First isolation and characterization of SARS-CoV-2 from COVID-19 patient of North East India.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) responsible for the current pandemic has resulted in over 5 million deaths globally. More than a year has passed, still SARS-CoV-2 panic the public life. Virus isolation is of paramount importance for development of vaccines, in-vitro screening of antiviral compounds, pathogenesis studies, etc., Many cell lines were studied for amplification and replication of SARS-CoV-2 and Vero cells were found to be ideal cell lines for isolation. In May 2020, ICMR-Regional Medical Research Centre, NE region, India, successfully established the SARS-CoV-2 culture system in Vero CCL-81 cell lines. Phylogenetic analyses of the whole genome sequences of the SARS-CoV-2 isolate (EPI_ISL_2501532 | 2020-05-19) showed monophyletic clade G and lineage B.1.1.

Presence of fimH and iss type 1, 2 and 3 genes in uropathogenic Escherichia coli isolates recovered from an apex medical institute in North India.

PURPOSE: To detect the presence of fimH and iss type 1, 2 and 3 genes in uropathogenic Escherichia coli (UPEC) isolates recovered from patients coming to the out patient department (OPD) of our hospital. METHODS: E. coli isolates recovered from patients who had symptoms of urinary tract infection (UTI) were processed for the presence of fimH and iss genes. DNA was extracted using an in house method after which conventional PCR using forward and reverse primers targeting the four genes was carried out. The amplified products were electrophoresed and visualized in a gel documentation imager. Relevant demographic details of the patients were recorded on a pre-designed pro-forma and antimicrobial susceptibility testing of the isolates was done by disc diffusion method. RESULTS: fimH was present in 87.5% of UPEC isolates whereas iss type 1 was seen in 7.3%, type 2 in 4.2% and iss type 3 in 71.9% isolates. Age of the patients ranged from 3 months to 82 â€‹yrs (mean 43.5 SD â€‹± â€‹18.20). UTI was more common in females (60.2%) as compared to males patients (39.8%). Dysuria (66.7%) was the most common symptom in the studied subjects and diabetes mellitus (42.6%) the most common co-morbidity. A total of 56.5% patients gave a history of prior antibiotic intake. The UPEC isolates were resistant to most of the antibiotics tested. However all the isolates were sensitive to polymyxin B and colistin. Fosfomycin resistance was seen in 9.5% of the UPEC isolates harbouring fimH gene. CONCLUSION: This is the first study that highlights the presence of iss type 3 gene in UPEC isolates along with the fimH and iss type 1 and 2 genes. The results of this study can serve as a stepping stone for future in depth research into the significance of the iss genes in causing UTI.

Norovirus gastroenteritis in children under-five years hospitalized for diarrhea in two cities of northeast India: A retrospective study.

PURPOSE: Norovirus gastroenteritis, known to cause 'winter vomiting disease' is increasingly being identified as a major cause of viral gastroenteritis worldwide. The impact and prevalence of this viral disease are lacking in many parts of India including northeast India. This study aimed to determine the prevalence and association of norovirus gastroenteritis among under-five-year-old hospitalized children in two cities in northeast India (Dibrugarh in Assam & Dimapur in Nagaland). MATERIALS AND METHODS: A retrospective analysis of 407 randomly selected diarrheal stool samples was conducted using a commercial multiplex probed-based real-time RT-PCR assay capable of detecting six-viral gastroenteritis pathogens including Norovirus GI, Norovirus GII, Rotavirus, Human Adenovirus, Human Astrovirus, and Sapovirus. RESULTS: Results showed that norovirus was detected in 18.4% of the samples (75/407; 95% CI: 14.8%-22.5%), with norovirus genogroup II being the predominant group in 97.3% of norovirus cases. A significant association of norovirus diarrhea was found with seasonality, with higher prevalence in colder months compared to warmer months (22.4% vs 9.1%, p-value:0.002). Additionally, 66.7% (50/75) of cases of norovirus gastroenteritis had reported vomiting as the major symptom and had a shorter duration of diarrhea (p-value 0.03). Co-infections with other viral pathogens were seen in 45.9% (187/407) of the cases. The detection of rotavirus was 67.1% (273/407), human adenovirus (45.9%; 187/407), sapovirus and astrovirus (5.9%, 24/407 each), and norovirus GI (0.5%, 2/407) among the cases. CONCLUSION: This study reports the prevalence of norovirus gastroenteritis in northeast India and further highlights that norovirus gastroenteritis is responsible for substantial cases of hospitalization of under-five years children in the region.

Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling.

BACKGROUND & OBJECTIVES: Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India. METHODS: Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (Ct) values was analyzed. RESULTS: A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the Ct value ≤30 cycles and 95.5 per cent for Ctvalues ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with Ct values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools. INTERPRETATION & CONCLUSIONS: Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.

Prevalence of campylobacter enteritis in children under 5 years hospitalised for diarrhoea in two cities of Northeast India.

Background: Campylobacter enteritis is the major cause of bacterial gastroenteritis worldwide. In recent years, there has been a rise in global incidence of campylobacteriosis. There are no available data on prevalence of Campylobacter diarrhoea from Northeast India. Materials and Methods: The study investigated archival stool samples collected between 2014 and 2016 from two hospitals of Northeast India. A total of 407 archival stool samples from cases of diarrhoea under 5 years of age were screened for Campylobacter spp. using commercial probe-based real-time polymerase chain reaction assay. Results: Campylobacter spp. was detected in overall 10.1% (41/407; 95% confidence interval: 7.4%-13.3%) in children under 5 years hospitalised for diarrhoea. The prevalence was significantly higher from Dibrugarh, Assam, compared to Dimapur, i.e., 13.4% (27/201) versus 6.8% (14/206), respectively (P = 0.02). Campylobacter detection was highest in the month of June and July compared to December and January (20%-18.8% vs. 8.9%-6.2%, respectively). Further, Campylobacter infection was higher in the age group below 24 months (11.7%) compared to above 24 months (7.0%). Campylobacter jejuni was detected in 80.5% of the positive cases. Conclusion: The present study reveals that Campylobacter infection is endemic in the studied regions of Northeast India and microbiological laboratories of the region should actively pursue the isolation or detection of Campylobacter spp. in cases of diarrhoea in routine stool cultures.

Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016.

Since its emergence in 2009, Influenza A/H1N1pdm09 virus has evolved continuously. Marked genetic variations have occurred in the HA1 domain of the hemagglutinin gene causing the emergence of new variants. The present study genetically characterized the hemagglutinin (HA) gene of Influenza A/H1N1pdm09 strains from Assam circulating in 2016 that caused a mild outbreak without any reported mortality. Sequence analysis of the HA gene of 20 positive Assam/H1N1pdm09 strains revealed 3 mutations (K180Q, S202T, S220T) at the antigenic sites along with several other reported mutations which are in close proximity to the antigenic sites and therefore might affect the viral antigenicity. Phylogenetically, the Assam/H1N1pdm09 strains clustered into genogroup 6B. These genetic variations highlight the importance of continuous surveillance and characterization of Influenza A/H1N1pdm09 virus activity to track the genetic makeup and diversification that may affect the behavior of the virus.