Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution (preprint)

Measures to control the COVID-19 pandemic such as antiviral therapy and vaccination have been challenged by ongoing virus evolution under antiviral and immune pressures. Understanding viral evolutionary dynamics is crucial for responding to SARS-CoV-2, and preparing for the next pandemic, by informing prediction of virus adaptation, public health strategies, and design of broadly effective therapies. Whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic enabled fine-grained studies of virus evolution in the human population. Serial passaging in vitro offers a controlled environment to investigate the emergence and persistence of genetic variants that may confer selective advantage. Nine virus lineages, including four "variants of concern" and three former "variants under investigation" as designated by the World Health Organisation, were chosen to investigate intra- and inter-lineage evolution through long-term serial passaging in Vero E6 cells. Viruses were sampled over at least 33 passages (range 33-100) and analysed using WGS to examine evolutionary dynamics and identify key mutations with implications for virus fitness, transmissibility, and immune evasion. All passages continued to replicate in culture, despite regular accumulation of mutations. There was evidence of convergent acquisition of mutations both across passage lines and compared with contemporaneous SARS CoV-2 clinical sequences from population studies. Some of these convergent mutations are hypothesised to be important in proliferation of SARS-CoV-2 lineages, such as by evading host immune responses (e.g. S:A67V, S:H655Y). Given these mutations arose in vitro, in the absence of a multicellular host immune response, this suggests virus genome mutation resulted from stochastic events, rather than immune-driven mutation. There was a regular gain and loss of low-frequency variants during serial passaging, but some became fixed in subsequent multiple passages, suggesting either a benefit of the mutation in vitro, or at least a lack of deleterious effect. Our findings reveal valuable insights into the evolution of SARS-CoV-2 by quantitatively investigating evolutionary dynamics of the virus over the greatest number of serial passages to date. Knowledge of these evolutionary trends will be useful for public health and the development of antiviral and vaccine measures to reduce the effects of SARS CoV-2 infection on the human population.

Measuring symptom burden in patients with cancer during a pandemic: the MD Anderson symptom inventory for COVID-19 (MDASI-COVID).

BACKGROUND: Symptom expression in SARS-CoV-2 infection (COVID-19) may affect patients already symptomatic with cancer. Patient-reported outcomes (PROs) can describe symptom burden during the acute and postacute stages of COVID-19 and support risk stratification for levels of care. At the start of the COVID-19 pandemic, our purpose was to rapidly develop, launch through an electronic patient portal, and provide initial validation for a PRO measure of COVID-19 symptom burden in patients with cancer. METHODS: We conducted a CDC/WHO web-based scan for COVID-19 symptoms and a relevance review of symptoms by an expert panel of clinicians treating cancer patients with COVID-19 to create a provisional MD Anderson Symptom Inventory for COVID-19 (MDASI-COVID). English-speaking adults with cancer who tested positive for COVID-19 participated in the psychometric testing phase. Patients completed longitudinal assessments of the MDASI-COVID and the EuroQOL 5 Dimensions 5 Levels (EQ-5D-5L) utility index and visual analog scale, which were presented through an electronic health record patient portal. To test the validity of the MDASI-COVID to distinguish between known groups of patients, we hypothesized that patients hospitalized, including having a hospitalization extended, for COVID-19 versus those not hospitalized would experience higher symptom burden. Correlation of mean symptom severity and interference scores with relevant EQ-5D-5L scores tested concurrent validity. The reliability of the MDASI-COVID was evaluated by calculating Cronbach alpha coefficients and test-retest reliability was evaluated by calculating Pearson correlation coefficients between the initial assessment and a second assessment no more than 14 days later. RESULTS: The web-based scan found 31 COVID-19-related symptoms; rankings of a 14-clinician expert panel reduced this list to 11 COVID-specific items to be added to the core MDASI. Time from literature scan start in March 2020 to instrument launch in May 2020 was 2 months. Psychometric analysis established the MDASI-COVID's reliability, known-group validity, and concurrent validity. CONCLUSIONS: We were able to rapidly develop and electronically launch a PRO measure of COVID-19 symptom burden in patients with cancer. Additional research is needed to confirm the content domain and predictive validity of the MDASI-COVID and define the symptom burden trajectory of COVID-19.

Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA vaccination in adolescents aged 12-17 years: A systematic review and meta-analysis.

The rapid emergence of COVID-19 variants of concern (VOCs) has hindered vaccine uptake. To inform policy, we investigated the effectiveness of the BNT162b2 vaccination among adolescents against symptomatic and severe COVID-19 diseases using mostly real-world data (15 studies). We searched international databases until May 2022 and used Cochrane's risk of bias tools for critical appraisal. Random effects models were used to examine overall vaccine effectiveness (VE) across studies (general inverse-variance) and the effect of circulating VOCs on VE (log relative ratio and VE). Meta-regression assessed the effect of age and time on VE (restricted-maximum likelihood). BNT162b2 VE against PCR-confirmed SARS-CoV-2 was 82.7% (95%CI: 78.37-87.31%). VE was higher for severe (88%) than non-severe (35%) outcomes and declining over time improved following booster dose in omicron era [73%(95%CI:65-81%)]. Fully vaccinated adolescents are protected from COVID-19 circulating VOCs by BNT162b2 especially for the need of critical care or life support.

Systematic review and meta-analysis of myocarditis and pericarditis in adolescents following COVID-19 BNT162b2 vaccination.

Myocarditis and pericarditis are frequent complications of COVID-19, but have also been reported following vaccination against COVID-19 in adolescents. To build vaccine confidence and inform policy, we characterized the incidence of myocarditis/pericarditis in adolescents following BNT162b2 vaccination and explored the association with dose and sex. We searched national and international databases for studies reporting the incidence of myocarditis/pericarditis following BNT162b2 vaccination as the primary endpoint. The intra-study risk of bias was appraised, and random-effects meta-analyses were performed to estimate the pooled incidence by dose stratified by sex. The pooled incidence of myocarditis/pericarditis was 4.5 (95%CI: 3.14-6.11) per 100,000 vaccinations across all doses. Compared to dose 1, the risk was significantly higher after dose 2 (RR: 8.62, 95%CI: 5.71-13.03). However, adolescents experienced a low risk after a booster dose than after dose 2 (RR: 0.06; 95%CI: 0.04-0.09). Males were approximately seven times (RR: 6.66, 95%CI: 4.77-4.29) more likely than females to present myocarditis/pericarditis. In conclusion, we found a low frequency of myocarditis/pericarditis after BNT162b2, which occurred predominantly after the second dose in male adolescents. The prognosis appears to be favorable, with full recovery in both males and females. National programs are recommended to adopt the causality framework to reduce overreporting, which undercuts the value of the COVID-19 vaccine on adolescent life, as well as to extend the inter-dose interval policy, which has been linked to a lower frequency of myocarditis/pericarditis.

Immunogenicity and reactogenicity of COVID-19 Pfizer-BioNTech (Bnt162b2) mRNA vaccination in immunocompromised adolescents and young adults: a systematic review and meta-analyses.

BACKGROUND: This study aimed to evaluate the safety and effectiveness of the BNT162b2 vaccine in immunocompromised adolescents and young adults. RESEARCH DESIGN AND METHODS: The study conducted a meta-analysis of post-marketing studies examining BNT162b2 vaccination efficacy and safety among immunocompromised adolescents and young adults worldwide. The review included nine studies and 513 individuals aged between 12 and 24.3 years. The study used a random effect model to estimate pooled proportions, log relative risk, and mean difference, and assessed heterogeneity using the I2 test. The study also examined publication bias using Egger's regression and Begg's rank correlation and assessed bias risk using ROBINS-I. RESULTS: The pooled proportions of combined local and systemic reactions after the first and second doses were 30% and 32%, respectively. Adverse events following immunization (AEFI) were most frequent in rheumatic diseases (40%) and least frequent in cystic fibrosis (27%), although hospitalizations for AEFIs were rare. The pooled estimations did not show a statistically significant difference between immunocompromised individuals and healthy controls for neutralizing antibodies, measured IgG, or vaccine effectiveness after the primary dose. However, the evidence quality is low to moderate due to a high risk of bias, and no study could rule out the risk of selection bias, ascertainment bias, or selective outcome reporting. CONCLUSIONS: This study provides preliminary evidence that the BNT162b2 vaccine is safe and effective in immunocompromised adolescents and young adults, but with low to moderate evidence quality due to bias risk. The study calls for improved methodological quality in studies involving specific populations.

Capillary driven microfluidic sequential flow device for point-of-need ELISA: COVID-19 serology testing.

A capillary-driven microfluidic sequential flow device, designed for eventual at-home or doctor's office use, was developed to perform an enzyme-linked immunosorbent assay (ELISA) for serology assays. Serology assays that detect SARS-CoV-2 antibodies can be used to determine prior infection, immunity status, and/or individual vaccination status and are typically run using well-plate ELISAs in centralized laboratories, but in this format SARs-CoV-2 serology tests are too expensive and/or slow for most situations. Instead, a point-of-need device that can be used at home or in doctor's offices for COVID-19 serology testing would provide critical information for managing infections and determining immune status. Lateral flow assays are common and easy to use, but lack the sensitivity needed to reliably detect SARS-CoV-2 antibodies in clinical samples. This work describes a microfluidic sequential flow device that is as simple to use as a lateral flow assay, but as sensitive as a well-plate ELISA through sequential delivery of reagents to the detection area using only capillary flow. The device utilizes a network of microfluidic channels made of transparency film and double-sided adhesive combined with paper pumps to drive flow. The geometry of the channels and storage pads enables automated sequential washing and reagent addition steps with two simple end-user steps. An enzyme label and colorimetric substrate produce an amplified, visible signal for increased sensitivity, while the integrated washing steps decrease false positives and increase reproducibility. Naked-eye detection can be used for qualitative results or a smartphone camera for quantitative analysis. The device detected antibodies at 2.8 ng mL-1 from whole blood, while a well-plate ELISA using the same capture and detection antibodies could detect 1.2 ng mL-1. The performance of the capillary-driven immunoassay (CaDI) system developed here was confirmed by demonstrating SARS-CoV-2 antibody detection, and we believe that the device represents a fundamental step forward in equipment-free point-of-care technology.

The Impact of Coronavirus Disease 2019 on Viral, Bacterial, and Fungal Respiratory Infections

Although coronavirus disease 2019 (COVID-19) remains an ongoing threat, concerns regarding other respiratory infections remain. Throughout the COVID-19 pandemic various epidemiologic trends have been observed in other respiratory viruses including a reduction in influenza and respiratory syncytial virus infections following onset of the COVID-19 pandemic. Observations suggest that infections with other respiratory viruses were reduced with social distancing, mask wearing, eye protection, and hand hygiene practices. Coinfections with COVID-19 exist not only with other respiratory viruses but also with bacterial pneumonias and other nosocomial and opportunistic infections. Coinfections have been associated with increased severity of illness and other adverse outcomes.

Performance of the PanbioTM COVID-19 Ag rapid test in a health care setting in Ouagadougou, Burkina Faso

This study aimed to evaluate the performance of the PanbioTM Covid-19 Ag Rapid Test (Abbott) in a medical center in Ouagadougou. The PanbioTM COVID-19 Ag test was evaluated from January 26 to March 31, 2021 in symptomatic and asymptomatic patients in the medical Centre of Kossodo. A total of 268 individuals were tested by both SARS-CoV-2 RT-PCR, and antigen RDT. Of these 268 individuals, 52 were positive and 216 were negative for COVID-19 RT-PCR. The performance parameters of the test and its Kappa agreement with the RT-PCR were calculated according to the presence or absence of symptoms in the patients on one hand, and according to the time onset of symptoms on the other hand. The sensitivity of the PanbioTM COVID-19 Ag Rapid Test ranged from 29.63% (95% CI: 13.75 to 50.18) among COVID-19 asymptomatic patients, to 87.5% (95% CI: 52.91 to97.76) among symptomatic patients with symptom onset time of 1-5 days. Similarly, the PanbioTM COVID-19 Ag Rapid Test specificity was 97.3% (95% CI: 90.58 to 99.67) and 96.4% (95% CI: 91.81 to 98.82) in symptomatic and asymptomatic RT PCR negative patients. The PanbioTM COVID-19 Ag Rapid Test shows good performance in detecting COVID-19 cases in patients with a symptom onset time of less than seven (7) days. This performance is even better when the symptom onset is reduced to five (5) days. The results show that the antigen RDT is not suitable for COVID-19 detection among asymptomatic patients.

A longitudinal study of olfactory dysfunction and parosmia in mild COVID-19 cases.

Background: COVID-19-related olfactory dysfunction (OD) can persist long after patients recover from acute infection, yet few studies have investigated the long-term progression of this complication. Moreover, existing studies are focused on hyposmia/anosmia but parosmia is becoming an increasingly recognized long-term symptom. Methods: We completed a longitudinal study about OD in individuals with mild cases of COVID-19. Participants completed a questionnaire and Brief Smell Identification Test (BSIT) one week, one month and one year after diagnosis. At one-year, participants completed an additional survey about parosmia. Results: We obtained questionnaires and psychophysical olfactory testing information from participants at one week (n=45), one month (n=38), and one year (n=33) post COVID-19 diagnosis. At one-year, 15.2% of participants had persistent OD and 66.7% of participants reported experiencing parosmia at some point following COVID-19 diagnosis. The mean onset of parosmia was 1.3 weeks (SD: 1.9 weeks) after diagnosis, although two patients reported delayed onset (>4 weeks after diagnosis). Eight patients (24.2%) reported ongoing parosmia one year after diagnosis. Of the patients whose parosmia resolved, the mean duration of symptoms was 7.2 weeks (SD: 7.3 weeks). Conclusion: Decreased sense of smell associated with COVID-19 infection has received significant recognition in both the media and in the medical literature. Symptoms of OD and parosmia were common in our patients with COVID-19. Hyposmia, anosmia, and parosmia, all decrease quality of life, necessitating continued research to understand the pathogenesis, course of symptoms, and possible treatment for these complications.

Immunomodulatory Agents for Coronavirus Disease-2019 Pneumonia.

Morbidity and mortality from COVID-19 is due to severe inflammation and end-organ damage caused by a hyperinflammatory response. Multiple immunomodulatory agents to attenuate this response have been studied. Corticosteroids, specifically dexamethasone, have been shown to reduce mortality in hospitalized patients who require supplemental oxygen. Interleukin-6 antagonist, tocilizimab, and Janus kinase inhibitors have also been shown to reduce mortality. However, patients who have severe pulmonary end-organ damage requiring mechanical ventilation or extracorporeal membrane oxygenation appear not to benefit from immunomodulatory therapies. This highlights the importance of appropriate timing to initiate immunomodulatory therapies in the management of severe COVID-19 disease.

Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level.

BACKGROUND: The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. METHODS: Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. FINDINGS: In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are uniquely dominant in this region in the later months of 2022. INTERPRETATION: Whilst the appearance of a diverse range of omicron lineages has led to primary or partial resistance to clinically approved monoclonal antibodies, the maturation of the antibody response across both cohorts and a large donor pools importantly observes increasing breadth in the antibody neutralisation responses over time with a trajectory that covers both current and known emerging variants. FUNDING: This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.

Coronaviruses, Lysosomes, and Secondary Bacterial Infections: Coronaviruses Outsmart the Host.

Lysosomes are key organelles that contribute to homeostatic functions such as autophagy-mediated recycling of cellular components and innate immune response through phagocytosis-mediated pathogen killing during infections. Viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has developed unique adaptation to not only avoid lysosome-mediated destruction but also actively utilize lysosomal machinery to both enter and exit cells. To survive the highly hostile lysosomal environment, coronaviruses deacidify the lysosomes, potentially by manipulating H+ ion exchange across the lysosomal lumen, ensuring coronavirus survival. At the same time, this deacidification not only impairs cellular homeostatic functions such as autophagy but also renders the host susceptible to secondary bacterial infections. Furthermore, lysosomal enzymes promote extensive cell death and tissue damage during secondary bacterial infections. Thus, targeting lysosomal pathways provide a great opportunity to limit both viral replication and subsequent negative impact on host immunity against secondary bacterial infections.

Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2.

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In this study, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 µM and 9.0 µM. In addition, three compounds inhibited PLpro with IC50 ranging from 1.9 µM to 3.3 µM. To verify the specificity of Mpro and PLpro inhibitors, our experiments included an assessment of common causes of false positives such as aggregation, high compound fluorescence, and inhibition by enzyme oxidation. Altogether, we confirmed novel classes of specific Mpro and PLpro inhibitors. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.

The Impact of Coronavirus Disease 2019 on Viral, Bacterial, and Fungal Respiratory Infections.

Although coronavirus disease 2019 (COVID-19) remains an ongoing threat, concerns regarding other respiratory infections remain. Throughout the COVID-19 pandemic various epidemiologic trends have been observed in other respiratory viruses including a reduction in influenza and respiratory syncytial virus infections following onset of the COVID-19 pandemic. Observations suggest that infections with other respiratory viruses were reduced with social distancing, mask wearing, eye protection, and hand hygiene practices. Coinfections with COVID-19 exist not only with other respiratory viruses but also with bacterial pneumonias and other nosocomial and opportunistic infections. Coinfections have been associated with increased severity of illness and other adverse outcomes.

Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak.

Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta-ORF7aΔ17del) in most Australian outbreak cases. Studies from early in the COVID-19 pandemic suggest that frameshift-inducing deletions in ORF7a do not persist for long in the population; therefore, Delta-ORF7aΔ17del genomes should have disappeared early in the Australian outbreak. In this study, we conducted a retrospective analysis of global Delta genomes to characterise the dynamics of Delta-ORF7aΔ17del over time, determined the frequency of all ORF7a deletions worldwide, and compared global trends with those of the Australian Delta outbreak. We downloaded all GISAID clade GK Delta genomes and scanned them for deletions in ORF7a. For each deletion we identified, we characterised its frequency, the number of countries it was found in, and how long it persisted. Of the 4,018,216 Delta genomes identified globally, 134,751 (~3.35%) possessed an ORF7a deletion, and ORF7aΔ17del was the most common. ORF7aΔ17del was the sole deletion in 28,014 genomes, of which 27,912 (~99.6%) originated from the Australian outbreak. During the outbreak, ~87% of genomes were Delta-ORF7aΔ17del, and genomes with this deletion were sampled until the outbreak's end. These data demonstrate that, contrary to suggestions early in the COVID-19 pandemic, genomes with frameshifting deletions in ORF7a can persist over long time periods. We suggest that the proliferation of Delta-ORF7aΔ17del genomes was likely a chance founder effect. Nonetheless, the frequency of ORF7a deletions in SARS-CoV-2 genomes worldwide suggests they might have some benefit for virus transmission.

Integrating civil liberty and the ethical principle of autonomy in building public confidence to reduce COVID-19 vaccination inequity in Africa.

Concerns regarding the safety of COVID-19 vaccination have caused hesitancy and lowered uptake globally. While vaccine hesitancy is documented globally, some continents, countries, ethnic groups and age groups are disproportionately affected, resulting in significant global inequities. To date, Africa has the lowest COVID-19 coverage globally, with only 22% of its population completely vaccinated. It might be argued that the difficulty with COVID-19 vaccine acceptance in Africa was triggered by the anxiety created by misinformation on social media platforms, particularly with the misinformation regarding depopulating Africa, given the significance of maternity in the continent. In this work, we examine numerous determinants of poor vaccination coverage that have received little attention in primary research and that may need to be considered by various stakeholders engaged in the COVID-19 vaccine strategy at the national and continental levels. Our study also emphasizes the importance of a multidisciplinary team when introducing a new vaccine, for people to trust that the vaccine is truly helpful to them and to be convinced that immunization is, all things considered, worthwhile.

Nonutility of procalcitonin for diagnosing bacterial pneumonia in patients with severe COVID-19.

Background: Patients hospitalized with COVID-19 are at significant risk for superimposed bacterial pneumonia. However, diagnosing superinfection is challenging due to its clinical resemblance to severe COVID-19. We therefore evaluated whether the immune biomarker, procalcitonin, could facilitate the diagnosis of bacterial superinfection. Methods: We retrospectively identified 185 patients hospitalized with severe COVID-19 who underwent lower respiratory culture; 85 had evidence of bacterial superinfection. Receiver operating characteristic curve and area under the curve (AUC) analyses were performed to assess the utility of procalcitonin for diagnosing superinfection. Results: This approach demonstrated that procalcitonin measured at the time of culture was incapable of distinguishing patients with bacterial infection (AUC, 0.52). The AUC not affected by exposure to antibiotics, treatment with immunomodulatory agents, or timing of procalcitonin measurement. Conclusion: Static measurement of procalcitonin does not aid in the diagnosis of superinfection in severe COVID-19.

PD-1highCXCR5-CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection.

T cell-B cell interaction is the key immune response to protect the host from severe viral infection. However, how T cells support B cells to exert protective humoral immunity in humans is not well understood. Here, we use COVID-19 as a model of acute viral infections and analyze CD4+ T cell subsets associated with plasmablast expansion and clinical outcome. Peripheral helper T cells (Tph cells; denoted as PD-1highCXCR5-CD4+ T cells) are significantly increased, as are plasmablasts. Tph cells exhibit "B cell help" signatures and induce plasmablast differentiation in vitro. Interestingly, expanded plasmablasts show increased CXCR3 expression, which is positively correlated with higher frequency of activated Tph cells and better clinical outcome. Mechanistically, Tph cells help B cell differentiation and produce more interferon γ (IFNγ), which induces CXCR3 expression on plasmablasts. These results elucidate a role for Tph cells in regulating protective B cell response during acute viral infection.