Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1.177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.

Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey

The Office for National Statistics COVID-19 Infection Survey is a large household-based surveillance study based in the United Kingdom. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing sequenced samples collected up until 13th November 2021. We observed four distinct sweeps or partial-sweeps, by lineages B.1.177, B.1.1.7/Alpha, B.1.617.2/Delta, and finally AY.4.2, a sublineage of B.1.617.2, with each sweeping lineage having a distinct growth advantage compared to their predecessors. Evolution was characterised by steady rates of evolution and increasing diversity within lineages, but with step increases in divergence associated with each sweeping major lineage, leading to a faster overall rate of evolution and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly as routine PCR testing is phased out or in settings where large-scale sequencing is not feasible.

Comparison of oral Candida species prevalence and carriage among gutka-chewers and betel-quid chewers.

OBJECTIVE: To compare prevalence and carriage of Candida species among gutka-chewers and betel-quid-chewers. METHODS: The cross-sectional case-control study was conducted between January and December, 2015 at the Oral Surgery department of Abbasi Shaheed Hospital and the Dental department of Jinnah Postgraduate Medical Centre, Karachi, and comprised oral yeast samples of gutka-chewers, betel-quid-chewers, and non-chewers. A standardised questionnaire was used to gather demographic data and oral hygiene maintenance information. Oral Candida strains were collected, cultured and identified using standard techniques and yeast identification system. In all groups, unstimulated whole salivary flow rate was determined. Lesions on the tongue and oral mucosa were clinically investigated and numbers of missing teeth were recorded. SPSS 20 was used for data analysis. RESULTS: Of the total 185 samples, 50(27%) were from gutka-chewers, 50(27%)betel-quid-chewers, and 85(46%) non-chewers. Oral Candida carriage was comparable among betel-quid-chewers (18 [36%])and gutka-chewers (20 [40%]), but it was significantly higher than the non-chewers (11 [12.9%]) (p<0.05).Candida species were isolated from 45 (90%) of gutka-chewers and 45 (90%) of BQ-chewers. Among the groups, Candida albicans was the most commonly isolated yeast species (38% in gutka-chewers and 12.9% non-chewers). Mean numbers of missing teeth were significantly higher among BQ-chewers (6.8±0.4 teeth [range: 5-10]) (p<0.01) and gutka-chewers 6.8±0.6 teeth (range: 5-10) (p<0.01) than non-chewers (2.2±0.3 teeth [range: 0-3 teeth]). There was no significant difference in unstimulated whole salivary flow rate and the number of missing teeth among gutka-chewers and betel-quid-chewers (p>0.05). CONCLUSIONS: Prevalence and carriage of Candida species were comparable between betel-quid-chewers and gutka-chewers compared to non-chewers.