James Kelly

Bio: James Kelly is an academic researcher. The author has contributed to research in topics: Medicine & Viral shedding. The author has an hindex of 2, co-authored 3 publications receiving 24 citations.

The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories

Abstract: Introduction Non-pharmaceutical interventions (NPIs) are used to reduce transmission of SARS coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, empirical evidence of the effectiveness of specific NPIs has been inconsistent. We assessed the effectiveness of NPIs around internal containment and closure, international travel restrictions, economic measures, and health system actions on SARS-CoV-2 transmission in 130 countries and territories. Methods We used panel (longitudinal) regression to estimate the effectiveness of 13 categories of NPIs in reducing SARS-CoV-2 transmission with data from January - June 2020. First, we examined the temporal association between NPIs using hierarchical cluster analyses. We then regressed the time-varying reproduction number (Rt) of COVID-19 against different NPIs. We examined different model specifications to account for the temporal lag between NPIs and changes in Rt, levels of NPI intensity, time-varying changes in NPI effect and variable selection criteria. Results were interpreted taking into account both the range of model specifications and temporal clustering of NPIs. Results There was strong evidence for an association between two NPIs (school closure, internal movement restrictions) and reduced Rt. Another three NPIs (workplace closure, income support and debt/contract relief) had strong evidence of effectiveness when ignoring their level of intensity, while two NPIs (public events cancellation, restriction on gatherings) had strong evidence of their effectiveness only when evaluating their implementation at maximum capacity (e.g., restrictions on 1000+ people gathering were not effective, restrictions on Conclusion Understanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications taking into account these effects, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many although not all the actions policy-makers are taking to respond to the COVID-19 pandemic.

Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study

Abstract: The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0-9.0) in unvaccinated participants to 6 days (IQR: 5.0-8.0) in those vaccinated (P=0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19-0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset.

Post-acute sequelae and adaptive immune responses in people living with HIV recovering from SARS-COV-2 infection.

Abstract: BACKGROUND Limited data are available on the long-term clinical and immunologic consequences of SARS-CoV-2 infection in people with HIV (PWH). METHODS We measured SARS-CoV-2-specific humoral and cellular responses in people with and without HIV recovering from COVID-19 (n = 39 and n = 43, respectively) using binding antibody, surrogate virus neutralization, intracellular cytokine staining, and inflammatory marker assays. We identified individuals experiencing post-acute sequelae of SARS-CoV-2 infection (PASC) and evaluated immunologic parameters. We used linear regression and generalized linear models to examine differences by HIV status in the magnitude of inflammatory and virus-specific antibody and T cell responses, as well as differences in the prevalence of PASC. RESULTS Among PWH, we found broadly similar SARS-CoV-2-specific antibody and T cell responses as compared with a well-matched group of HIV-negative individuals. PWH had 70% lower relative levels of SARS-CoV-2-specific memory CD8+ T cells (p = 0.007) and 53% higher relative levels of PD-1+ SARS-CoV-2-specific CD4+ T cells (p = 0.007). Higher CD4/CD8 ratio was associated with lower PD-1 expression on SARS-CoV-2-specific CD8+ T cells (0.34-fold effect, p = 0.02). HIV status was strongly associated with PASC (odds ratio 4.01, p = 0.008), and levels of certain inflammatory markers (IL-6, TNF-alpha, and IP-10) were associated with persistent symptoms. CONCLUSIONS We identified potentially important differences in SARS-CoV-2-specific CD4+ and CD8+ T cells in PWH and HIV-negative participants that might have implications for long-term immunity conferred by natural infection. HIV status strongly predicted the presence of PASC. Larger and more detailed studies of PASC in PWH are urgently needed.

Vaccine hesitancy and access to psoriasis care during the COVID‐19 pandemic: findings from a global patient‐reported cross‐sectional survey

Abstract: Background: COVID-19 vaccination is efficacious at protecting against severe COVID-19 outcomes in the general population. However, vaccine hesitancy (unwillingness for vaccination despite available vaccination services) threatens public health. Individuals taking immunosuppression for psoriasis have been prioritised for COVID-19 vaccination, however there is a paucity of information on vaccine hesitancy in this population, including contributing factors. While global healthcare has been severely disrupted in the pandemic, the impact on access to psoriasis care and whether this may negatively influence vaccine uptake, is underexplored. Objectives: To explore organisational and individual factors associated with COVID-19 vaccine hesitancy in individuals with psoriasis. Methods: Individuals with psoriasis, identified through global patient organisations and social media, completed a cross-sectional self-reported online survey. The primary outcome was COVID-19 vaccine hesitancy. Logistic regression was used to examine the association between predictor variables (organisational and individual factors) and outcome. Results: Self-reported data from 802 individuals with psoriasis across 89 countries were available (65.6% female, median age 51 years [IQR 37-61], 43.7% taking systemic immunosuppression). Eight percent (n=63) reported vaccine hesitancy. Those reporting vaccine hesitancy were younger, more likely to be of non-white ethnicity, non-UK resident, have a lower BMI, not taking systemic immunosuppression and with shorter disease duration compared to those not reporting vaccine hesitancy. The commonest reasons for vaccine hesitancy were concerns regarding vaccine side-effects, that the vaccine is too new or that psoriasis may worsen post-vaccination. Forty percent (n=322) reported that their psoriasis care had been disrupted by the pandemic. These individuals were younger, of non-white ethnicity, with shorter duration and more severe psoriasis. Disruption to psoriasis care was associated with vaccine hesitancy (unadjusted OR 2.97 (95%CI 1.23-7.13), p=0.015), although not statistically significant in the adjusted model. Conclusion: A minority of individuals with psoriasis from our study reported COVID-19 vaccine hesitancy. Similar to general population trends, vaccine hesitancy in our psoriasis sample is most common in younger age and ethnic minority groups. Our data highlight patient concerns regarding COVID-19 vaccination, which are important to address during patient-clinician interactions to help optimise vaccine uptake and mitigate risks from the ongoing pandemic in individuals with psoriasis.

Tuning Trend-Following Strategies with Macro ESG Data

Abstract: This article seeks to tilt traditional macro trend-following strategies toward countries with high Environmental, Social, and Governance (ESG) scores. The integration incorporates both ESG levels and changes (improvements or deteriorations in sustainability). Notably, the authors find that the international ESG exposure of the macro portfolios can be substantially increased without any cost in performance for both long-only and long–short portfolios. In some cases, transaction cost–adjusted Sharpe ratios can even benefit from a minor shift toward more ESG exposure. Key Findings ▪ Cross-country and cross-asset momentum-based strategies are reweighted to favor countries with high or improving ESG ratings. ▪ All portfolios can sustain small tilts toward sustainability without any impact on their Sharpe ratios, with up to 70% increase in ESG exposure. ▪ For long-only portfolios small tilts increase the overall Sharpe ratio, while larger tilts can become detrimental.

Ranking the effectiveness of worldwide COVID-19 government interventions.

Abstract: Assessing the effectiveness of non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 is critical to inform future preparedness response plans. Here we quantify the impact of 6,068 hierarchically coded NPIs implemented in 79 territories on the effective reproduction number, Rt, of COVID-19. We propose a modelling approach that combines four computational techniques merging statistical, inference and artificial intelligence tools. We validate our findings with two external datasets recording 42,151 additional NPIs from 226 countries. Our results indicate that a suitable combination of NPIs is necessary to curb the spread of the virus. Less disruptive and costly NPIs can be as effective as more intrusive, drastic, ones (for example, a national lockdown). Using country-specific ‘what-if’ scenarios, we assess how the effectiveness of NPIs depends on the local context such as timing of their adoption, opening the way for forecasting the effectiveness of future interventions. Analysing over 50,000 government interventions in more than 200 countries, Haug et al. find that combinations of softer measures, such as risk communication or those increasing healthcare capacity, can be almost as effective as disruptive lockdowns.

Inferring the effectiveness of government interventions against COVID-19.

Abstract: Governments are attempting to control the COVID-19 pandemic with nonpharmaceutical interventions (NPIs). However, the effectiveness of different NPIs at reducing transmission is poorly understood. We gathered chronological data on the implementation of NPIs for several European, and other, countries between January and the end of May 2020. We estimate the effectiveness of NPIs, ranging from limiting gathering sizes, business closures, and closure of educational institutions to stay-at-home orders. To do so, we used a Bayesian hierarchical model that links NPI implementation dates to national case and death counts and supported the results with extensive empirical validation. Closing all educational institutions, limiting gatherings to 10 people or less, and closing face-to-face businesses each reduced transmission considerably. The additional effect of stay-at-home orders was comparatively small.

Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study

Abstract: Summary Background Since the coronavirus disease 2019 outbreak began in the Chinese city of Wuhan on Dec 31, 2019, 68 imported cases and 175 locally acquired infections have been reported in Singapore. We aimed to investigate options for early intervention in Singapore should local containment (eg, preventing disease spread through contact tracing efforts) be unsuccessful. Methods We adapted an influenza epidemic simulation model to estimate the likelihood of human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a simulated Singaporean population. Using this model, we estimated the cumulative number of SARS-CoV-2 infections at 80 days, after detection of 100 cases of community transmission, under three infectivity scenarios (basic reproduction number [R0] of 1·5, 2·0, or 2·5) and assuming 7·5% of infections are asymptomatic. We first ran the model assuming no intervention was in place (baseline scenario), and then assessed the effect of four intervention scenarios compared with a baseline scenario on the size and progression of the outbreak for each R0 value. These scenarios included isolation measures for infected individuals and quarantining of family members (hereafter referred to as quarantine); quarantine plus school closure; quarantine plus workplace distancing; and quarantine, school closure, and workplace distancing (hereafter referred to as the combined intervention). We also did sensitivity analyses by altering the asymptomatic fraction of infections (22·7%, 30·0%, 40·0%, and 50·0%) to compare outbreak sizes under the same control measures. Findings For the baseline scenario, when R0 was 1·5, the median cumulative number of infections at day 80 was 279 000 (IQR 245 000–320 000), corresponding to 7·4% (IQR 6·5–8·5) of the resident population of Singapore. The median number of infections increased with higher infectivity: 727 000 cases (670 000–776 000) when R0 was 2·0, corresponding to 19·3% (17·8–20·6) of the Singaporean population, and 1 207 000 cases (1 164 000–1 249 000) when R0 was 2·5, corresponding to 32% (30·9–33·1) of the Singaporean population. Compared with the baseline scenario, the combined intervention was the most effective, reducing the estimated median number of infections by 99·3% (IQR 92·6–99·9) when R0 was 1·5, by 93·0% (81·5–99·7) when R0 was 2·0, and by 78·2% (59·0 −94·4) when R0 was 2·5. Assuming increasing asymptomatic fractions up to 50·0%, up to 277 000 infections were estimated to occur at day 80 with the combined intervention relative to 1800 for the baseline at R0 of 1·5. Interpretation Implementing the combined intervention of quarantining infected individuals and their family members, workplace distancing, and school closure once community transmission has been detected could substantially reduce the number of SARS-CoV-2 infections. We therefore recommend immediate deployment of this strategy if local secondary transmission is confirmed within Singapore. However, quarantine and workplace distancing should be prioritised over school closure because at this early stage, symptomatic children have higher withdrawal rates from school than do symptomatic adults from work. At higher asymptomatic proportions, intervention effectiveness might be substantially reduced requiring the need for effective case management and treatments, and preventive measures such as vaccines. Funding Singapore Ministry of Health, Singapore Population Health Improvement Centre.

HIV and Sexually Transmitted Infections Among Persons with Monkeypox — Eight U.S. Jurisdictions, May 17–July 22, 2022

Abstract: High prevalences of HIV and other sexually transmitted infections (STIs) have been reported in the current global monkeypox outbreak, which has affected primarily gay, bisexual, and other men who have sex with men (MSM) (1-5). In previous monkeypox outbreaks in Nigeria, concurrent HIV infection was associated with poor monkeypox clinical outcomes (6,7). Monkeypox, HIV, and STI surveillance data from eight U.S. jurisdictions* were matched and analyzed to examine HIV and STI diagnoses among persons with monkeypox and assess differences in monkeypox clinical features according to HIV infection status. Among 1,969 persons with monkeypox during May 17-July 22, 2022, HIV prevalence was 38%, and 41% had received a diagnosis of one or more other reportable STIs in the preceding year. Among persons with monkeypox and diagnosed HIV infection, 94% had received HIV care in the preceding year, and 82% had an HIV viral load of <200 copies/mL, indicating HIV viral suppression. Compared with persons without HIV infection, a higher proportion of persons with HIV infection were hospitalized (8% versus 3%). Persons with HIV infection or STIs are disproportionately represented among persons with monkeypox. It is important that public health officials leverage systems for delivering HIV and STI care and prevention to reduce monkeypox incidence in this population. Consideration should be given to prioritizing persons with HIV infection and STIs for vaccination against monkeypox. HIV and STI screening and other recommended preventive care should be routinely offered to persons evaluated for monkeypox, with linkage to HIV care or HIV preexposure prophylaxis (PrEP) as appropriate.