Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022.

Early detection of increased infections or new variants of SARS-CoV-2 is critical for public health response. To determine whether cycle threshold (Ct) data from PCR tests for SARS-CoV-2 could serve as an early indicator of epidemic growth, we analyzed daily mean Ct values in England, UK, by gene target and used iterative sequential regression to detect break points in mean Ct values (and positive test counts). To monitor the epidemic in England, we continued those analyses in real time. During September 2020-January 2022, a total of 7,611,153 positive SARS-CoV-2 PCR test results with Ct data were reported. Spike (S) gene target (S+/S-)-specific mean Ct values decreased 6-29 days before positive test counts increased, and S-gene Ct values provided early indication of increasing new variants (Delta and Omicron). Our approach was beneficial in the context of the first waves of the COVID-19 pandemic and can be used to support future infectious disease monitoring.

Poor outcomes among critically ill HIV-positive patients at hospital discharge and post-discharge in Guinea, Conakry: A retrospective cohort study.

INTRODUCTION: Optimal management of critically ill HIV-positive patients during hospitalization and after discharge is not fully understood. This study describes patient characteristics and outcomes of critically ill HIV-positive patients hospitalized in Conakry, Guinea between August 2017 and April 2018 at discharge and 6 months post-discharge. METHODS: We carried out a retrospective observational cohort study using routine clinical data. Analytic statistics were used to describe characteristics and outcomes. RESULTS: 401 patients were hospitalized during the study period, 230 (57%) were female, median age was 36 (IQR: 28-45). At admission, 229 patients (57%) were on ART, median CD4 was 64 cells/mm3, 166 (41%) had a VL >1000 copies/ml, and 97 (24%) had interrupted treatment. 143 (36%) patients died during hospitalisation. Tuberculosis was the major cause of death for 102 (71%) patients. Of 194 patients that were followed after hospitalization a further 57 (29%) were lost-to-follow-up (LTFU) and 35 (18%) died, 31 (89%) of which had a TB diagnosis. Of all patients who survived a first hospitalisation, 194 (46%) were re-hospitalised at least once more. Amongst those LTFU, 34 (59%) occurred immediately after hospital discharge. CONCLUSION: Outcomes for critically ill HIV-positive patients in our cohort were poor. We estimate that 1-in-3 patients remained alive and in care 6 months after their hospital admission. This study shows the burden of disease on a contemporary cohort of patients with advanced HIV in a low prevalence, resource limited setting and identifies multiple challenges in their care both during hospitalisation as well as during and after re-transitioning to ambulatory care.

Early onset of neurological features differentiates two outbreaks of Lassa fever in Ebonyi state, Nigeria during 2017-2018.

Lassa fever (LF) is an acute viral haemorrhagic illness with various non-specific clinical manifestations. Neurological symptoms are rare at the early stage of the disease, but may be seen in late stages, in severely ill patients.The aim of this study was to describe the epidemiological evolution, socio-demographic profiles, clinical characteristics, and outcomes of patients seen during two Lassa fever outbreaks in Ebonyi State, between December 2017 and December 2018. Routinely collected clinical data from all patients admitted to the Virology Centre of the hospital during the period were analysed retrospectively. Out of a total of 83 cases, 70(84.3%) were RT-PCR confirmed while 13 (15.7%) were probable cases. Sixty-nine (83.1%) patients were seen in outbreak 1 of whom 53.6% were urban residents, while 19%, 15%, and 10% were farmers, students and health workers respectively. There were 14 (16.8%) patients, seen in second outbreak with 92.9% rural residents. There were differences in clinical symptoms, signs and laboratory findings between the two outbreaks. The case fatality rates were 29.9% in outbreak 1 and 85.7% for outbreak 2. Neurological features and abnormal laboratory test results were associated with higher mortality rate, seen in outbreak 2. This study revealed significant differences between the two outbreaks. Of particular concern was the higher case fatality during the outbreak 2 which may be from a more virulent strain of the Lassa virus. This has important public health implications and further molecular studies are needed to better define its characteristics.

Feasibility of using Determine TB-LAM to diagnose tuberculosis in HIV-positive patients in programmatic conditions: a multisite study.

Background: Determine TB-LAM is a urine-based point-of-care assay for diagnosis of tuberculosis (TB). Objective: To assess the feasibility of using LAM to diagnose TB in adult HIV-positive patients in resource-limited settings. Methods: We performed a multi-centric mixed-methods cross-sectional descriptive study in the Democratic Republic of Congo, Malawi, and Mozambique. We used the study and program monitoring tools to estimate user workload, turn-around time (TAT), and proportion of patients with LAM and sputum-based results. We conducted semi-structured interviews to assess the user acceptability of the LAM. Results: The duration of the LAM testing activity per patient was 27 min (IQR 26-29); staff continued with other duties whilst waiting for the result. More patients had a LAM versus a sputum-based result: 168/213 (78.9%) vs 77/213 (36.1%), p < 0.001 in DRC; 691/695 (99.4%) vs 429/695 (61.7%), p < 0.001 in Malawi; and 646/647 (99.8%) vs 262/647 (40.5%), p < 0.001 in Mozambique. The median TAT in minutes when LAM was performed in the consultation room was 75 (IQR 45-188) in DRC, 29 (IQR 27-39) in Malawi, and 36 (IQR 35-41) in Mozambique. In comparison, the overall median TAT for sputum-based tests (smear or GeneXpert) was 2 (IQR 1-3) days. The median time to the first anti-TB drug dose for LAM-positive patients was 155 (IQR 90-504) minutes in DRC and 90 (IQR 60-117) minutes in Mozambique. The overall inter-reader agreement for the interpretation of the LAM result as positive or negative was 98.9%, kappa 0.97 (95%CI 0.96-0.99). Overall, LAM users found the test easy to perform. Major concerns were use of the reading card and the prior requirement of CD4 results before LAM testing. Conclusion: It is feasible to implement the LAM test in low resource settings. The short TAT permitted same day initiation of TB treatment for LAM-positive patients.

Care requirements for clients who present after rape and clients who presented after consensual sex as a minor at a clinic in Harare, Zimbabwe, from 2011 to 2014.

STUDY GOALS: To describe the differences between clients presenting after rape and clients who have consented to sex as a minor to an SGBV clinic in Harare, Zimbabwe, and how these differences affect their care requirements. BACKGROUND: Adolescents and adults presenting at the specialized Sexual and Gender Based Violence clinic in Harare are offered a standardised package of free medical and psychosocial care. Zimbabwe has an HIV prevalence of 14%, so prevention of HIV infection using PEP for those that present within 72 hours is a key part of the response. STI treatment, emergency contraceptive pills, referral for termination of pregnancy, psychological, social and legal support is also provided. METHODS: This is a retrospective descriptive study of routine programmatic data collected at the Edith Opperman polyclinic in Mbare SGBV clinic from 2011 to 2014. Chi-square tests and logistic regression were used to describe the different experiences and the differences in uptake of care between clients presenting for rape compared to those who consented to sex as a minor. RESULTS: During the study period a total of 3617 clients presented to the clinic. 2242 (62%) sought care after rape, 602 (17%) for having consented to sex as a minor and 395 (11%) for suspected sexual abuse. 1615 (45%) of people presenting were 12-15 year olds. Minors who consented to sex compared to survivors of rape were less likely to report within 72 hours- 156 (26%) vs 894 (40%) p<0.001; less likely to report that they delayed due to fear- 68 (17%) vs 472 (40%) p<0.001, less likely to have experienced accompanying violence- 9 (1%) vs 176 (8%) p<0.001 or physical trauma-34 (6%) vs 427 (19%) p<0.001; and less likely to display psychological symptoms at presentation 51 (8%) vs 411 (18%) p<0.001. Minors who consented to sex compared to those who were raped were less likely to start PEP if eligible-123 (80%) vs 751 (93%) p<0.001, less likely to take emergency contraceptives if eligible-125 (81%) vs 598 (88%) p<0.001, more likely to be pregnant- 132 (23%) vs 241 (15%) p<0.001; less likely to request a termination of pregnancy if pregnant-10 (8%) vs 74 (31%) p<0.001; and less likely to come for at least one follow up 281 (47%) vs 1304 (58%) p<0.001. CONCLUSION: The experiences of those who consent to sex as a minor and those that have experienced forced sex were very different. The standardised SGBV medical response does not fully meet the needs to protect minors who have consented to sex from HIV or unwanted pregnancies. Clients who present for having consented to sex as a minor might benefit more from being offered long-term family planning or being assessed as a sero-discordant couple rather than simply PEP and ECP as is relevant for clients who have been raped. More provision of health care is needed for minors to ensure they have access to enough information and protection from HIV, other STIs and unwanted pregnancy, before they decide to engage in sexual intercourse, rather than as an emergency at an SGBV clinic.

Investigating a Non-Mesh Mosquito Net Among Outdoor Sleeping Nomadic Communities in Kenya.

Rising reports of exophagic malaria vectors make even more pressing the need for alternatives to traditional, mesh, long-lasting insecticidal nets (LLINs) designed for indoor sleeping and often inadequate in the protection of outdoor-sleeping populations. This study tests and evaluates the retention, utilization, and durability of novel, non-mesh nets designed for outdoor use. Longitudinal, cross-sectional surveys were conducted, the physical condition of nets was assessed, and bio-efficacy and insecticide content were tested. At 22 months, retention was 98.0%; 97.1% of nets fell within the World Health Organization (WHO) category of being in "good" condition; none were in the "torn" category. At 18 months post-distribution, 100% of nets had at least WHO Pesticide Evaluation Scheme (WHOPES)-acceptable levels of insecticide, this proportion was 66.7% at 22 months. This novel mosquito net has the potential to provide a durable and context-specific tool to prevent malaria among traditionally hard-to-protect and highly vulnerable populations.