SARS-CoV-2 human challenge reveals single-gene blood transcriptional biomarkers that discriminate early and late phases of acute respiratory viral infections. (preprint)

Evaluation of host-response blood transcriptional signatures of viral infection have so far failed to test whether these biomarkers reflect different biological processes that may be leveraged for distinct translational applications. We addressed this question in the SARS-CoV-2 human challenge model. We found differential time profiles for interferon (IFN) stimulated blood transcriptional responses represented by measurement of single genes. MX1 transcripts correlated with a rapid and transient wave of type 1 IFN stimulated genes (ISG) across all cell types, which may precede PCR detection of replicative infection. Another ISG, IFI27, showed a delayed but sustained response restricted to myeloid peripheral blood mononuclear cells, attributable to gene and cell-specific epigenetic regulation. These findings were reproducible in diverse respiratory virus challenges, and in natural infection with SARS-CoV-2 or unselected respiratory viruses. The MX1 response achieved superior diagnostic accuracy in early infection, correlation with viral load and identification of virus culture positivity, with potential to stratify patients for time sensitive antiviral treatment. IFI27 achieved superior diagnostic accuracy across the time course of symptomatic infection. Compared to blood, measurement of these responses in nasal mucosal samples was less sensitive and did not discriminate between early and late phases of infection.

Human SARS-CoV-2 challenge resolves local and systemic response dynamics (preprint)

The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the cellular disease dynamics remains limited. In our unique COVID-19 human challenge study we used single cell genomics of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in 16 seronegative individuals challenged with preAlpha-SARS-CoV-2. Our analyses revealed rapid changes in cell type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific timepoints or infection status. We observed that the interferon response in blood precedes the nasopharynx, and that nasopharyngeal immune infiltration occurred early in transient but later in sustained infection, and thus correlated with preventing sustained infection. Ciliated cells showed an acute response phase, upregulated MHC class II while infected, and were most permissive for viral replication, whilst nasal T cells and macrophages were infected non-productively. We resolve 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our novel computational pipeline (Cell2TCR) identifies activated antigen-responding clonotype groups and motifs in any dataset. Together, we show that our detailed time series data (covid19cellatlas.org) can serve as a 'Rosetta stone' for the epithelial and immune cell responses, and reveals early dynamic responses associated with protection from infection.

Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi (preprint)

Background. The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions. Methods. We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Primary sampling units (PSU) were selected using probability proportionate to the number of households based on the 2018 national census, followed by second-stage sampling units that were selected from listed households. A random systematic sample of households was selected from each PSU within the 7 districts. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalizations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. Results. Serum samples were analysed from 4619 participants (57% female; 65% aged 14 to 50 years), of whom 1018 (22%) had received a COVID-19 vaccine. The overall assay-adjusted seroprevalence was 86.3% (95% confidence interval (CI), 85.1% to 87.5%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18 to 50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (96% vs. 77%; risk ratio, 6.65; 95% CI, 4.16 to 11.40). Urban residents were more likely to test seropositive than those living in rural settings (91% vs. 78%; risk ratio, 2.81; 95% CI, 2.20 to 3.62). National COVID-19 data showed that at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalization, 10.7% (95% CI, 10.2 to 11.3) vs 4.86% (95% CI, 4.52 to 5.23), p<0.0001; deaths, 3.48% (95% CI, 3.18 to 3.81) vs 1.15% (95% CI, 1.00 to 1.34), p<0.0001). Conclusion. We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence but low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of at-risk populations.

Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi. (preprint)

Introduction: Understanding human mixing patterns relevant to infectious diseases spread through close contact is vital for modelling transmission dynamics and optimisation of disease control strategies. Mixing patterns in low-income countries like Malawi are not well understood. Methodology: We conducted a social mixing survey in urban Blantyre, Malawi between April and July 2021 (between the 2nd and 3rd wave of COVID-19 infections). Participants living in densely-populated neighbourhoods were randomly sampled and, if they consented, reported their physical and non-physical contacts within and outside homes lasting at least 5 minutes during the previous day. Age-specific mixing rates were calculated, and a negative binomial mixed effects model was used to estimate determinants of contact behaviour. Results: Of 1,201 individuals enrolled, 702 (58.5%) were female, the median age was 15 years (interquartile range [IQR] 5-32) and 127 (10.6%) were HIV-positive. On average, participants reported 10.3 contacts per day (range: 1-25). Mixing patterns were highly age-assortative, particularly those within the community and with skin-to-skin contact. Adults aged 20-49y reported the most contacts (median:11, IQR: 8-15) of all age groups; 38% (95%CI: 16-63) more than infants (median: 8, IQR: 5-10), who had the least contacts. Household contact frequency increased by 3% (95%CI 2-5) per additional household member. Unemployed participants had 15% (95%CI: 9-21) fewer contacts than other adults. Among long range (>30 meters away from home) contacts, secondary school children had the largest median contact distance from home (257m, IQR 78-761). HIV-positive status in adults >18 years-old was not associated with increased contact patterns (1%, 95%CI -9-12). During this period of relatively low COVID-19 incidence in Malawi, 301 (25.1%) individuals stated that they had limited their contact with others due to COVID-19 precautions; however, their reported contacts were not fewer (8%, 95%CI 1-13). Conclusion: In urban Malawi, contact rates, are high and age-assortative, with little behavioural change due to either HIV-status or COVID-19 circulation. This highlights the limits of contact-restriction-based mitigation strategies in such settings and the need for pandemic preparedness to better understand how contact reductions can be enabled and motivated. Keywords: Social contacts, Transmission, Mixing data, Infectious disease, Malawi, Africa

Dynamics of SARS-CoV-2 exposure in Malawian blood donors: a retrospective seroprevalence analysis between January 2020 and February 2021 (preprint)

BackgroundAs at end of July 2021, the COVID-19 pandemic has been less severe in sub-Saharan Africa than elsewhere. In Malawi, there have been two subsequent epidemic waves. We therefore aimed to describe the dynamics of SARS-CoV-2 exposure in Malawi. MethodsWe measured the seroprevalence of anti-SARS-CoV-2 antibodies among randomly selected blood donor sera in Malawi from January 2020 to February 2021. In a subset, we also assesed in vitro neutralisation against the original variant (D614G WT) and the Beta variant. FindingsA total of 3586 samples were selected from the blood donor database, of which 2685 (74.9%) were male and 3132 (87.3%) were aged 20-49 years. Of the total, 469 (13.1%) were seropositive. Seropositivity was highest in October 2020 (15.7%) and February 2021 (49.7%) reflecting the two epidemic waves. Unlike the first wave, both urban and rural areas had high seropositivity by February 2021, Balaka (rural, 37.5%), Blantyre (urban, 54.8%), Lilongwe (urban, 54.5%) and Mzuzu (urban, 57.5%). First wave sera showed potent in vitro neutralisation activity against the original variant (78%[7/9]) but not the Beta variant (22% [2/9]). Second wave sera potently neutralised the Beta variant (73% [8/11]). InterpretationThe findings confirm extensive SARS-CoV-2 exposure in Malawi over two epidemic waves with likely poor cross-protection to reinfection from the first on the second wave. Since prior exposure augments COVID-19 vaccine immunity, prioritising administration of the first dose in high SARS-CoV-2 exposure settings could maximise the benefit of the limited available vaccines in Malawi and the region. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed on August 16, 2021, with no language restrictions, for titles and abstracts published between Jan 1, 2020, and August 16, 2021, using the search terms: "SARS-CoV-2 seroprevalence in Africa"[Title/Abstract]) OR "SARS-CoV-2 seroprevalence in blood donors" [Title/Abstract] OR "SARS-CoV-2 seroprevalence in Malawi", and found 15 records. There are limited SARS-CoV-2 seroprevalence studies in sub Saharan Africa, however the few that are available report high seroprevalence than can be deduced from the respective national reported COVID-19 cases and deaths. Only two published SARS-CoV-2 serosurveys were done on blood donors, from Kenya and Madagascar. Blood donor serosurveys have been recommended by the WHO as an important tool for assessing the spread of SARS-CoV-2 and estimating the burden of COVID-19 pandemic. Added value of this studyUnlike previous SARS-CoV-2 blood donor serosurveys in African populations that were conducted for a maximum period of 9 months, our study covers a full year from January 2020 to February 2021, capturing potential introduction of SARS-CoV-2 into Malawi as well as the two epidemic waves. This study provides evidence against the speculation that SARS-CoV-2 had been circulating more widely in sub-Saharan Africa before the first detected cases. It also provides supporting evidence suggesting that the Beta variant was the likely driver of the second wave that resulted in high SARS-CoV-2 seropositivity in January to February 2021 in Malawi. Implications of all the available evidenceOur results show extensive community transmission of SARS-CoV-2 in Malawi as reflected in the blood donors serosurvey, with almost half the sample population being seropositive for anti-SARS-CoV-2 antibodies by February 2021. This has implications for COVID-19 vaccination policy in sub-Saharan Africa (SSA), where there are limited available vaccine doses. Considering that prior exposure to SARS-CoV-2 augments COVID-19 vaccine immunity, strategies to maximise administration of the first vaccine dose, while waiting for more vaccines to become available, could maximise the benefits of the limited available vaccines in high SARS-CoV-2 exposure settings in SSA such as Malawi.

Low seropositivity and sub-optimal neutralisation rates in patients fully vaccinated against COVID-19 with B cell malignancies. (preprint)

Patients with haematological malignancies are at increased risk of severe disease and death from COVID-19 and are less likely to mount humoral immune responses to COVID-19 vaccination, with the B cell malignancies a particularly high-risk group. Our COV-VACC study is evaluating the immune response to COVID-19 vaccination in patients with B cell malignancies. Eligible patients were either receiving active treatment or had received treatment within the last 24 months. Patients were vaccinated with either the BNT162b2 (Pfizer-BioNTech) (n=41) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) (n=14) vaccines. The median age of participants was 60 years (range: 27-82) and 50% were receiving systemic anti-cancer therapy (SACT) at the time of vaccination. This interim analysis from the first 55 participants describes anti-S seropositivity rates, neutralising antibody activity and association with peripheral lymphocyte subsets. After the first vaccine dose, 36% overall had detectable anti-S antibodies rising to 42% after the second dose. Sera from seropositive patients was assessed for neutralisation activity in vitro. Of the seropositive patients after first dose (n=17), only 41% were able to neutralise SARS-CoV-2 pseudotyped virus with a 50% inhibitory dilution factor (ID50) of >1:50. After two doses (n=21) 57% of the seropositive patients had detectable neutralisation activity (median ID50 of 1:469, range 1:70 - 1:3056). Total blood lymphocyte, CD19, CD4 and CD56 counts were significantly associated with seropositivity. Patients vaccinated more than 6 months after completing therapy were significantly more likely to develop antibodies than those within 6 months of treatment or on active treatment; OR: 5.93 (1.29 - 27.28). Our data has important implications for patients with B cell malignancies as we demonstrate a disconnect between anti-S seropositivity and virus neutralisation in vitro following vaccination against COVID-19. Urgent consideration should be given to revaccinating patients with B-cell malignancies after completion of anti-cancer treatment as large numbers currently remain at high risk of infection with the increasing transmission of SARS-CoV-2 in many countries.