The Florida Department of Health's Bureau of Public Health Laboratories in Jacksonville has developed a protocol for the Next Generation Sequencing (NGS) of HIV, primarily for the purpose of drug-resistant mutation identification. This HIV-1 protocol uses amplicon-based sequencing based on primers designed by the BEEHIVE Consortium (https://www.beehive.ox.ac.uk/). The amplified pol gene regions can be used in both genotyping and drug resistance determination. Our protocol utilizes newer enzymes

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... with higher fidelity for sequencing and Illumina sequencing technology. We have cross verified 3 different Illumina Sequencing platforms to ensure that all produce equivalent results so that in the event of a surge samples can be sequenced quickly and in mixed-species pools. The NGS data generated can also be used in surveillance and outbreak monitoring, giving epidemiologist more information about circulating viral genomes. There is also the potential that this protocol can be expanded to whole genome sequencing for HIV-1. The imminent sunsetting of ViroSeq (Abbott Molecular) has required many labs to look for new methods to continue identifying HIV-1 drug resistance strains for both clinical management and epidemiological study. NGS was chosen as it is more cost effective than investing in a single pathogen platform. NGS allows for one sample to produce results and data that can aid not just a patient but an entire population.