Nanomicroarray and multiplex next-generation sequencing for simultaneous identification and characterization of influenza viruses.

Jiangqin Zhao,Indira Hewlett,Viswanath Ragupathy,Zhiping Ye,Sai Vikram Vemula,Xue Wang,Haja Sittana El Mubarak,Jikun Liu,Marie L Landry

doi:10.3201/eid2103.141169

Abstract

Conventional methods for detection and discrimination of influenza viruses are time consuming and labor intensive. We developed a diagnostic platform for simultaneous identification and characterization of influenza viruses that uses a combination of nanomicroarray for screening and multiplex next-generation sequencing (NGS) assays for laboratory confirmation. The nanomicroarray was developed to target hemagglutinin, neuraminidase, and matrix genes to identify influenza A and B viruses. PCR amplicons synthesized by using an adapted universal primer for all 8 gene segments of 9 influenza A subtypes were detected in the nanomicroarray and confirmed by the NGS assays. This platform can simultaneously detect and differentiate multiple influenza A subtypes in a single sample. Use of these methods as part of a new diagnostic algorithm for detection and confirmation of influenza infections may provide ongoing public health benefits by assisting with future epidemiologic studies and improving preparedness for potential influenza pandemics.

Highlights

Human cases of avian influenza A(H7N9) virus infection to date A total of 375 laboratory-confirmed cases of human infection with avian influenza A(H7N9) virus, including 115 deaths, have been reported to WHO: 367 cases by China National Health and Family Planning Commission, two cases by the Taipei Centers for Disease Control (Taipei CDC), five cases by the Centre for Health Protection, China, Hong Kong SAR, and one case in a Chinese traveller, reported from Malaysia
The cases occurred in a first wave (n=133) from February to May 2013; two cases were reported in July and August; and from October 2013 a second wave of human cases has been occurring (n= 240 to date
The age distribution in the second wave is very similar to the first wave, with most cases occurring in middle-aged and older men, few in children and even fewer in teenagers and young adults

Summary

Summary of surveillance and investigation findings

Human cases of avian influenza A(H7N9) virus infection to date A total of 375 laboratory-confirmed cases of human infection with avian influenza A(H7N9) virus, including 115 deaths, have been reported to WHO: 367 cases by China National Health and Family Planning Commission, two cases by the Taipei Centers for Disease Control (Taipei CDC), five cases by the Centre for Health Protection, China, Hong Kong SAR, and one case in a Chinese traveller, reported from Malaysia. The cases occurred in a first wave (n=133) from February to May 2013; two cases were reported in July and August; and from October 2013 a second wave of human cases has been occurring (n= 240 to date) (fig 1). Around 80% of human cases report a history of exposure to birds or live poultry markets. The viruses isolated from humans are avian influenza viruses and genetically similar to those isolated from birds and the environment. Current evidence suggests that these avian influenza A(H7N9) viruses do not transmit from poultry or environments to humans, their transmissibility may be greater compared with highly pathogenic avian influenza A(H5N1) viruses. With the exception of the family clusters, enhanced surveillance has not revealed additional human infections among contacts of confirmed cases so far in the second wave. Considering that a few cases of H7N9 infection since October were detected through influenza-like illness (ILI) surveillance, continued vigilance is warranted

Risk assessment

Findings

What should countries do?