metabolism, which can predict immune strength and correlate with disease severity.

Genetically identical cells produce variable levels of a given protein at a given time, termed 'noise' in gene expression. The dynamics of such noise over time has now been followed in human cancer cells. The work reveals surprisingly long-lasting 'memories' of individual cell states, which can last for more than two generations in culture.

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.

The Omicron BA.2.86 subvariant differs from previous variants by over 30 spike mutations. Here, the authors report that BA.2.86 likely evolved in Southern Africa and that its immune escape is not larger than recently circulating SARS-CoV-2 strains. Neither its replication nor its pathogenicity are enhanced in vitro.

The spike protein of the Omicron variant of SARS-CoV-2 has a higher affinity for ACE2 than Delta, and a marked change in its antigenicity increases Omicron’s evasion of therapeutic and vaccine-elicited neutralizing antibodies.

Creating international viral biosafety guidelines are key to clearing up confusion, regaining trust and ensuring that essential research continues.

Emerging SARS-CoV-2 Omicron sub-lineages BA.4 and BA.5 raise concerns about potential immune evasion. Here, Khan et al. show that both BA.4 and BA.5 are able to escape immune response induced by prior BA.1 infection, but that this effect is less pronounced in vaccinated individuals.

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.

There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.

Comprenhensive analysis of human antibody responses to SARS-CoV-2 variants and animal sarbecoviruses finds that Omicron escapes neutralization more readily than distantly related animal sarbecoviruses.

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.

Understanding the heterogeneity of HIV infection, such as in persons with non-suppressible HIV-1 viremia despite adherence to antiretroviral treatment, is crucial to better tailor therapeutic interventions to abrogate HIV-1 persistence.

Understanding the effect of vaccination on emerging SARS-CoV-2 variants of concern is of increasing importance. Here, James et al. report that two doses of vaccination with the Pfizer-BioNTech vaccine induce more robust immune responses to the B.1.1.7 and B.1.351 SARS-CoV-2 lineages than does natural infection.

In this Review, Sigal et al. explore SARS-CoV-2 persistence mechanisms, the frequency of persistent infections, their role in accelerated evolution and their link to variant emergence hot spots. The Review also addresses symptoms, management and the connection between persistence and post-COVID conditions.

At the population level we are seeing milder disease during the Omicron wave of the SARS-CoV-2 pandemic. Is this due to the virus or pre-existing immunity, and what should we expect next?

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.

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.

The Omicron variant of SARS-CoV-2 has been reported to cause milder disease in adults but lead to increased hospital admissions in children. How can we compare disease severity in Omicron and Delta infections, and how should differences be interpreted?

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.

Kolloli et al. examine whether aggregation contributes to enhanced pathogenicity of Mycobacterium tuberculosis in a rabbit model of pulmonary infection. They demonstrate that aggregation increases the ability of M. tuberculosis to grow robustly and promote inflammation and host cell death in the rabbit lungs, thus increasing disease burden.

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.

The neutralization of SARS-CoV-2 and variants of concern by nine monoclonal antibodies (mAb) isolated from convalescent donors infected with the Wuhan-Hu-1 strain alongside structural characterization of two of the mAbs in complex with the RBD and spike are presented.