A retrospective analysis of serological & molecular testing data on dengue fever in Kolkata & adjacent districts during 2016-2019

Background & objectives: Regional Virus Research and Diagnostic Laboratory established at ICMR-National Institute of Cholera and Enteric Diseases (NICED) regularly receives samples for dengue screening and serotyping from patients of acute febrile illness (AFI) from Kolkata and adjacent districts. In this study, data over a three year period (August 2016-July 2019) was retrospectively analyzed to provide insight into the epidemiological trends of dengue fever in this region. Methods: Serological screening of dengue was performed by detection of NS1 antigen and/or immunoglobulin M (IgM) antibody. Dengue serotyping was done by conventional or real-time reverse transcriptase–PCR. The data were analyzed to describe the distribution of dengue with respect to age of patient, duration of fever on the day of blood collection and month of the year. Zip codes were used for spatial plotting. Results: Out of the 24,474 samples received from Kolkata and its adjacent districts (Hooghly, Howrah, North and South 24 Parganas), 38.3 per cent (95% confidence interval: 37.7-38.9%) samples were screened positive for dengue. The correlation between age and dengue positivity was found to be weak. A combination of dengue NS1 antigen and dengue IgM antibody detection may be a better option for detecting dengue positivity compared to a single test. Most AFI cases were tested from August to November during the study period, with maximum dengue positivity noted during September (45.9%). The predominant serotype of 2016, dengue virus serotype 1 (DENV-1), was almost entirely replaced by DENV-2 in 2017 and 2018. Interpretation & conclusions: Dengue continues to be an important cause of AFI in the region and round-the-year preventive measures are required for its control. Serotype switching is alarming and should be monitored routinely.

Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal andoropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2aclade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were alsodetected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz.G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutationsreside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S2 domain,which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observedbetween these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations ofmiRNA binding and structure were also predicted for these mutations. More importantly, the possibleimplications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of Sprotein have also been discussed. Results report for the first time a bird’s eye view on the accumulation ofmutations in SARS-CoV-2 genome in Eastern India.

Occurrence, significance & molecular epidemiology of cholera outbreaks in West Bengal.

BACKGROUND & OBJECTIVE: Diarrhoeal disease outbreaks are causes of major public health emergencies in India. We carried out investigation of two cholera outbreaks, for identification, antimicrobial susceptibility testing, phage typing and molecular characterization of isolated Vibrio cholerae O1, and to suggest prevention and control measures. METHODS: A total of 22 rectal swabs and 20 stool samples were collected from the two outbreak sites. The V. cholerae isolates were serotyped and antimicrobial susceptibility determined. Pulsed- field gel electrophoresis (PFGE) was performed to identify the clonality of the V. cholerae strains which elucidated better understanding of the epidemiology of the cholera outbreaks. RESULTS: Both the outbreaks were caused by V. cholerae O1 (one was caused by serotype Ogawa and the other by serotype Inaba). Clinically the cases presented with profuse watery diarrhoea and dehydration. All the tested V. cholerae isolates were sensitive to tetracycline, gentamycin and azithromycin but resistance for ampicillin, co-trimoxazole, nalidixic acid, and furazolidone. PFGE pattern of the isolates from the two outbreaks revealed that they were clonal in origin. Stoppage of the source of water contamination and chlorination of drinking water resulted in terminating the two outbreaks. INTERPRETATION & CONCLUSION: The two diarrhoeal outbreaks were caused by V. cholerae O1 (Inaba/Ogawa). Such outbreaks are frequently seen in cholera endemic areas in many parts of the world. Vaccination is an attractive disease (cholera) prevention strategy although long-term measures like improvement of sanitation and personal hygiene, and provision of safe water supply are important, but require time and are expensive.

Phage typing, biotyping & antimicrobial resistance profile of Salmonella enterica serotype Typhi from Kolkata.

BACKGROUND & OBJECTIVE: Kolkata and its suburbs in eastern India are known to be endemic for typhoid fever. The objective of this study was to determine phage types, biotypes and antimicrobial resistance patterns of Salmonella enterica serotype Typhi isolated during the period 2003-2005 from a prospective surveillance for typhoid fever in two urban slums in Kolkata. METHODS: A total of 195 Salmonella enterica serotype Typhi isolated from blood cultures were phage typed, biotyped and tested for their antimicrobial susceptibility profile. RESULTS: Phage type E1 was the most common (60.3%) followed by phage type A among five phage types identified. Biotype I (95%) was predominant, 28 isolates were multidrug resistant (MDR) and most of the MDR strains belonged to phage type E1 and biotype I. INTERPRETATION & CONCLUSION: A single phage type and biotype were prevalent among the Salmonella enterica serotype Typhi isolates studied from Kolkata, India.