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. 2023 Oct 20:11:1218292.
doi: 10.3389/fpubh.2023.1218292. eCollection 2023.

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

Varsha Potdar #  1 , Neetu Vijay #  2 , Labanya Mukhopadhyay #  2 , Neeraj Aggarwal #  2 , Sumit Dutt Bhardwaj  1 , Manohar Lal Choudhary  1 , Nivedita Gupta  2 , Harmanmeet Kaur  2 , Jitendra Narayan  2 , Prabhat Kumar  3 , Harpreet Singh  3 , Rizwan Suliankatchi Abdulkader  4 , Manoj Murhekar  4 , Meena Mishra #  5 , Sundararajan Thangavel #  6 , K Nagamani #  7 , Rahul Dhodapkar #  8 , Bashir Ahmad Fomda #  9 , Umesh Varshney #  10 , Agniva Majumdar #  11 , Shanta Dutta #  11 , P Vijayachari #  12 , Jyotirmayee Turuk #  13 , Tapan Majumdar #  14 , Ganesh Chandra Sahoo #  15 , Krishna Pandey #  15 , Anudita Bhargava #  16 , Sanjay Singh Negi #  16 , Prabhat K Khatri #  17 , Usha Kalawat #  18 , Debasis Biswas #  19 , Neeta Khandelwal #  20 , Biswajyoti Borkakoty #  21 , S Manjushree #  22 , Mini P Singh #  23 , Jyoti Iravane #  24 , K Kaveri #  25 , G B Shantala #  26 , Megha Brijwal #  27 , Aashish Choudhary #  27 , Lalit Dar #  27 , Bharti Malhotra #  28 , Amita Jain #  29 ; ILI-SARI Surveillance Team
Affiliations

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

Varsha Potdar et al. Front Public Health. .

Abstract

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.

Keywords: ILI; SARI; SARS-CoV-2; influenza; integrated surveillance.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Laboratories (n = 26) in the ILI/SARI surveillance network.
Figure 2
Figure 2
ILI/SARI testing protocol.
Figure 3
Figure 3
(A) Monthly distribution of influenza and SARS-CoV-2 detected among ILI cases. (B) Monthly distribution of influenza and SARS-CoV-2 detected among SARI cases. (C) Monthly distribution of influenza virus sub types.
Figure 4
Figure 4
(A) Influenza virus subtype wise % positivity among ILI cases. (B) Influenza virus subtype wise % positivity among SARI cases.
Figure 5
Figure 5
Regional trends of influenza and SARS-CoV-2 positivity across India.
Figure 6
Figure 6
Phylogenetic analysis of A(H1Nl)pdm09 from 2021 and 2022. The strains in red are 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylocenetic analysis of A(H3N2) from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylogenetic analysis of influenza B viruses: B/Victoria lineage from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue.
Figure 6
Figure 6
Phylogenetic analysis of A(H1Nl)pdm09 from 2021 and 2022. The strains in red are 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylocenetic analysis of A(H3N2) from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylogenetic analysis of influenza B viruses: B/Victoria lineage from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue.
Figure 6
Figure 6
Phylogenetic analysis of A(H1Nl)pdm09 from 2021 and 2022. The strains in red are 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylocenetic analysis of A(H3N2) from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue. Phylogenetic analysis of influenza B viruses: B/Victoria lineage from 2021 and 2022. The strain in red is 2022–23 vaccine component strains. The 2022 strains are denoted in blue.
Figure 7
Figure 7
Flowchart depicting different subsets of patients used for analysis of clinical data.
See this image and copyright information in PMC

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