Viral Diagnosis: Mucocutaneous, Enteric, Systemic, Immunocompromised, and Travel-Related Infections

Pathogenesis predicts lesion distribution: direct inoculation causes localized mucocutaneous lesions (molluscum, HPV, HSV, hand-foot-mouth disease/herpangina); hematogenous dissemination causes generalized exanthems (measles, rubella, parvovirus B19, human herpesvirus 6); VZV can do both. HIV diagnostic algorithms, staging, and monitoring, and viral-hepatitis serologic algorithms, are owned by Immunology. Those algorithms still need microbiology-facing information about specimens, NAAT, culture, and antigen applications.

Skin and mucosal manifestations

Molluscum contagiosum virus is a poxvirus that replicates only in human epidermis and spreads by direct contact. It occurs mainly in childhood; sexual transmission or immunocompromise explains most adult cases. Lesions are small (3-5 mm), skin-colored, dome-shaped, umbilicated papules; large or widespread (“giant molluscum”) lesions occur in immunocompromised hosts. Diagnosis is clinical; biopsy, if performed, shows lobulated endophytic epidermal hyperplasia with magenta cytoplasmic inclusions (Henderson-Paterson bodies). No routine viral or serologic testing is indicated. Extensive or persistent disease without another explanation should prompt evaluation for HIV. Zoonotic poxviruses (mpox, cowpox, orf) also cause human infection and require outbreak surveillance.

Human papillomavirus (HPV) is a nonenveloped, circular double-stranded DNA virus. Low-risk mucosal types HPV-6 and HPV-11 cause anogenital warts and, through vertical transmission, recurrent respiratory papillomatosis in children. High-risk mucosal types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59 are associated with cervical, anogenital, and oropharyngeal cancer. Cutaneous types produce common warts. High-risk HPV testing uses NAAT, hybrid capture/signal amplification, or in situ hybridization for localization. Assays that target L1 can miss integrated virus because integration frequently deletes L1, which is when oncogenic risk is highest.

Enteroviral exanthems. Hand-foot-mouth disease (oral vesicular enanthem plus a hand/foot/limb/buttock exanthem, most often coxsackievirus A16 or enterovirus A71) and herpangina (abrupt fever with painful posterior oropharyngeal vesicles, no skin lesions) are both usually diagnosed clinically. Rare neurologic or cardiovascular complications are linked to enterovirus A71 and coxsackievirus A6.

Measles morbillivirus is highly contagious, spread by respiratory droplet/aerosol, with an 11- to 13-day incubation period. The classic sequence is fever with cough/coryza/conjunctivitis (“3 Cs”), then Koplik spots on the buccal mucosa, then a maculopapular rash beginning on the face and behind the ears and spreading downward while coalescing. CDC recommends collecting serum for IgM and a nasopharyngeal or throat swab (preferred over urine) for rRT-PCR at first contact. Serum IgM may be negative in the first 72 hours after rash onset; if that early IgM is negative and rRT-PCR is negative or not done, collect a second serum 3-10 days after onset. rRT-PCR is most sensitive from rash day 0-3 and may remain positive as late as 10-14 days. A negative early IgM does not exclude measles. Laboratory confirmation supports airborne-precaution and outbreak-control decisions even when the clinical picture is classic.¹

Postnatal rubella produces a fine, noncoalescing, pink-red maculopapular rash spreading from face/neck to trunk/limbs within 24 hours. Parvovirus B19 causes erythema infectiosum (“fifth disease”), a slapped-cheek facial rash followed by a lacy, reticular rash on the trunk and limbs; IgG/IgM testing is used to assess fetal hydrops risk after exposure during pregnancy. Human herpesvirus 6 causes roseola infantum (“sixth disease”), with several days of high fever followed by a rash as the fever breaks; serology has limited clinical utility given near-universal seropositivity by adulthood.

Viral gastroenteritis

Viruses are a leading cause of gastroenteritis, spread mainly by the fecal-oral route from contaminated food, water, or surfaces (norovirus has also caused airborne hospital outbreaks).

Norovirus has an unusually low infectious dose and prolonged environmental survival; it can be severe in older adults and chronic in immunocompromised hosts. Molecular stool panels are the standard diagnostic approach; standalone antigen immunoassays are used mainly for outbreak investigation.

Viral hepatitis

Five hepatotropic viruses share a tropism for the liver and overlapping clinical presentation. All five can cause acute hepatitis. Hepatitis A remains an acute infection; chronic infection with hepatitis E is rare outside immunocompromised hosts. Detailed serologic algorithms belong to Immunology; the table below summarizes the microbiology-facing diagnostic information for these infections.

Human immunodeficiency virus

HIV (family Retroviridae, genus Lentivirus) comprises HIV-1, responsible for the global pandemic, and HIV-2, largely restricted to West Africa. Group M divides into ten recognized subtypes (A, B, C, D, F, G, H, J, K, L); subtype B predominates in the U.S. and Europe. Groups O and N are geographically restricted to West/Central Africa.

After mucosal entry, the virus spreads to lymphoid organs and establishes a persistent reservoir. Cell entry requires gp120/gp41 to bind CD4 together with a coreceptor: R5 viruses use CCR5; X4 viruses use CXCR4 and are more often associated with late or T-cell-tropic variants. Reverse transcriptase converts the RNA genome to cDNA, which integrates as a provirus.

HIV RNA becomes detectable by NAAT at about day 10 after exposure, marking the end of the eclipse period. Antigen/antibody immunoassays turn positive at a median of about 16 days. The window period, during which the person is infected and infectious but immunoassay-negative, extends beyond 3 weeks for older, antibody-only assays. After acute viremia, viral load falls to a set point that marks the start of the asymptomatic latent phase, with progressive CD4 depletion culminating in AIDS-defining illness.

The CDC/APHL laboratory algorithm, with APHL October 2025 fourth-edition reporting language, remains a three-step sequence. Immunology owns clinical interpretation; the laboratory sequence is:

1. FDA-approved HIV-1/2 antigen/antibody (fourth-generation) immunoassay. Nonreactive → no further testing (repeat later if acute exposure is still suspected). CDC recommends simultaneous antigen/antibody and HIV RNA testing when PrEP use is known.
2. Reactive → HIV-1/HIV-2 antibody differentiation immunoassay (Geenius or VioOne HIV Profile). HIV-1 positive → HIV-1 confirmed. HIV-2 positive, including HIV-2 positive with HIV-1 cross-reactivity → HIV-2 confirmed. Both positive / untypable → dual reactivity reported.
3. Differentiation assay negative or indeterminate despite a reactive screen → HIV nucleic acid test (HIV-1 RNA or an FDA-cleared HIV-1/HIV-2 qualitative NAAT). RNA detected → acute infection of the detected type. RNA not detected → antibodies not confirmed; if differentiation remains HIV-2 indeterminate or undifferentiated, refer for supplemental HIV-2 testing or repeat the algorithm on a new specimen in 2-4 weeks.

FDA-cleared diagnostic NAATs now include cobas HIV-1/HIV-2 Qualitative, Aptima HIV-1 Quant Dx, and Alinity m HIV-1. Dual-claim assays may report a quantitative result on plasma only; serum is acceptable for qualitative diagnosis but not for viral load. CDC’s 2023 technical update also describes limited circumstances in which a diagnostic NAAT may be used as the second step (recent exposure with symptoms; vaccine or neutralizing-antibody prevention trials), with antibody differentiation then completing the algorithm if RNA is not detected.²

Point-of-care tests (finger-stick or oral fluid, under 40 minutes, including an antigen/antibody format) are less sensitive than laboratory-based assays but valuable when a rapid preliminary result changes immediate management.

Viral load is obtained at entry to care and whenever a change in suppression is in question. Most assays report undetectable below 50 copies/mL. Untreated, clinically stable patients show about 0.3 log₁₀ unit of natural variation, so a change must exceed threefold (0.5 log₁₀ unit) to be considered significant. Transient increases after intercurrent infection or vaccination resolve within a month.

Genotypic resistance testing is performed at entry to care and whenever virologic failure or suboptimal suppression occurs (requires a viral load of at least 500-1,000 copies/mL). Sanger sequencing of the protease gene and part of the reverse transcriptase gene detects resistant variants down to about 20% of the viral population; next-generation sequencing detects minority variants below 1%. Tropism testing is added before a CCR5 antagonist is considered, and baseline hepatitis B and C serology is obtained routinely.

Blood-donor screening combines a risk-factor questionnaire, HIV-1/2 antibody testing, and minipool NAAT (6-16 pooled specimens). Maternal antigen/antibody screening is performed as early as possible in pregnancy and repeated in the third trimester if the initial result was negative and risk factors persist. Current NIH perinatal guidance tests HIV-exposed infants by NAAT at birth, 14-21 days, 1-2 months, and 4-6 months; an additional NAAT 2-6 weeks after infant antiretroviral drugs are stopped commonly falls at 2-3 months. Antibody testing before 18 months detects passively transferred maternal IgG and cannot diagnose infant infection.³

Virus-associated neoplasia

Circulating cell-free EBV DNA is used to screen for nasopharyngeal carcinoma in endemic areas.

Viral infections in immunocompromised hosts

Transplant recipients face viral risk from donor-derived virus, reactivation of the recipient’s own latent virus, and newly acquired community- or healthcare-associated infection. Infection risk in solid-organ transplant is highest in the first 6 months; in hematopoietic cell transplant, risk tracks engraftment and immune reconstitution.

Pretransplant donor and recipient screening establishes baseline risk. The usual screening includes CMV and EBV IgG (donor and recipient), HSV and VZV IgG (recipient), HIV/HBV/HCV serology with NAAT if positive, HTLV serology (donor), and optional BK, HHV-8, and West Nile testing. A seropositive donor paired with a seronegative recipient signals highest donor-transmitted risk; a seropositive recipient predicts reactivation. NAAT of blood is the primary post-transplant monitoring method; a WHO international standard has improved cross-laboratory comparability of quantitative results, though asymptomatic shedding still complicates a positive result.

CMV presentation ranges from undifferentiated fever to pneumonitis, enteritis, hepatitis, or retinitis. Donor-positive/recipient-negative pairs and lung or small-bowel recipients carry the highest reactivation risk. EBV is usually asymptomatic in transplant recipients, but a high viral load predicts PTLD, whose risk is highest in seronegative (often pediatric) allogeneic HCT recipients and those with more intensive T-cell suppression. HSV reactivation typically occurs earlier than other herpesviruses, usually as oropharyngeal or genital ulcers. Dermatomal zoster is the most common VZV manifestation. HHV-6 reactivation is common; a small fraction of the population (<1%) carries chromosomally integrated HHV-6, producing persistently high viral loads that can be mistaken for active infection. Adenovirus severe-disease risk is highest in pediatric patients, allogeneic HCT recipients, and those with intensive T-cell suppression. Circulating BK viral load correlates with nephropathy risk, supporting prospective plasma qPCR in kidney transplant recipients.

CMV resistance develops most often with prolonged or incomplete antiviral exposure. Ganciclovir, foscarnet, and cidofovir all target the viral DNA polymerase; only ganciclovir requires initial phosphorylation by the viral UL97 kinase. The most common resistance pathway begins with a UL97 kinase mutation (ganciclovir resistance); a subsequent UL54 DNA polymerase mutation can extend resistance to multiple drugs. Genotypic testing by Sanger sequencing typically requires a viral load above 1,000 copies/mL. HSV acyclovir/foscarnet resistance is tested phenotypically in reference laboratories and requires isolate growth in cell culture.

Viral infections in returning travelers

Epidemiologic risk, exposure history, and incubation period together narrow the differential in a febrile returning traveler. Several of these pathogens are highly transmissible person-to-person and require heightened biosafety precautions.

Dengue, Zika, and chikungunya share an Aedes mosquito vector and overlapping tropical/subtropical distribution. RT-PCR of blood is most sensitive during acute illness; IgM capture ELISA is useful once viremia clears, though flavivirus cross-reactivity can complicate interpretation.

Ebola, Marburg, Lassa, and Crimean-Congo hemorrhagic fever viruses are designated select agents requiring BSL-4 containment. High viral loads at presentation give RT-PCR high clinical sensitivity.

SARS-CoV and MERS-CoV are bat-origin coronaviruses that established zoonotic-to-human transmission (civets for SARS-CoV; dromedary camels as an ongoing MERS-CoV reservoir), with subsequent person-to-person spread. Diagnosis for both relies on RT-PCR of respiratory, blood, and stool specimens.

Japanese encephalitis virus (mosquito-borne, Culex vector, maintained in pigs and wading birds) is a leading cause of viral encephalitis in Asia; low viral loads in human infection favor serologic over molecular diagnosis. Nipah virus (zoonotic, Pteropus bat reservoir, with documented person-to-person transmission) causes severe pulmonary and/or CNS disease; testing (serology and RT-PCR) is available through CDC.

Molecular diagnostic reference

HPV L1-targeted amplification can miss integrated virus. Coinfection with multiple HPV types can also suppress amplification of one type by another. Influenza’s high mutation and reassortment rate can shift both primer-binding sites and antigenic determinants within a single season. Single-target assays for rapidly evolving viruses therefore require periodic review of primer and probe sequences.