Highly pathogenic avian influenza (HPAI) H5N1 has caused severe illnesses in poultry and in humans. More than 15,000 outbreaks in domestic birds from 2005 to 2018 and 861 human cases from 2003 to 2019 were reported across the world to OIE (Office International des Epizooties) and WHO (World Health Organization), respectively. We reviewed and summarized the spatial and temporal distribution of HPAI outbreaks in South Asia. During January 2006 to June 2019, a total of 1063 H5N1 outbreaks in birds and 12 human cases for H5N1 infection were reported to OIE and WHO, respectively. H5N1 outbreaks were detected more in the winter season than the summer season (RR 5.11, 95% CI: 4.28–6.1). Commercial poultry were three times more likely to be infected with H5N1 than backyard poultry (RR 3.47, 95% CI: 2.99–4.01). The highest number of H5N1 outbreaks was reported in 2008, and the smallest numbers were reported in 2014 and 2015. Multiple subtypes of avian influenza viruses and multiple clades of H5N1 virus were detected. Early detection and reporting of HPAI viruses are needed to control and eliminate HPAI in South Asia.

As the COVID-19 pandemic erupted, the WHO recommended the use of nasopharyngeal or throat swabs for the detection of SARS-CoV-2 etiology of COVID-19. The collection of NPS causes discomfort because of its invasive collection procedure.

The Nanopore MinION-based influenza sequencing approach we are proposing makes it possible to sequence the influenza A virus, irrespective of its diverse serotypes, directly from clinical and environmental swab samples, so that we are not limited to virus culture. This third-generation, portable, multiplexing, and real-time sequencing strategy is highly convenient for local sequencing, particularly in low- and middle-income countries like Bangladesh.

Several species of Plasmodium are responsible for causing malaria in humans. Proper diagnoses are crucial to case management, because severity and treatment varies between species. Diagnoses can be made using rapid diagnostic tests (RDTs), which detect Plasmodium proteins. Plasmodium falciparum causes the most virulent cases of malaria, and P. falciparum histidine-rich protein 2 (PfHRP2) is a common target of falciparum malaria RDTs. Here we report a case in which a falciparum malaria patient in Bangladesh tested negative on PfHRP2-based RDTs. The negative results can be attributed to a deletion of part of the pfhrp2 gene and frameshift mutations in both pfhrp2 and pfhrp3 gene. This finding may have implications for malaria diagnostics and case management in Bangladesh and other regions of South Asia.

Nipah virus (NiV) is a deadly zoonotic pathogen in Southeast Asia causing severe respiratory and encephalitis symptoms with a high fatality rate. Whole-genome sequencing (WGS) is crucial for tracking transmission, conducting epidemiological analyses, and understanding NiV’s adaptive evolution. WGS is essential for analyzing genomes, particularly in understanding pathogen nature, and pathogenesis and aiding in the development of therapeutics. However, sequencing this highly contagious virus directly from samples is challenging in low- and middle-income countries lacking BSL-4 facilities. This study developed and optimized a culture-independent, high-throughput multiplex PCR-based third-generation sequencing protocol for NiV using the Oxford Nanopore Technology platform and a proposed bioinformatics pipeline to generate consensus genome sequences directly from environmental and clinical specimens. We amplified 12 NiV RT-PCR-positive specimens (11 clinical, one environmental) to produce 60 amplicons, each approximately 400 bp, covering the entire ~18.2 kb genome. Using a two-step reverse transcriptase PCR approach, libraries were prepared with a ligation sequencing kit. Raw sequence data were then analyzed using bioinformatics tools. A minimum of 10,000 total reads per sample provided a nearly complete coverage (>95%) of the NiV genome, even with low virus concentrations (Ct ≤ 32), with an average quality score of 10.2. The WGS of 12 NiV-positive samples achieved coverage between 95.71% (Ct 29.54) and 99.3% (Ct 22.34). The entire process, from RNA extraction to finished sequences, took only 24 h. We developed a portable, culture-independent, high-throughput sequencing workflow suitable for resource-limited settings, aiding in real-time monitoring, outbreak investigation, and detection of new NiV strains and genetic evolution. IMPORTANCE: The development of a culture-independent, high-throughput whole-genome sequencing (WGS) protocol for Nipah virus (NiV) using the Oxford Nanopore MinION technology marks a significant advancement in outbreak response, surveillance, and genomic analysis of NiV. NiV is an RG4 category C pathogen; working with the NiV virus is a deep concern of biosafety and biosecurity. It demands the development of biologically safe procedures to get genetic information. This protocol utilizes biologically safe samples that were collected into recommended lysis solution, multiplex PCR, and third-generation sequencing, effectively addressing challenges in sequencing NiV. This optimized workflow achieved over 95% genome coverage without the need for virus culture. It is a cost-effective, rapid, and efficient approach to the WGS of NiV, making it suitable for resource-limited settings like Bangladesh. The method enhances the capacity for outbreak investigations, epidemiological analyses, and monitoring virus, aiding in detecting emerging strains. This work contributes significantly to global pandemic preparedness and response efforts.

Background: Norovirus is a major cause of endemic acute gastroenteritis (AGE) worldwide. We described the epidemiology, risk factors, and genotypic distribution of noroviruses among hospitalized patients of all ages in Bangladesh. Methods: From March 2018 to October 2021, 1250 AGE case patients and controls (age, sex, season, and site matched) were enrolled at 10 hospitals. Demographic and clinical information was collected; real-time reverse-transcriptase polymerase chain reaction (RT-PCR) used to test stool specimens, and positive samples were genotyped. Results: Norovirus was detected in 9% of cases (111 of 1250) and 15% (182 of 1250) of controls. Eighty-two percent of norovirus-positive cases were in children <5 years old. Norovirus-positive AGE hospitalizations occurred year-round, with peaks in April and October. Risk factors for norovirus included age <5 years (adjusted odds ratio, 3.1 [95% confidence interval, 1.9–5.2]) and exposure to a patient with AGE in the 10 days before enrollment (3.8 [1.9–7.2]). GII.3[P16] and GII.4 Sydney[P16] were the predominant genotypes. Conclusions: We highlight the burden of norovirus in hospital settings. Young age and recent exposure to a patient with AGE were risk factors for norovirus. A high prevalence of norovirus among controls might represent asymptomatic reinfections or prolonged shedding from a previous infection; carefully designed longitudinal studies are needed to improve our understanding of norovirus infections in Bangladesh.