COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition (preprint)

Newborns can acquire immunological protection to SARS-CoV-2 through vaccine-conferred antibodies in human breast milk. However, there are some concerns around lactating mothers with regards to potential short- and long-term adverse events and vaccine-induced changes to their breast milk microbiome composition, which helps shape the early-life microbiome. Here, we recruited 49 lactating mothers from Hong Kong who received two doses of BNT162b2 vaccine between June 2021 and August 2021. Breast milk samples were self-collected by participating mothers pre-vaccination, one week post-first dose, one week post-second dose, and one month post-second dose. The levels of SARS-CoV-2 spike-specific IgA and IgG in breast milk peaked at one week post-second dose. Subsequently, the levels of both antibodies rapidly waned in breast milk, with IgA levels returning to baseline levels one month post-second dose. The richness and composition of human breast milk microbiota changed dynamically throughout the vaccination regimen, but the abundances of beneficial microbes such as Bifidobacterium species did not significantly change after vaccination. In addition, we found that baseline breast milk bacterial composition can predict spike-specific IgA levels at one week post-second dose (Area Under Curve: 0.72, 95% confidence interval: 0.58–0.85). Taken together, our results suggest that infants may acquire immunological protection from breast milk from SARS-CoV-2-vaccinated mothers by both the vertical transmission of antibodies and beneficial microbiota.

Altered ISGylation drives aberrant macrophage-dependent immune responses during SARS-CoV-2 infection (preprint)

Interferon stimulated gene 15 (ISG15) is a ubiquitin like modifier frequently induced during virus infections and involved in versatile host defense mechanisms. Not surprisingly, many viruses including SARS-CoV-2 have evolved de-ISGylating activities to antagonize its effect. In this study we compared ISG15-driven macrophage responses upon infection by influenza, Zika and SARS-CoV-2 viruses. ISG15 and its modifying enzymes were upregulated in human macrophages after infection with all three viruses. While influenza and Zika viruses induced cellular ISGylation, SARS-CoV-2 triggered hydrolysis of ISG15 modifications instead, to generate free, extracellular ISG15 from macrophages and dendritic cells, but not from bronchial epithelial cells. Extracellular ISG15 was released independent of the conventional secretory pathway or cell death, but instead, depended on a non-classical autophagy-related secretory process. Increase of extracellular ISG15 was also reflected in serum samples from COVID-19 patients. The high ratio of free versus conjugated ISG15 in SARS-CoV-2 infected cells triggered macrophage polarization towards a M1 phenotype, increased secretion of pro-inflammatory cytokines, e.g. MCP-1 (CCL2), IL-1, TNF and IL-6, and attenuated antigen presentation. Depleting ISG15 conjugating enzymes Ube1L and HERC5 further increased free ISG15 and exacerbated this effect. We could recapitulate this phenomenon by expressing the wild-type but not the catalytically inactive PLpro de-ISGylating enzyme of SARS-CoV-2. Proteomic analyses of the secretome from SARS-CoV-2 infected macrophages revealed that besides ISG15, it displayed significant enrichment in non-classical secretory proteins and inflammatory responses, which was further amplified by free ISG15. Collectively, our results indicate that increased proportions of free ISG15 dramatically alter macrophage responses and is likely a key feature of cytokine storms triggered by highly pathogenic respiratory viruses such as influenza and SARS-CoV-2.

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients (preprint)

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.