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Hantavirus hemorrhagic fever with renal syndrome (HFRS) is an emerging zoonotic disease in Europe and Asia, which is clinically indistinguishable from leptospirosis. A total of 1,032 patients with clinical suspicion of HFRS-like illness were included in the analysis from March 2013 to March 2021. Of these, 168 were positive for hantavirus immunoglobulin M (IgM) antibodies. Thirty-one of 35 patients had a 4-fold increase in IgG antibody titer with paired serum, confirming acute hantavirus infections. The detected antibodies showed a diverse pattern, strongly cross-reacting with the Seoul, Hantaan, and Puumala virus antigens. All the IgM-positive patients had no serological evidence of acute dengue or leptospirosis and had classical features of HFRS, including fever, thrombocytopenia, and renal involvement. More than 90% of patients had a history of rodent exposure 2-3 weeks prior to the onset of the fever. The highest number of positive cases was diagnosed in the Western and North Central Provinces of Sri Lanka during the paddy harvesting seasons. A significant number of patients develop severe complications with high mortality rates. Therefore, hantavirus infection should be considered as a differential diagnosis for leptospirosis-like illnesses in Sri Lanka.

During the 2017 outbreak of severe dengue in Sri Lanka, dengue virus (DENV) serotypes 2, 3, and 4 were found to be co-circulating. Our previous study of 295 patients from the National Hospital Kandy in Sri Lanka between March 2017 and January 2018 determined that the dominant infecting serotype was DENV-2. In this study, we aimed to characterize the DENV-3 strains from non-severe and severe dengue patients from our previous study population. Patients’ clinical records and previous laboratory tests, including dengue-specific nonstructural protein 1 antigen rapid test and IgM-capture and IgG enzyme-linked immunosorbent assays, were analyzed together with the present results of real-time reverse transcription polymerase chain reaction and next-generation sequencing of DENV-3. Complete genome analysis determined that DENV-3 isolates belonged to 2 different clades of genotype I and were genetically close to strains from Indonesia, China, Singapore, Malaysia, and Australia. There were 16 amino acid changes among DENV-3 isolates, and a greater number of changes were found in nonstructural proteins than in structural proteins. The emergence of DENV-3 genotype I was noted for the first time in Sri Lanka. Continuous monitoring of this newly emerged genotype and other DENV serotypes and genotypes is needed to determine their effects on future outbreaks and understand the molecular epidemiology of dengue., Japanese Journal of Infectious Diseases, 74(5), pp. 443-449; 2021

Background Classical hantavirus infections present as haemorrhagic fever with renal syndrome (HFRS) in Euro-Asia and as hantavirus pulmonary syndrome (HPS) in America. Mixed clinical features have been reported from certain novel hantavirus infections. In the north-central part of Sri Lanka, clusters of patients with fever and non-cardiogenic pulmonary edema have been reported in recent years. Objectives To detect hantavirus infection among clinically suspected patients and to describe clinical and demographic features of hantavirus infection in north-central Sri Lanka. Study design Clinically suspected patients with HFRS and HPS like illness admitted to two leading hospitals in the north-central part of the country from December 2013 to November 2015 and from March 2016 to February 2018 were included in the study. Acute phase blood samples were tested for the presence of anti-hantavirus IgM. Convalescent blood samples were taken from available cases and both acute and convalescent sera were subjected to IgG titre detection. Results Seventy-two patients were included in the study. Twenty-nine (40.28%) were positive for hantavirus IgM. Of them, 20 (68.97%) presented with pulmonary symptoms with no or mild nephritis. Five (17.24%) had pulmonary symptoms with prominent nephritis and 04 (13.79%) had classic features of HFRS. Conclusion In the north-central part of Sri Lanka, most hantavirus infection was associated with pulmonary symptoms complicated with non-cardiogenic pulmonary edema, which was different from clinical presentation reported previously from other parts of the country. HPS like hantavirus infection in the study area could be due to a Puumala-like virus or a novel virus.

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 values40) 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.

Purpose of review Hantavirus infection is an emerging zoonosis and there are two main clinical presentations, hemorrhagic fever with renal syndrome (HFRS) and Hantavirus pulmonary syndrome (HPS). Although Hantavirus infections have a worldwide distribution with a high mortality rate, a safe and effective vaccine or an antiviral drug against the Hantavirus disease is yet to be available. This review summarizes all the efforts undertaken to develop medical countermeasures in vitro, in vivo, and human clinical trials against Hantavirus infections. Recent findings Multiple antivirals are shown to be effective with limited evidence and recent studies on immunotherapy were not very conclusive. There are multiple vaccine candidates with evidence of conferring long protective immunity against Hantaviruses. Some of these had been already trialed on humans. Summary At present, severe HPS or HFRS case management is purely based on supportive treatments, often in an intensive care unit. Rodent control and public health education and promotion play a major role in preventing Hantavirus infection.

Dengue has now become endemic in almost all districts of Sri Lanka. An increase in the percentage contribution from North Central Province (NCP) to dengue incidence in the country has been noted since the 2015 dengue outbreak. During the year 2017, 338 patients per 100,000 population were reported to have clinically suspected dengue according to the epidemiology unit records. The daily records available at the dengue control unit of regional director of health services office, Anuradhapura, and the freely available data at the epidemiology unit, which comprised of weekly cases of dengue, were extracted and analysed against the meteorological parameters and the vector density data. According to our observations, a statistically significant association between daily rainfall and daily temperature and clinically diagnosed dengue cases does not exist in Anuradhapura. The monthly vector indices did not show any correlation with the monthly incidence of dengue in the medical officer of health area with the highest overall incidence of dengue. The proportion of paediatric patients were also very low in the Anuradhapura district (9%) compared to other districts. Based on these observations, the authors suggest that imported cases of dengue to this district is a major cause of increased incidence of dengue, rather than indigenous transmission in the area.

Background Sri Lanka experienced its largest dengue outbreak in 2017 with more than 185,000 dengue cases including at least 250 fatalities. Objectives Our study aimed to characterize the clinical, immunological and virological features of confirmed dengue patients in Sri Lanka during the outbreak in 2017 when unusual manifestations of severe dengue were observed. Study design Sera from 295 patients who were admitted to Teaching Hospital Kandy, Kandy, Sri Lanka between March 2017- January 2018 were subjected to NS1 antigen, IgM and IgG ELISAs, virus isolation, conventional and real time RT-PCR and next generation sequencing. Results Primary and secondary infections were detected in 48.5 % and 51.5 % of the study population, respectively. Two hundred twenty five DENV strains were isolated (219 DENV-2, one DENV-3, two DENV-4, two mixed infections of DENV-2 and -3 and one mixed infection of DENV-2 and -4). Unusual and severe manifestations such as encephalitis, encephalopathy, liver failure, kidney failure, myocarditis, Guillain–Barre syndrome and multi-organ failure were noted in 44 dengue patients with 11 deaths. The viraemia levels in patients with primary infection and unusual manifestations were significantly higher compared to those in patients with secondary infection. A new clade of DENV-2 Cosmopolitan genotype strains was observed with the strains closely related to those from China, Malaysia, Indonesia, Singapore and Taiwan. Conclusions The new clade of DENV-2 cosmopolitan genotype observed in Sri Lanka in 2017 caused an unprecedented, severe dengue outbreak. The emergence of DENV-3 and DENV-4 in the 2017 outbreak might cause future outbreaks in Sri Lanka.

In 2013 in Myanmar, dengue epidemic occurred with 20,255 cases including 84 deaths. This study aimed to determine the serological and molecular characteristics of dengue virus (DENV) infection among children with clinical diagnosis of dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS) during this period. Single acute serum samples were collected from 300 children in Mandalay Children Hospital, Mandalay, Myanmar. Out of the 300 children, 175 (58.3%) and 183 (61%) were positive for anti-dengue IgM and anti-dengue IgG, respectively. Among the IgM positives, 41 (23.4%) had primary DENV infection. Thirty-nine DENV strains (23 DENV-1, 10 DENV-2 and 6 DENV-4) were successfully isolated after inoculation of the patient serum samples onto C6/36 cells. DENV 1 was the dominant serotype in the 2013 epidemic. There was no correlation between the infecting serotypes and clinical severities. The DENV-1 strains belonged to three lineages of the genotype 1; the DENV-2 strains were of the Asian I genotype and were separated into two lineages; and DENV-4 strains belonged to the same lineage of genotype I. It is of interest to note the diversity of DENV-1 and -2 circulating in the same location during June-August 2013. These DENV isolates were genetically close (98%-100%) to the other previously reported isolates from Myanmar and its neighboring countries, namely China, Thailand, Sri Lanka, Cambodia and Vietnam. Primary DENV infection was still high among the severe dengue cases. Different serotypes of DENV were co-circulating in 2013, however, genotype shift was not observed. Additionally, amino acid mutations were detected in the study strains not seen in the previously reported strains from other countries and Myanmar. This paper provided information on the circulating serotypes for the last 15years and the recent dengue situation in Mandalay, Myanmar after 2006.

Dengue virus (DENV) infection remains a major public health concern in many parts of the world, including Southeast Asia and the Americas. Sri Lanka experienced its largest dengue outbreak in 2017. Neurological symptoms associated with DENV infection have increasingly been reported in both children and adults. Here, we characterize DENV type 2 (DENV-2) strains, which were isolated from cerebrospinal fluid (CSF) and/or serum of patients with dengue encephalitis. Acute serum and CSF samples from each patient were subjected to dengue-specific non-structural protein 1 (NS1) antigen test, IgM and IgG enzyme-linked immunosorbent assay (ELISA), virus isolation, conventional and real-time polymerase chain reaction (PCR), and next-generation sequencing (NGS). Among the 5 dengue encephalitis patients examined, 4 recovered and 1 died. DENV-2 strains were isolated from serum and/or CSF samples of 3 patients. The highest viral genome levels were detected in the CSF and serum of the patient who succumbed to the illness. A phylogenetic tree revealed that the DENV-2 isolates belonged to a new clade of cosmopolitan genotype and were genetically close to strains identified in China, South Korea, Singapore, Malaysia, Thailand, and the Philippines. According to the NGS analysis, greater frequencies of nonsynonymous and synonymous mutations per gene were identified in the nonstructural genes. The full genomes of serum- and CSF-derived DENV-2 from the same patient shared 99.7% similarity, indicating that the virus spread across the blood-brain barrier. This is the first report to describe neurotropic DENV-2 using whole-genome analysis and to provide the clinical, immunological, and virological characteristics of dengue encephalitis patients during a severe dengue outbreak in Sri Lanka in 2017., PLOS ONE, 15(6), art.no.e0234508; 2020

Epidemics of the Chikungunya virus (CHIKV) from 2004 onwards were caused by the East/Central/South African (ECSA) genotype. However, the pathogenesis of the genotype infection has not been fully explained. In this study, we examined the pathogenic potential of CHIKV ECSA genotype M-30 (M-30) by comparing it with that of African genotype S-27 (S-27) in mice. Following low titer infections in type-I IFN receptor KO (A129) mice, we found that the M-30 infection caused high and acute fatality compared with the S-27 infection. M-30-infected A129 mice showed higher viral loads in their central nervous systems and peripheral organs, and increased levels of IFN- responses in their brains. Interestingly, M-30-infected mice did not show the hypophagia and reductions in weight which were observed in S-27-infected mice. Our observations provide a novel explanation of the pathogenic mechanisms attributed to virus proliferation, anti-type-II IFN response and metabolic activity in the CHIKV ECSA virus in mice., Viruses, 12(2), art.no.169; 2020

Acute encephalitis syndrome (AES) is associated with high morbidity and mortality, and affects both children and adults. The main etiologic agent is Japanese encephalitis virus (JEV); however, there are also reports of Dengue virus (DENV) encephalitis. The objectives of this study were to determine the proportion of patients with encephalitis due to JEV during the 2014 outbreak in Son La Province in Vietnam and to explore the association of DENV in non-JEV viral encephalitis cases. Of 90 patients, 6 (6.7%) were positive for anti-JEV immunoglobulin M (IgM), 5 (5.6%) were positive for anti-DENV IgM, 30 (33.3%) were positive for both anti-JEV and anti-DENV IgM, and 56 (62.2%) were positive for flavivirus immunoglobulin G (IgG). In 5 patients with AES, who had positive anti-DENV IgM results in at least one of the paired serum samples, DENV was confirmed by neutralization testing. The incidence of JEV infection was high. There is still a need to maintain and strengthen the national JEV immunization program. This noticeable occurrence of DENV infection was not reported in Son La Province in 2013?2014. Our data suggested that in addition to JEV, DENV was also a causative agent of AES in 2014 in Son La Province, and this finding also confirmed the local occurrence of DENV infection., Japanese Journal of Infectious Diseases, 70(4), pp.357-361; 2017