Coinfection connectors

Connectors model interactions between co-circulating diseases. They run each timestep and adjust agents’ relative susceptibility (rel_sus) and relative transmissibility (rel_trans) on a target disease module, based on their state in another disease.

Why connectors?

A multi-STI simulation is not just a sum of independent diseases — biological evidence supports several coinfection effects:

• HIV ↔︎ ulcerative STIs (syphilis, GUD): Ulcers increase HIV acquisition and transmission risk.
• HIV ↔︎ non-ulcerative STIs (gonorrhea, chlamydia, trichomoniasis): Inflammation increases HIV transmissibility; HIV-induced immunosuppression can prolong STI infection.
• HIV ↔︎ BV: Dysbiosis is associated with elevated HIV acquisition risk.
• GUD ↔︎ syphilis: Syphilitic chancres are a primary cause of GUD; the connector links syphilis stage to GUD prevalence.

Each effect is implemented as a connector class so that users can mix and match.

Available connectors

Class	Diseases	Effect
sti.hiv_syph	HIV ↔︎ syphilis	Bidirectional. Syphilis raises HIV rel_sus (default 2.67×) and rel_trans (1.2×); HIV/AIDS state can modify syphilis rel_sus / rel_trans
sti.hiv_tv	trichomoniasis → HIV	Trichomoniasis infection raises HIV rel_sus (default 1.5×)
sti.hiv_ng	gonorrhea → HIV	Gonorrhea infection raises HIV rel_sus (default 1.2×) and rel_trans (1.2×)
sti.hiv_ct	chlamydia → HIV	Chlamydia infection raises HIV rel_sus (default 1× — placeholder)
sti.hiv_bv	BV → HIV	CST-IV state raises HIV rel_sus (default 2×) and rel_trans (2×)
sti.gud_syph	syphilis → GUD	Syphilis stage drives GUD prevalence

Most connectors are unidirectional (the STI affects HIV but not vice versa); hiv_syph is the exception.

Adding connectors

Connectors are passed explicitly when constructing an sti.Sim. By default, STIsim automatically wires connectors if connectors=True (the default). Alternatively, provide an explicit list of connectors instead:

hiv = sti.HIV()
syph = sti.Syphilis()
sim = sti.Sim(
    diseases=[hiv, syph],
    connectors=[sti.hiv_syph(hiv_module=hiv, syphilis_module=syph, rel_sus_hiv_syph=3.0)],
)

Writing a custom connector

A connector is a subclass of ss.Connector that overrides step() to update rel_sus / rel_trans arrays:

class my_connector(ss.Connector):
    def __init__(self, disease_a, disease_b, **kwargs):
        super().__init__()
        self.a = disease_a
        self.b = disease_b
        self.define_pars(rel_sus_a_b=2.0)
        self.update_pars(**kwargs)

    def step(self):
        infected_b = self.b.infected
        self.a.rel_sus[infected_b] = self.pars.rel_sus_a_b
        self.a.rel_sus[~infected_b] = 1.0

Connectors run after disease step() and before transmission, so changes to rel_sus / rel_trans take effect on the same timestep.