Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis.

Background: Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods: In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings: Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation: The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories.

Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.

Study of biofilm formation in bacterial isolates from contact lens wearers.

Purpose: To detect biofilm forming capacity of bacterial isolates obtained from the conjunctiva, contact lens and accessories of contact lens wearers using phenotypic and genotypic methods. Methods: Bacterial strains were collected from the conjunctiva, contact lens and lens storage cases of contact lens wearers. The phenotypic detection of biofilm production was done using the tube method and congo red agar method. The biofilm-forming related genes, icaA, of Coagulase negative Staphylococcus (CONS) and Staphylococcus aureus, and pslA, of P. aeruginosa, were detected using PCR. Results: A total of 265 bacterial isolates which included S. aureus, CONS, Pseudomonas, Nil-fermenter Gram-negative bacilli (NFGNB), Bacillus spp, Diphtheroids, Micrococci, Klebsiella pneumonia, Klebsiella oxytoca, E. coli, Proteus mirabilis, Proteus vulgaris, Citrobacter koseri, Citrobacter freundii, Enterobacter cloacae, Moraxella were obtained. Of the 265 isolates, 53.5% were moderately positive, 33.2% strongly positive and 13.2% negative for biofilm production by tube method and 36.6% were moderately positive, 40% strongly positive and 23.3% negative for biofilm production by congo red agar method. Of the four S. aureus isolates, two (50%) showed the presence of icaA gene. Of the 23 CONS isolates, three (13%) showed the presence of icaA gene. All the Pseudomonas isolates were negative for presence pslA (1119 bp) gene though most of them were phenotypically positive for biofilm formation. Conclusion: Most of the bacterial isolates obtained from contact lens wearers had the potential to produce biofilms. Tube method and Congo red agar method exhibited significant statistical correlation (P-value = 0.006) and picked up a good number of biofilm-forming isolates, hence may be used for detection of biofilm production. The absence of biofilm-forming gene did not rule out the possibility for phenotypic biofilm production by bacteria.

Geographical distribution of primary & secondary dengue cases in India - 2017: A cross-sectional multicentric study.

Background & objectives: Dengue virus infection is endemic in India with all the four serotypes of dengue virus in circulation. This study was aimed to determine the geographic distribution of the primary and secondary dengue cases in India. Methods: A multicentre cross-sectional study was conducted at Department of Health Research / Indian Council of Medical Research (DHR)/(ICMR) viral research and diagnostic laboratories (VRDLs) and selected ICMR institutes located in India. Only laboratory-confirmed dengue cases with date of onset of illness less than or equal to seven days were included between September and October 2017. Dengue NS1 antigen ELISA and anti-dengue IgM capture ELISA were used to diagnose dengue cases while anti-dengue IgG capture ELISA was used for identifying the secondary dengue cases. Results: Of the 1372 dengue cases, 897 (65%) were classified as primary dengue and 475 (35%) as secondary dengue cases. However, the proportion varied widely geographically, with Theni, Tamil Nadu; Tirupati, Andhra Pradesh and Udupi-Manipal, Karnataka reporting more than 65 per cent secondary dengue cases while Srinagar, Jammu and Kashmir reporting as low as 10 per cent of the same. The median age of primary dengue cases was 25 yr [interquartile range (IQR 17-35] while that of secondary dengue cases was 23 yr (IQR 13.5-34). Secondary dengue was around 50 per cent among the children belonging to the age group 6-10 yr while it ranged between 20-43 per cent among other age groups. Interpretation & conclusions: Our findings showed a wide geographical variation in the distribution of primary and secondary dengue cases in India. It would prove beneficial to include primary and secondary dengue differentiation protocol in the national dengue surveillance programme.

Comparison of microbiome isolated from the conjunctiva, contact lens and lens storage case of symptomatic and asymptomatic contact lens users.

BACKGROUND AND OBJECTIVES: Contact lenses (CLs) are increasingly being used for cosmetic or therapeutic purposes. Lack of compliance and poor hygiene towards lens care is strongly associated with microbial contamination and has been proved to result in eye infections. The present study was done to compare the microbial flora between symptomatic and asymptomatic contact lens users. The study also attempts to analyze the contact lens hygiene practices of CL users. MATERIALS AND METHODS: Six samples each were collected from both the eyes, CLs and lens cases of 40 CL users (n=240) divided into two groups based on symptoms present asasymptomatic CL users and symptomatic CL users. Organisms were identified using standard microbiological techniques. RESULTS: The proportion GNB obtained in symptomatic CL users was significantly higher when compared to asymptomatic CL users (p-value= <0.003). In 56.2% eyes, the microbial flora of conjunctiva was similar to either the contact lens isolate/storage case. Enterococcal microbial keratitis was seen in one case. CONCLUSION: There was significant microbial contamination present in CL users despite compliance to contact lens hygiene practices. There were a significant number of bacteria (p-value <0.001) present which were resistant to ampicillin, amoxicillin-clavulanate, and cefotaxime in both the groups.