Rohitha Muthugala

BACKGROUND Sand fly fever virus (SFFV) infection is an acute self-limiting febrile illness caused by phleboviruses and transmitted by sand flies of the Phlebotomus species. The disease has been reported in the Mediterranean region, North Africa, the Middle East, and the Indian subcontinent, and is now considered to be expanding into new geographic areas. Clinically, SFFV infection closely resembles acute dengue fever. AIM To detect other possible infection including SSFV in patients with clinically suspected dengue fever with negative serology results for NS1 antigen. METHODS In this study, a total of 757 serum samples were collected from patients clinically suspected of dengue fever and admitted to three major hospitals in Sri Lanka between January and August 2023. Patients were from the Colombo and Kandy District, and demographic information was obtained from laboratory request forms, although detailed individual-level demographic data were limited due to anonymization in this laboratory-based study. All samples were initially screened for dengue NS1 antigen negativity and further tested for a panel of pathogens including SFFV immunoglobulin (Ig) M, hantavirus IgM, chikungunya IgM, and leptospira IgM antibodies, as well as molecular detection of hantavirus, flavivirus, and alphavirus RNA. RESULTS From tested samples, two samples were serologically positive for SFFV-specific IgM using a commercial immunoblot assay, while all other tests for dengue, chikungunya, leptospira, hantavirus, and related RNA viruses were negative. These two SFFV-positive cases were from Kandy District and included one child (6-8 years) and one adult (40-50 years), both presenting with uncomplicated dengue-like illness. CONCLUSION This study provides the first evidence of SFFV infection in Sri Lanka. Given the high endemicity of dengue in the country, SFFV infections may be clinically misdiagnosed as dengue and therefore remain under-recognized. Further studies involving febrile patients and sand fly vector surveillance are required to determine the true burden and epidemiological significance of SFFV in Sri Lanka.

BACKGROUND In tropical Asia, arbovirus-induced encephalitis continues to be a serious public health issue. Encephalitis is caused by wide range of neurotropic pathogens, and flaviviruses are one of the main causative agents in the area. Sri Lanka reports a considerable number of central nervous system infections annually. Both dengue and Japanese encephalitis are endemic, and cases of Zika and West Nile virus infections were reported occasionally in Sri Lanka. Although reported number of Japanese encephalitis cases has reduced in the past, aetiological diagnosis in majority of encephalitis cases is still unknown. AIM To detect dengue virus (DENV) infections in individuals in the central region of Sri Lanka who were clinically suspected of having encephalitis. METHODS A retrospective observational analysis was conducted on 99 cerebrospinal fluid samples received to a virology laboratory from patients in the central part of Sri Lanka who were clinically suspected of having encephalitis. Samples were analyzed using reverse transcriptase polymerase chain reaction (RT-PCR) with universal flavivirus primers to detect flaviviral RNA followed by DENV serotyping real-time RT-PCR, and an immunoglobulin M (IgM) detection enzyme-linked immunosorbent assay to detect IgM antibodies indicative of a possible recent DENV infection. RESULTS DENV aetiology was detected in 6 (6.06%) cerebrospinal fluid samples, and all were confirmed as DENV infections. A single positive result (1.01%) was yielded through RT-PCR and was identified as DENV serotype 3. Serology testing detected 05 (5.05%) anti-dengue IgM positives and further investigation indicated probable DENV aetiology. Among positives 02 (33.33%) were children (aged less than 14 years), and rest were adults. CONCLUSION These findings underscore the presence of DENV-associated central nervous system infections and highlight the need for broader surveillance and more advanced diagnostic approaches in the future.

Acute respiratory infections (ARIs) are the main cause of morbidity and mortality worldwide, especially among children. The human bocavirus (HBoV) is a non-enveloped DNA virus that was recently identified as a respiratory pathogen associated with respiratory tract infections (RTIs), predominantly in infants and young children. It is also detected from the gastrointestinal tract in children. The prevalence of HBoV1 acute respiratory tract infection varies across age groups, ranging from 10.3% to 12.51% in individuals under 3 years of age. The spectrum of clinical presentation includes mild upper RTIs, acute exacerbation of asthma, bronchitis, bronchiolitis, pneumonia, and multi-organ failure. Although HBoV is often detected in patients with ARIs who have other respiratory viruses (17%-85%), recent studies have identified it as the sole aetiology for mild to severe ARIs. Children with pre-existing medical conditions infected with HBoV often have a risk of severe illness. HBoV infection is diagnosed primarily by detecting viral DNA in respiratory samples using molecular methods. Currently, there is no specific antiviral treatment for HBoV infections and the cases are managed symptomatically. General preventive measures used for the prevention of viral RTIs are applicable, as there is no effective vaccine against this virus. The HBoV has been implicated in RTIs, particularly in children, and has also been detected in cases of gastroenteritis. Despite its global prevalence, the exact pathogenic role of HBoV remains unclear due to frequent co-infections with other viruses. This mini-review discusses the virology, epidemiology, clinical manifestations, diagnosis, and potential treatment approaches related to HBoV infections.

Background. Influenza C virus (ICV) is a lesser known member of the Orthomyxoviridae family, primarily causing respiratory tract infections in children. Co-infection with WU polyomavirus (WUPyV), a recently identified human polyomavirus, has been rarely reported. This study presents the first laboratory-confirmed case of ICV infection in Sri Lanka and its co-infection with WUPyV. Methods. Nasopharyngeal and oropharyngeal swabs were collected from children aged 3 months to 14 years with respiratory tract symptoms between November 2022 and February 2023. Samples were screened using multiplex real-time PCR (RT-PCR) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RT-PCR. A nasopharyngeal swab from a 14-month-old infant showing an insignificant curve in respiratory PCR was subjected to whole-genome sequencing using the Illumina platform. Data were analysed for genomic characterization, and phylogenetic analysis was performed using the haemagglutinin-esterase gene of ICV. Results. Full-genome sequencing identified ICV and WUPyV in the sample. Phylogenetic analysis revealed that the ICV isolate belonged to the C/Sao Paulo lineage. The patient presented with mild symptoms, including fever, cough and cold, with normal inflammatory markers, and recovered with supportive care. Discussion. This case highlights the importance of considering ICV in paediatric respiratory illnesses, despite its under-diagnosis due to limited diagnostic tools. Unlike influenza A and B, ICV lacks neuraminidase, rendering neuraminidase inhibitors ineffective. The absence of ICV in current influenza vaccines further complicates preventive strategies. Co-detection of WUPyV raises questions about its role as a co-pathogen, with its clinical significance requiring further investigation. Conclusion. This report underscores the need for enhanced molecular diagnostic techniques and surveillance to better understand the epidemiology and clinical impact of ICV and its co-infections.

Human bocavirus-1 (HBoV1) is a respiratory virus linked to various respiratory illnesses, but its prevalence and role in acute respiratory infections in Sri Lanka are not well investigated. This study investigated the prevalence of HBoV1 in respiratory samples from individuals suspected of having respiratory tract infections in the Western Province, Sri Lanka. Two hundred systematically selected nasopharyngeal swab samples from suspected COVID-19 patients from January 2022 to May 2022 with acute respiratory tract infection (ARTI) symptoms from a total of 1,507 samples were included. PCR was performed to amplify the non-structural protein 1 gene region of HBoV. The positive sample was subjected to complete genomic sequencing by using the Illumina sequencing platform. HBoV was detected in one sample from a 9-month-old infant who presented with cough, fever and sore throat. This sample was negative for other respiratory viruses and atypical bacteria. The sequence was aligned with reference sequences available in GenBank, which confirmed that the sample belongs to the HBoV1 genotype, with a nucleotide identity of 99.14%. This study was able to detect HBoV1 infections in a patient with ARTI as a sole pathogen and genomic characterization of the isolate. This detection in a symptomatic infant highlights the importance of comprehensive respiratory pathogen testing.

Human bocavirus-1 (HBoV1) is a respiratory virus linked to various respiratory illnesses, but its prevalence and role in acute respiratory infections in Sri Lanka is not well investigated. This study investigated the prevalence of HBoV1 in respiratory samples from individuals suspected of having respiratory tract infections in the Western Province, Sri Lanka. Two hundred systematically selected nasopharyngeal swab samples from suspected COVID-19 patients from January 2022 to May 2022 with acute respiratory tract infection (ARTI) symptoms from total of 1507 samples were included. Polymerase chain reaction (PCR) was performed to amplify the Nonstructural protein 1(NP1) gene region of HBoV. The positive sample was subjected to complete genomic sequence by using the Illumina sequencing platform. HBoV was detected in one sample from a nine-month-old infant who presented with cough, fever, and sore throat. This sample was negative for other respiratory viruses and atypical bacteria. The sequence was aligned with reference sequences available in GenBank, which confirmed that the sample belongs to the HBoV1 genotype, with a nucleotide identity of 99.14%. This study was able to detect HBoV1 infections in a patient with acute respiratory tract infection (ARTI) as a sole pathogen and genomic characterization of the isolate. This detection in a symptomatic infant highlights the importance of comprehensive respiratory pathogen testing.

Acute febrile illnesses, including dengue fever, are common causes of hospitalization in Sri Lanka. However, a significant proportion of clinically suspected dengue cases tested negative for dengue-specific markers, raising concerns about alternative infectious causes such as hantavirus. This study aimed to detect hantavirus infections among patients clinically suspected of dengue who tested negative for dengue NS1 and IgM antibodies and to analyze the epidemiology of hantavirus infections in febrile patients. A descriptive cross-sectional study was conducted at the Department of Virology, National Hospital Kandy, from January to August 2023. A total of 415 serum samples from clinically suspected dengue patients who tested negative for dengue NS1 and IgM antibodies were selected. Hantavirus detection was performed using real-time RT-PCR and IgM antibody testing. Additional tests for flavivirus, alphavirus, and leptospirosis were also conducted. Demographic, clinical, and laboratory data were collected from hantavirus-positive cases. Among the 415 samples, 21 (5.1%) tested positive for hantavirus IgM antibodies. None of the samples tested positive for hantavirus RNA. The demographic analysis revealed no significant difference in age or gender between hantavirus-positive and negative patients. Co-infection with leptospirosis was observed in one patient. In addition to fever, clinical features of hantavirus infection included dry cough (41.2%), vomiting (35.3%), and shortness of breath (23.5%). Laboratory findings showed elevated liver enzymes (AST: 61.5%, ALT: 53.8%), elevated creatinine (50%), and elevated CRP (72.7%). The putative 5.1% hantavirus seropositivity rate among clinically suspected dengue patients suggests that hantavirus should be considered in differential diagnoses. Although no hantavirus RNA was detected, the presence of IgM antibodies and negativity to other potential infections indicates a potential recent infection or probable cases. The study highlights the challenge of diagnosing hantavirus due to its similar presentation to dengue fever and the need for improved diagnostic testing. Early diagnosis and tailored management can improve patient outcomes and guide public health responses. Further studies and expanded diagnostic capabilities are recommended to better understand hantavirus prevalence and to improve clinical care for affected patients.

Introduction Human metapneumovirus (hMPV), first identified in 2001, is one of the major respiratory pathogens causing acute respiratory tract infections (ARTIs). 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 January 2021 to December 2023. Methods A total of 1582 respiratory samples from patients with ARTIs were enrolled from four tertiary care hospitals. Nasopharyngeal swab samples were subjected to real-time reverse transcriptase polymerase chain reaction (rtRT-PCR) to test for hMPV using a commercial multiplex assay. Demographic and clinical data were extracted from the patients’ clinical records. 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% (26/1582) patients with majority being children under five 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 (URTI) 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 (LRTI). Continuous surveillance on hMPV infection may help in monitoring the hMPV activity, which will help in tracking the emergence of hMPV infections.

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.