Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting.

The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar's test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.

Prospective Surveillance of Respiratory Infections in British Antarctic Survey Bases During the COVID-19 Pandemic.

BACKGROUND: The British Antarctic bases offer a semiclosed environment for assessing the transmission and persistence of seasonal respiratory viruses. METHODS: Weekly swabbing was performed for respiratory pathogen surveillance (including SARS-CoV-2), at 2 British Antarctic Survey bases, during 2020: King Edward Point (KEP, 30 June to 29 September, 9 participants, 124 swabs) and Rothera (9 May to 6 June, 27 participants, 127 swabs). Symptom questionnaires were collected for any newly symptomatic cases that presented during this weekly swabbing period. RESULTS: At KEP, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (2), adenovirus (1), parainfluenza 3 (1), and respiratory syncytial virus B (1). At Rothera, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (3), adenovirus (2), parainfluenza 4 (1), and human metapneumovirus (1). All bacterial agents identified were considered to be colonizers and not pathogenic. CONCLUSIONS: At KEP, the timeline indicated that the parainfluenza 3 and adenovirus infections could have been linked to some of the symptomatic cases that presented. For the other viruses, the only other possible sources were the visiting ship crew members. At Rothera, the single symptomatic case presented too early for this to be linked to the subsequent viral detections, and the only other possible source could have been a single nonparticipating staff member.

Psychobehavioral Responses and Likelihood of Receiving COVID-19 Vaccines during the Pandemic, Hong Kong.

To access temporal changes in psychobehavioral responses to the coronavirus disease (COVID-19) pandemic, we conducted a 5-round (R1-R5) longitudinal population-based online survey in Hong Kong during January-September 2020. Most respondents reported wearing masks (R1 99.0% to R5 99.8%) and performing hand hygiene (R1 95.8% to R5 97.7%). Perceived COVID-19 severity decreased significantly, from 97.4% (R1) to 77.2% (R5), but perceived self-susceptibility remained high (87.2%-92.8%). Female sex and anxiety were associated with greater adoption of social distancing. Intention to receive COVID-19 vaccines decreased significantly (R4 48.7% to R5 37.6%). Greater anxiety, confidence in vaccine, and collective responsibility and weaker complacency were associated with higher tendency to receive COVID-19 vaccines. Although its generalizability should be assumed with caution, this study helps to formulate health communication strategies and foretells the initial low uptake rate of COVID-19 vaccines, suggesting that social distancing should be maintained in the medium term.

Will achieving herd immunity be a road to success to end the COVID-19 pandemic?

As the COVID-19 pandemic continues, the availability of several different new vaccines, their varying supply levels, effectiveness, and immunity duration across different ethnic populations, together with natural infection rates, will have an impact on when each country can reach herd immunity (ranging from 15.3% to 77.1%). Here we estimate the population proportions still required to gain immunity (ranging from 0.01% to 48.8%) to reach an overall herd immunity level to stop the exponential virus spread in 32 selected countries.

Retrospective SARS-CoV-2 IgG screening during the first wave (March-June 2020) of the COVID-19 pandemic in the United Kingdom.

During the "first wave" of the coronavirus disease 2019 (COVID-19) pandemic in the United Kingdom (March-June 2020), the city of Leicester was particularly hard hit, resulting in reimposed lockdown measures. Although initial polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was attempted within the community, testing was soon abandoned due to an inability to keep up with demand by local laboratories. It is therefore feasible that undiagnosed transmission of COVID-19 in the community by asymptomatic individuals was a real possibility. Therefore, retrospective SARS-CoV-2 immunoglobulin G (IgG) testing of archived sera from out-patients visiting University Hospitals of Leicester NHS Trust service was performed to investigate the transmission of SARS-CoV-2 in the community. A total of 1779 sera samples were tested from samples collected between 16th March and 3rd June 2020, of which 202 (11.35%) were SARS-CoV-2 IgG positive. Positivity was lowest in March (2.54%) at the beginning of the pandemic before peaking in April (17.16%) before a decline in May and June (11.16% and 12.68%, respectively). This retrospective screening offers some insight into the early patterns of SARS-CoV-2 transmission within a sampled community population during the first wave of the COVID-19 pandemic; supporting the argument for more community screening during high incidences of pandemics.

Retrospective serosurveillance for anti-SARS-CoV-2 immunoglobulin during a time of low prevalence: A cautionary tale.

We performed a retrospective screening of 428 serum samples for anti-SARS-CoV-2  immunoglobulin during a period of low prevalence. Employing two different serological tests yielded discrepant results for 10 samples; highlighting an increased risk of potential  false positive results and the need for further confirmatory testing before publication of data.

COVID-19 multisystem inflammatory syndrome in three teenagers with confirmed SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) is generally a relatively mild illness in children. An emerging disease entity coined as pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) has been reported recently, but is very rare and only affects a very small minority of children. Here we describe the clinical presentations and outcomes of three teenagers with serologically-confirmed SARS-CoV-2 infection admitted to a pediatric intensive care unit for PIMS-TS. Although their initial presentations were very similar, their COVID-19-related disease varied in severity.