Zoning in on Zika

  • Zika Virus Infection is Spreading from Africa and South East Asia to Brazil, UK and USA
  • Early Detection is Enabled by Quantitative RT-PCR
  • Smart Surveillance Systems are Available, But not Likely to be Used

Zika virus (ZIKV) has rapidly become print headline and TV breaking news for several important reasons that make it blogworthy here, in my opinion. First and foremost is that ZIKV, which is transmitted by infected Aedes aegypti mosquitoes, has been linked to 4,000 cases of microcephaly in the past year in Brazil alone. Microcephaly is a serious and often fatal condition in which babies are born with unusually small heads. Guillain-Barré paralyzing syndrome may also be associated with ZIKV.

A researcher in Brazil with Aedes aegypti mosquitoes. Taken from nytimes.com  

A researcher in Brazil with Aedes aegypti mosquitoes. Taken from nytimes.com

Much controversy over Rio 2016. Taken from dailystomer.com

Much controversy over Rio 2016. Taken from dailystomer.com

Secondly, concerns over the spread of the virus prompted the U.S. Centers for Disease Control and Prevention to recently issue travel alerts urging pregnant women to avoid 14 destinations. These include popular vacation destinations such as Mexico, Puerto Rico, Barbados, St. Martin, and—obviously—Brazil, which is expected to host more than 500,000 foreign visitors during the 2016 Summer Olympics.

ZIKV has now spread outside of Brazil. Three UK residents have been infected, and the US has had about a dozen confirmed cases in California, Florida, Hawaii, Illinois, New Jersey and Texas. One baby in Hawaii was born with microcephaly. All of those infected had traveled to countries where ZIKV is present.

ZIKV Origin and PCR Detection

While I found considerable and up-to-date-information about ZIKV in Wikipedia, my PubMed search of titles/abstracts for “Zika” gave 164 references to peruse. Historically, ZIKV was first characterized following its isolation from serum of a monkey that developed fever after being caged in the Zika Forest (zika meaning “overgrown”) in Entebbe, Uganda. It was subsequently isolated from a human in Nigeria in 1954. From its discovery until the last decade, confirmed cases of ZIKV infection from Africa and Southeast Asia were rare.

My guess is that once ZIKV reached Southeast Asia and Brazil, which have a combined population of nearly 1 billion—and countless zillions of mosquitos—as well as more international visitors than Africa, the current spreading of ZIKV was inevitable.

The complete coding sequence of ZIKV from a French Polynesia outbreak in 2013 was assembled from >130,000 Ion Torrent reads, as reported the following year. Sequence assembly produced a 10,617-nt-long consensus contig, including the virus complete open reading frame (ORF) sequence (10,272 nt). The ORF encodes a polyprotein with three structural proteins—capsid (C), membrane (M), and envelope (E)—and seven nonstructural (NS) proteins—NS1 through NS5—as depicted below, together with peptidase and protease cleavage sites. All of this is characteristic of a flavivirus.

Taken from microbewiki.kenyon.edu

Taken from microbewiki.kenyon.edu

Like Ebola virus, about which I’ve previously commented, ZIKV is a single-stranded, positive-sense RNA genome. Consequently, like Ebola, ZIKV is best detected by one-step quantitative reverse-transcription PCR (qRT-PRC) using virus-specific probes. Sub-searching the aforementioned PubMed “Zika” references for “PCR” led to the following qRT-PCR assay for ZIKV.

In 2013, researchers at Institut Pasteur Dakar in Senegal (Africa) reported that qRT-PCR provides a more rapid (3 hr), specific and sensitive method for early diagnosis of ZIKV infection, compared to detection of specific antibodies or virus isolation from animals or mosquitoes, which is labor intensive, time consuming and requires appropriate containment.

The NS5 protein coding regions of African ZIKV isolates were sequenced and aligned with representative flavivirus sequences from GenBank to design primers and probe from conserved regions. As a technical note, one of the primers included two “Y” positions (aka wobble sites) involving mixed-coupling of T or C, as did one position in the dual-labeled fluorogenic probe.

ZIKV single-stranded RNA is reverse-transcribed (not show) into cDNA that is amplified with forward and reverse primers into double-stranded DNA for detection using a double-labeled (R and Q) fluorogenic probe. Taken from eurofinsgenomics.eu

ZIKV single-stranded RNA is reverse-transcribed (not show) into cDNA that is amplified with forward and reverse primers into double-stranded DNA for detection using a double-labeled (R and Q) fluorogenic probe. Taken from eurofinsgenomics.eu

Smarter Surveillance Systems

Importantly, the aforementioned study validated that the qRT-PCR assay was able to specifically detect RNA extracted from ZIKV-bearing mosquitos caught in the field in Senegal. To me, this suggests that this ZIKV-specific surveillance method is “smarter” in the sense that it can quantitate the amount of ZIKV that may be present in trapped mosquitos, regardless of species—i.e. Aedes aegypti or not—and whether these bear any other type of virus, including the closely related Dengue virus.

Taken from intechopen.com

Taken from intechopen.com

In researching this idea of qRT-PCR-enabled smart surveillance systems for ZIKV, I came across a report by NIH and Brazilian agencies entitled Cost-effectiveness of Novel System of Mosquito Surveillance and Control, Brazil that’s worth mentioning here. In a nut shell, a new trap (Mosquitrap) designed to chemically attract potentially Dengue- or ZIKV-bearing Aedes aegypti mosquitos was implemented in 21 cities in Minas Gerais, Brazil. Traps for adult female mosquitoes were spaced at 300-m intervals throughout each city. In cities that used this trap, mosquito abatement was conducted specifically at high-risk sites (indicated by mosquito count—not qRT-PCR for Dengue) through daily updates. In control cities, mosquito abatement followed established guidelines.

Amazingly to me, it was estimated that these traps prevented 27,191 cases of Dengue fever and saved an average of $227 (median $58) per case prevented. That equates to approximately $364,517 in direct costs (health care and vector control) and $7,138,940 in lost wages (societal effect) annually.

Ideally, these traps, in combination with multiplex qRT-PCR for Dengue virus and ZIKV, will soon be adopted worldwide. Practically speaking, however, my guess is that this ideal will not be achieved due to the usual issues surrounding who’s responsible (i.e. who pays) for implementation—notwithstanding the aforementioned evidence that it would actually save money.

Current CDC Advice for ZIKV

Being a strong believer in Ben Franklin’s sage opinion that “an ounce of prevention is worth a pound of cure,” I thought it apropos to conclude with what preventative information is available for ZIKV. My “go to” sources for authoritative health and epidemiological information are NIH and CDC, respectively. Rather than try to paraphrase the latter’s website advice for ZIKV, here are active links to “What’s New” postings.

As always, your comments are welcomed.


6 thoughts on “Zoning in on Zika

  1. Wonderful and concise report, Jerry! Am sure to retweet, since the Zika virus is now a worldwide concern. Thanks, John

    • Thank you, John, and to your point, I’ll add that health officials in Arkansas and Virginia confirmed Tuesday 1/26 that residents of those states had tested positive for the mosquito-born Zika virus; see this link:



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