Viral Factors Associated With the High Mortality Related to Human Infections With Clade 2.1 Influenza A/H5N1 Virus in Indonesia

Abstract

Background Since their emergence in Indonesia in 2005, 200 human infections with clade 2.1 highly pathogenic avian influenza A/H5N1 virus have been reported, associated with exceptionally high mortality (84%) compared to regions affected by other genetic clades of this virus. To provide potential clues towards understanding this high mortality, detailed clinical virological analyses were performed in specimens from 180 H5N1 patients, representing 90% of all Indonesian patients and 20% of reported H5N1-infected patients globally. Methods H5N1 RNA was quantified in available upper- and lower-respiratory tract specimens as well as fecal and blood samples from 180 patients with confirmed infection between 2005 and 2017. Mutations in the neuraminidase and M2 genes that confer resistance to oseltamivir and adamantanes were assessed. Fatal and nonfatal cases were compared. Results High viral RNA loads in nasal and pharyngeal specimens were associated with fatal outcome. Mortality increased over time during the study period, which correlated with increasing viral RNA loads on admission. Furthermore, the prevalence of amantadine resistance–conferring M2 mutations increased over time, and viral loads were higher in patients infected with viruses that harbored these mutations. Compared to observations from other regions, viral RNA was detected more frequently in feces (80%) and particularly in blood (85%), and antiviral responses to oseltamivir appeared less pronounced. Conclusions These observations confirm the association of viral load with outcome of human H5N1 infections and suggest potential differences in virulence and antiviral responses to oseltamivir that may explain the exceptionally high mortality related to clade 2.1 H5N1 infections in Indonesia.

Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015

“…However, none of the newly isolated viruses encoded known NAI resistance mutations (i.e., V116A, I117V, E119V, G136K, V149A, R156K, D198N, S246N, H275Y, R293K, N295S (N1 numbering)) [64]. This corresponds with our earlier study showing that acquisition of NAI resistance is extremely rare in H5N1-infected individuals in Indonesia, be it before or during treatment [11]. Of note, Q136H was observed in 14 of the 35 isolates.…”

“…Interestingly, isolates in this study collected in more recent years often encode resistance mutations in both positions 27 and 31. These results indicate that Indonesian H5N1 viruses are sensitive to NA inhibitors but resistant to M2 inhibitor, despite the absence of amantadine treatment [11].…”

“…200 human infections with HPAI H5N1 viruses have been reported in Indonesia so far with higher case fatality rates among reported cases (84%) compared to the rest of the world afflicted by the virus. We previously showed that high nasopharyngeal viral load was associated with more severe outcome of human H5N1 infections in Indonesia and that the virus was more commonly detected in blood relative to other geographical regions affected by HPAI H5N1 [11,12]. Strikingly, although the number of detections in humans peaked in [2005][2006] in Indonesia and subsequently declined in the following years, the case fatality rate in Indonesia increased over time from 65% in 2005 to 100% since 2012.…”

“…Strikingly, although the number of detections in humans peaked in [2005][2006] in Indonesia and subsequently declined in the following years, the case fatality rate in Indonesia increased over time from 65% in 2005 to 100% since 2012. This increase was associated with higher viral load prior to treatment and the presence of mutations in the matrix protein that confers adamantane resistance [11]. However, reasons for the higher viral load and case fatality rate are still unclear.…”

“…We previously showed that substitutions related to amantadine resistance are common in H5N1 viruses in Indonesia [11] even though amantadine treatment is not administered anymore. The prevalence of amantadine resistance-related substitutions increased over time from 37.5% in 2005, to 95% in 2009 and 100% during subsequent years [11]. Various amantadine resistance substitutions in the M2 protein were also found in all 35 isolates, including V27A (34 viruses), V27T (1 virus), S31G (1 virus), and S31N (5 viruses).…”