Detecting SARS-CoV-2 using a simple real time molecular assay will be helpful for the mitigation efforts in low / middle income countries during the pandemic. We have developed and validated a rapid and simple real time loop mediated isothermal amplification assay (LAMP) for screening of SARS-CoV-2 infection in known infected and non-infected individuals. Six sets of primers were designed targeting the N-gene of the SARS-CoV-2 (Accession ID MN994468). LAMP reactions were performed using Warm Start 2X Master Mix and real-time PCR machine at 65 °C for 60 cycles with 15 s for each cycle. Results were read by visualizing turbidity under ultraviolet light and real time fluorescence detection through FAM channel of the real time PCR machine. We tested a total of 320 including 240 SARS CoV-2 positive (Ct values <40) and 80 SARS CoV-2 negative samples as tested by a real time RT-PCR using the newly developed LAMP assay. A total of 206 out of 240 SARS CoV-2 positive samples were tested positive by the newly developed LAMP assay with a sensitivity of 86%. All 80 SARS CoV-2 negative samples were tested negative by the newly developed LAMP assay with a specificity of 100%. The newly developed real time LAMP assay has a sensitivity of 86% and specificity of 100% compared to the real time RT-PCR for the detection of SARS CoV-2. The new assay will be useful to screen large number of samples if adopted to minimize the time and cost.

Introduction: Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections, and HPV is an aetiological agent for cervical cancer (CC). In Sri Lanka, CC is the second most frequent cancer affecting women. The present study was undertaken to determine knowledge, attitude and practices (KAP) regarding HPV infection, vaccination and CC among paramedical students of the Faculty of Allied Health Sciences (FAHS), University of Peradeniya. Methods: A purposive sample of 200 students following 5 different degree programmes at FAHS including 128 females and 72 males were surveyed. A pre-tested questionnaire was used to assess the KAP, and the analysis scale used for KAP ranged from ‘satisfactory’ and ‘fair’ to ‘inadequate’. Results: Twelve percent of the study participants reached fair to satisfactory knowledge scores on HPV infection, vaccination and CC. A significant difference in the knowledge score was noted between males and females, academic year of study, and ethnicities. A percentage of 79.5 of the study participants reached fair to satisfactory attitude scores towards HPV infection, vaccination and CC. Attitude score also significantly differed between males and females. Only 12% of the participants reached a fair to satisfactory practice score and no significant difference was noted among different categories in the practice score. Conclusion: Overall, knowledge and practice scores regarding HPV infection, vaccination, CC and its preventive measures among the respondents were low. However, the majority of study participants had a positive attitude. As considerable gaps in KAP exists in many areas, and there is an urgent need for educational programmes to improve KAP related to the prevention of HPV infection and CC including vaccination among paramedical students.

Introduction. Human metapneumovirus (hMPV), first identified in 2001, is one of the major respiratory pathogens causing acute respiratory tract infections (ARTIs). In Sri Lanka, data on epidemiology and clinical characteristics of hMPV infections are limited. In this study, we aimed to investigate the epidemiology and clinical characteristics of hMPV infection in adults and children with ARTIs in different locations in Sri Lanka from January 2021 to December 2023. Methods. A total of 1,582 respiratory samples from patients with ARTIs were enrolled from four tertiary care hospitals. Nasopharyngeal swab samples were subjected to real-time reverse transcriptase PCR to test for hMPV using a commercial multiplex assay. Demographic and clinical data were extracted from the patients’ clinical records. A selected subset of positive samples was subjected to genomic sequencing using an amplicon-based approach with the Respiratory Pathogen ID/AMR Library Prep and Enrichment Kit using the Illumina platform. Results. hMPV infection was identified in 1.64% (26/1,582) of patients, with the majority being children under 5 years of age. The co-infection rate was 0.34% with other respiratory viruses. The most common clinical presentation in hMPV infection included acute upper respiratory tract infection with fever, cough and cold and sore throat. Conclusion. hMPV is an important respiratory pathogen in children, causing ARTIs. hMPV-infected patients showed a range of respiratory symptoms with varying severity ranging from common cold to life-threatening lower respiratory tract infections. Continuous surveillance on hMPV infection may help in monitoring the hMPV activity, which will help in tracking the emergence of hMPV infections.

Legionella pneumophila is commonly found in aquatic environments. L. pneumophila is a causative agent of severe community acquired pneumonia and the infection is acquired through inhalation of aerosols containing the bacteria. In Sri Lanka, serologically confirmed cases of L. pneumophila infection in patients have been reported. However, there are no published reports on legionellosis in humans with evidence of polymerase chain reaction (PCR) based molecular confirmation in Sri Lanka. We report a PCR confirmed case of L. pneumophila associated lower respiratory tract infection in a 16-year-old monk who presented to a District General Hospital in the Central Province of Sri Lanka during the COVID-19 pandemic.

A comprehensive analysis of the molecular epidemiology of SARS-CoV-2 in the Kandy District of Sri Lanka from November 2020 to March 2022 was conducted to address the limited genomic surveillance data available across the country. The study investigated the circulating SARS-CoV-2 lineages, their temporal dynamics, and the associated mutational profiles in the study area. A total of 280 SARS-CoV-2-positive samples were selected, and 252 complete genomes were successfully sequenced using Oxford Nanopore Technology. Lineage classification was performed using the EPI2ME tool, while phylogenetic relationships were inferred through maximum likelihood and time-scaled phylogenetic trees using IQ-TREE2 and BEAST, respectively. Amino acid substitutions were analyzed to understand lineage-specific mutation patterns. Fifteen SARS-CoV-2 lineages were identified, and of those B.1.411 (36%) was the most prevalent, followed by Q.8 (21%), AY.28 (9.5%), and the Delta and Omicron variants. The lineage distribution showed a temporal shift from B.1.411 to Alpha, Delta, and finally the Omicron, mirroring the global trends. Time to the most recent common ancestor analyses provided estimates for the introduction of major variants, while mutation analysis revealed the widespread occurrence of D614G in the spike protein and lineage-specific mutations across structural, non-structural, and accessory proteins.Detection of the Epsilon variant (absent in other national-level studies) in November 2020, highlighted the regional heterogeneity viral spread. This study emphasizes the importance of localized genomic surveillance to capture the true diversity and evolution of SARS-CoV-2, to facilitate containment strategies in resource-limited settings.